Wednesday, May 30, 2012

Why Mothers Prefer Boys

Phil Kitcher is a philosopher who is interested in the philosophy of science and he's also very interested in evolution. In his recent article on The Trouble with Scientism he gives and example of .... well, I'm not exactly sure what.
The emphasis on generality inspires scientific imperialism, conjuring a vision of a completely unified future science, encapsulated in a “theory of everything.” Organisms are aggregates of cells, cells are dynamic molecular systems, the molecules are composed of atoms, which in their turn decompose into fermions and bosons (or maybe into quarks or even strings). From these facts it is tempting to infer that all phenomena—including human actions and interaction—can “in principle” be understood ultimately in the language of physics, although for the moment we might settle for biology or neuroscience. This is a great temptation. We should resist it. Even if a process is constituted by the movements of a large number of constituent parts, this does not mean that it can be adequately explained by tracing those motions.

A tale from the history of human biology brings out the point. John Arbuthnot, an eighteenth-century British physician, noted a fact that greatly surprised him. Studying the registry of births in London between 1629 and 1710, he found that all of the years he reviewed showed a preponderance of male births: in his terms, each year was a “male year.” If you were a mad devotee of mechanistic analysis, you might think of explaining this—“in principle”—by tracing the motions of individual cells, first sperm and eggs, then parts of growing embryos, and showing how the maleness of each year was produced. But there is a better explanation, one that shows the record to be no accident. Evolutionary theory predicts that for many, but not all, species, the equilibrium sex-ratio will be 1:1 at sexual maturity. If it deviates, natural selection will favor the underrepresented sex: if boys are less common, invest in sons and you are likely to have more grandchildren. This means that if one sex is more likely to die before reaching reproductive age, more of that sex will have to be produced to start with. Since human males are the weaker sex—that is, they are more likely to die between birth and puberty—reproduction is biased in their favor.
In humans, the average sex ratio at birth is about 105 boys to every 100 girls but this ratio varies a lot from country to country and it depends on environmental conditions. There are many factors that affect fertilization and the survival of embryos and fetuses.

Is it reasonable to believe that the observed sex ratio (1.05) is the product of natural selection? You can't really answer that question until you know the mechanism of altered sex ratios. What is being selected? Is it the probability that a male sperm will reach the egg before a female sperm? If so, what kind of selective advantage would have to apply to change that probability from from 50% to 51% or 52%? How is it done? What alleles are involved?

Why does Philip Kitcher, a philosopher of science, think that a postulated adaptive explanation is a "better explanation" than a mechanistic one? Don't you actually have to "prove" your adaptive model at the level of genes, cells, and developing embryos before it can be accepted?


The Trouble with Scientism?

Philip Kitcher is a philosopher who specializes in the philsophy of science. He is a professor at Columbia University in New York, USA. He's well known in the atheist, skeptical community and he's an outspoken critic of creationism.

He just published an article in The New Republic entitled: The Trouble with Scientism: Why history and the humanities are also a form of knowledge.

Many of the debates on the issue of "scientism" depend on how you define "science." As you can see from the subtitle of his essay, it's about the two cultures. Kitcher separate the search for knowledge in the humanities from the search for knowledge in the natural sciences. Here's what he says ...
It is so easy to underrate the impact of the humanities and of the arts. Too many people, some of whom should know better, do it all the time. But understanding why the natural sciences are regarded as the gold standard for human knowledge is not hard. When molecular biologists are able to insert fragments of DNA into bacteria and turn the organisms into factories for churning out medically valuable substances, and when fundamental physics can predict the results of experiments with a precision comparable to measuring the distance across North America to within the thickness of a human hair, their achievements compel respect, and even awe. To derive one’s notion of human knowledge from the most striking accomplishments of the natural sciences easily generates a conviction that other forms of inquiry simply do not measure up. Their accomplishments can come to seem inferior, even worthless, at least until the day when these domains are absorbed within the scope of “real science.”
It's clear the he thinks of "science" as something that only natural scientists do. This is a different definition that the one I prefer. I think of "science" as a way of knowing that involves evidence, skepticism, and rationalism. I agree with Rush Holt [Rush Holt on Science and Critical Thinking] that critical thinking is an important part of science as a way of knowing and I agree with him that the scientific approach can be used everywhere—even in philosophy departments.

Kitcher's view is different. That leads him to define scientism as ...
The problem with scientism—which is of course not the same thing as science—is owed to a number of sources, and they deserve critical scrutiny. The enthusiasm for natural scientific imperialism rests on five observations. First, there is the sense that the humanities and social sciences are doomed to deliver a seemingly directionless sequence of theories and explanations, with no promise of additive progress. Second, there is the contrasting record of extraordinary success in some areas of natural science. Third, there is the explicit articulation of technique and method in the natural sciences, which fosters the conviction that natural scientists are able to acquire and combine evidence in particularly rigorous ways. Fourth, there is the perception that humanists and social scientists are only able to reason cogently when they confine themselves to conclusions of limited generality: insofar as they aim at significant—general—conclusions, their methods and their evidence are unrigorous. Finally, there is the commonplace perception that the humanities and social sciences have been dominated, for long periods of their histories, by spectacularly false theories, grand doctrines that enjoy enormous popularity until fashion changes, as their glaring shortcomings are disclosed.
That's a really stupid definition of scientism. I don't know anyone who actually thinks like that. Do you know any "natural science imperialists" who dismiss the humanities and the social sciences?1

I believe that people in the humanities and social sciences use the same approach as those in the natural sciences. I call that way of knowing "science" but if someone wants to come up with a better name, I'm all ears. As far as I'm concerned, science (as I define it) is the ONLY way of knowing that has actually been successful in discovering true knowledge. I guess that makes me guilty of "scientism."

It's very easy to refute scientism as I define it. All you have to do is show that there's some other way of knowing that produces universal truths or true knowledge. Perhaps philosophers have discovered truths using some other way of knowing?


1. I criticize evolutionary psychology. The reason why I'm so critical is precisely because they don't conform to the scientific way of knowing. They are not doing "good science" by any definition of the word "science."

Rush Holt on Science and Critical Thinking

I don't know Rush Holt from Adam. I'm told that he's a US Congressman from New Jersey but I find that difficult to believe. :-)

Here's an interview he gave with The Humanist: Thinking Like a Scientist.
The Humanist: How do you define critical thinking?

Rush Holt: Let me define instead what I like to call “thinking like a scientist.” It’s asking questions that can be answered based on evidence; it’s expressing questions in a way that allows someone to check your work. If you don’t have both of those elements, it’s too easy to fool yourself or to get lazy in your thinking. I wouldn’t say that critical thinking is hard thinking, because I don’t want to discourage people from doing it, but like anything else, it’s easier if you practice.

Third graders, for example, are often very good at thinking like scientists. Like scientists, they know that if you ask how something works, what something means, or how something happens, you should do it in a way that allows for more than just pure thinking. There should be some evidence, something empirical. You should form your question so that it allows someone else to ask that same question and observe the evidence to see if they get the same answer as you do. And that’s the essential part of critical thinking. If you say, “I’ve been thinking about this deeply and, by golly, now I understand it,” but then you try to explain it to someone else and can’t, then you probably don’t understand it … or it’s not very reliable knowledge.

I keep trying to get science taught in a way that, even if you can’t remember a single Latin term or are a klutz at solving equations, you’ve learned how to frame questions and sift evidence. I talk about verification but another way of putting it is: be ready for the cross-examination. Prepare to explain yourself.

The Humanist: How valuable is critical thinking to everyday life?

Holt: It’s invaluable, whether you’re making a consumer decision like which laundry detergent to buy or whether you’re trying to decide what career you want to pursue. There are ways to ask yourself both what you’re trying to accomplish and how to measure whether you’ve accomplished it. If you’re able to express it that way, then you’re thinking critically.

This is important on every level, not just on a personal level, not just in regards to consumer decisions or life choices. I think it’s quite likely we wouldn’t have invaded Iraq if more people in the CIA or in Congress had been thinking critically and asking, “What’s the evidence? You say Saddam Hussein is doing things that will hurt our national interests. Now tell me exactly: what is he doing? Does he have chemical weapons, nuclear weapons? Where’s the evidence?” Of course, there wasn’t any.
This is important stuff. I think of "science" as a way of knowing but it can also be thought of as a way of thinking. It's intimately associated with critical thinking.

In this sense, "science" is not confined to the so-called "natural sciences" but it can be applied to everything that requires a search for reliable truth. Everybody should be thinking like a scientist and that includes politicians and philosophers. In my experience, there is no other way of knowing that has a proven track record.


[Hat Tip: RichardDawkins.net]

Tuesday, May 29, 2012

Watch Jonathan Wells Screw Up

Here's Jonathan Wells attacking the concept of junk DNA during a lecture at Biola University in October 2010. It's remarkable because he repeats a false history that he knows is untrue because many people have corrected him. Pay attention to what he says about four minutes into the presentation.


Wells is talking about the history of junk DNA. He begins by falsely describing the Central Dogma of Molecular Biology, which, he says, is "DNA makes RNA, makes protein, makes us." He then quotes Jacques Monod as a supporter of this concept (4 minutes, 23 seconds).
With that, and the understanding of the random physical basis of mutation that molecular biology has provided, the mechanism of Darwinism is at last securely founded, and man has to understand that he is a mere accident.
Jacque Monod (1970) quoted in "The Eight Day of Creation" by Horace Freeland Judson (p. 192)
I looked up this passage and guess what I found? I discovered that when Monod said "with that" he was referring to the real Central Dogma—the one that Crick actually formulated. Only a few sentences earlier Monod is quoted as saying ...
This was what Francis Crick called the Central Dogma: no information goes from protein to DNA.
This is followed by a brief description of Lamarckism and why it conflicts with the Central Dogma. So Monod has it exactly right, the Central Dogma says that information can only flow from nucleic acid to protein and not vice versa. That rules out the inheritance of applied characteristics and makes "the mechanism of Darwinism ... securely founded."

Why is this important? Because Wells immediately follows this by claiming that ...
... biologists discovered that most human DNA does not code for proteins. Based on the Central Dogma that "DNA makes RNA makes protein makes us," this non-protein-coding DNA was dubbed "junk."
This is nonsense. Not only did the concept of junk DNA have nothing to do with the Central Dogma, it also had nothing to do with "non-coding DNA." By 1970, all knowledgeable molecular biologists knew that there was lots of perfectly functional DNA that did not encode protein. It's simply not true that the consensus opinion among the experts at the time was that all noncoding DNA was junk [Junk & Jonathan: Part 3—The Preface].

There are legitimate debates about the quantity of junk DNA in our genome. What I just don't understand is why IDiots feel they have to distort history in order to make their point. Wouldn't they be a lot more credible if they at least got the simple things right?

Are they pathological liars?


Three Big Questions

Here's John West at Biola University in October 2010. He's asking three big questions.
  1. Did God specifically direct the history of life?
  2. Did God create humans originally good?
  3. Can we see evidence of God's design in nature?
The answers, by the way, are no, no, and no. But you already knew that, didn't you?

John G. West is a Senior Fellow at the Discovery Institute. He is also Associate Director of Discovery's Center for Science & Culture and Vice President for Public Policy and Legal Affairs. In other words, he's one of the prime IDiots.

While watching the video, try and remember that Intelligent Design Creationism is not about God and criticism of "Darwinism" should be taught in the schools because it's part of science, not religion.




A troglodyte discovers a car ...

From GilDodgen at Uncommon Descent: Even IF the Genome is Full of “Junk”.
I enjoyed Jonathan’s presentation about junk DNA at the link provided above. Let us presume that the genome does include junk. What does this have to do with the evidence for design found elsewhere, such as in the highly sophisticated, functionally integrated, information-processing machinery about which we know a great deal?

I’m sure that Francis Collins is a very fine fellow. I have no doubt about his Christian conversion. (I underwent a similar one.) I have no doubt about his intellect or problem-solving IQ.

However, there is something missing in his reasoning, which basically goes like this:

A troglodyte discovers a car in a junkyard. The engine runs. The transmission works, and the car can be driven. But wait: The headlights don’t work and do nothing (of course, the troglodyte has no idea what a headlight is, but he sees such structures and assumes that they have no purpose).

Even if (and that’s a BIG if) the genome is full of junk (that is, degenerate stuff that provides no function), the existence of that junk has nothing to do with an inference to design from the stuff that is obviously not junk, but highly sophisticated technology.

Based upon my experience, design theorists are not the troglodytes who refuse to follow the evidence where it leads — Darwinists are.
You just can't make this stuff up.

There's an important point here. Up until now the IDiots have been drawing a line in the sand by claiming that junk DNA is inconsistent with Intelligent Design Creationism. Do I detect a bit of backpeddling?


[Image Credit: Troglodyte]

Searching for a Chair

Universities are very complex institutions. I'm sure the average person doesn't understand how they are run. The reason I'm so sure of this is because the average professor doesn't know either! In fact, I'm not sure anyone knows.

A typical large university is divided into several faculties like law, medicine, engineering, arts & humanities, science etc. Each faculty has a Dean who is head of the faculty. Large faculties contain many departments; for example, a faculty of science might have departments of physics, geology, chemistry, and biology. Each department has a chair who is responsible for the administration of the department and for making decisions about hiring, firing, promotions, salary increases etc.

My department is the Department of Biochemistry in the Faculty of Medicine. The position of departmental chair is a five year appointment that is renewable once for a total of ten years. The ten years are up for our current chair so we have to find a new one. This is always a traumatic time for a university department.

The process begins with an addvertisment that's placed in prominent science journals and distributed to various other departments in Canada.
Chair, Department of Biochemistry
University of Toronto, Faculty of Medicine
Toronto, ON

Posted: December 5th, 2011

Applications are invited for the position of Chair, Department of Biochemistry, Faculty of Medicine, University of Toronto, for a 5-year term on or before January 1, 2013.

The Department of Biochemistry at the University of Toronto is a diverse and highly-productive department with a broad range of research areas including protein structure and folding, cell biology, computational biology, and genomics/proteomics. The department has 60 faculty members located at the university’s St. George campus, The Hospital for Sick Children, Princess Margaret Hospital, Mount Sinai Hospital, and other sites in the University of Toronto community. The department is an important component of the University of Toronto academic health science complex, which is among the largest in North America. The department offers programs leading to MSc and PhD degrees, as well as a strong undergraduate program in biochemistry.

The University of Toronto academic health science complex is among the largest in North America. The Faculty of Medicine (http://www.facmed.utoronto.ca) and its nine fully-affiliated hospitals receive over CAN $700 million per annum in research funds.

In addition to a record of academic excellence, the successful candidate will possess outstanding leadership, administrative management, and communication skills to direct a geographically-dispersed department. The individual will bring entrepreneurial vision and execute strategies to enable the Department to build and to sustain effective partnerships. Candidates should have a track record of successful and innovative leadership in education and research. The successful candidate should be eligible for tenured academic appointment at the rank of full professor in the Department of Biochemistry. The next Chair must have the vision and ability to take the Department of Biochemistry to a new level of international recognition and achievement.

Applications consisting of a letter of interest and CV may be submitted online at www.jobs.utoronto.ca/faculty (Job # 1101059) or by sending to:

Prof. Catharine Whiteside, Dean
c/o Anastasia Meletopoulos, Academic Affairs Specialist
Office of the Dean, Faculty of Medicine, University of Toronto
Room 2109, Medical Sciences Building
1 King's College Circle
Toronto, Ontario M5S 1A8, CANADA
Fax: 416 978 1774
anastasia.meletopoulos@utoronto.ca

The closing date for this position is January 31, 2012, or until filled.

For detailed information on the department, visit its Web site at http://www.biochemistry.utoronto.ca.

The University of Toronto is strongly committed to diversity within its community and especially welcomes applications from visible minority group members, women, Aboriginal persons, persons with disabilities, members of sexual minority groups, and others who may contribute to the further diversification of ideas. All qualified candidates are encouraged to apply; however, Canadians and permanent residents will be given priority.
The applications are reviewed by a search committee chaired by the Dean. Other ex officio members are; a Vice-Dean of the Faculty of Medicine, a representative of the Graduate School, and the chair of a cognate department. The committee has an undergraduate from our department and a graduate student in the department. In addition, there are seven professors from our department on the committee. The departmental representatives are split between those in the academic core (on campus) and those who are employed by hospital research institutes but have an academic appointment in our department.

After reviewing all the applications, the search committee draws up a short list of suitable candidates. These candidates are then invited to visit the department and give a seminar on their work. After the seminar they meet with members of the department, faculty, staff, and students in a 45 minute forum where we can ask questions.

This is the stage we're at right now. The candidates will be arriving in a couple of weeks. We have two from Toronto and two from other cities in Canada.

During their visit, the candidates meet with the search committee where they will be asked a series of prepared questions. Each candidate will be asked the same questions. After all four candidates have been interviewed, the search committee will make a recommendation to the Dean. The Dean is not obliged to offer the job to the recommended candidate but it would be highly unusual if she were to ignore the recommendation by the search committee. The committee may decide that none of the candidates are suitable for the job.

Once a candidate has been recommended, the Dean negotiates a deal that the candidate is willing to accept. (Salary, research space, and various benefits to the department are usually on the table.) Negotiations can fail if the demands of the candidate aren't met. In this case, the offer will go to the second choice of the search committee, if there is one.

How does this process compare to other departments and universities?


Online Courses: The Great Courses

John Hawks has recently blogged about My foray into online education. He's posted videotapes of the lectures in his anthropology course: Principles of Biological Anthropology.

It's interesting to watch his lectures but I think he's avoiding the key question that concerns me about online courses. The question is, should we be delivering traditional "lectures" to students in our classrooms?

I would never allow anyone to videotape my classroom time and post it on the web. That's because my goal is to involve the students in the class and generate discussion. I don't want them to be intimidated by a camera and I certainly don't want the camera to record for posterity the interactions between students as they discuss the basic concepts and principles that come up in class. Sometimes I have to tell a student that there question was interesting but not on topic or, even worse, that it revealed a serious misunderstanding. Do we really want that posted on the course website?

Sometimes (often?) I say something really stupid. It's part of the risk we take when we have a course like the one I'm describing. These are not prepared and rehearsed lectures.

Monday's Molecule #172

Today's molecule (Tuesday's Molecule) should be quite easy for those of you who have been paying attention to the rules of nomenclature. Be sure to specify the stereochemistry. (The image shows two different views of the same molecule.)

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch with a very famous person, or me.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is β-D-glucopyranosyl 1,6-bisphosphate. The winners are Mike Hamilton and Dmitri Tchigvintsev but I'm being a bit generous with Mike because he called it "1,6-diphosphate" and that's not correct.

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


Monday, May 28, 2012

Denyse O'Leary: Catholics & Evolution

As I'm sure you all know, the Intelligent Design Creationists have a small bevy of really, really, smart people who strike fear and dread into the hearts of evolutionary biologists.

Here's Toronto's own Denyse O'Leary giving a lecture at Biola University in October 2010.




The Business of Online Education

John Hawks is interested in putting his lecture on the internet [My foray into online education]. I'll eventually get around to discussing whether this is a good idea or not. Today I want to question his sources.

John Hawks quotes an article by someone named Robert Tracinski as evidence that online education is the wave of the future. Let''s look at that article.

Robert Tracinski writes for The Intellectual Activist, which describes itself like this ...
The Intellectual Activist is especially dedicated to understanding and promoting the revolutionary ideas of the 20th-century novelist and philosopher Ayn Rand — the great champion of the power of reason, the supreme value of the individual, and the unfettered liberty of a capitalist society. TIA serves as a forum for those who are working to gain a deeper understanding of Ayn Rand's fiction and philosophy and applying her ideas to gain new insights in every field of human knowledge.
Rober Tracinski has been called The Intellectual Leader of the Tea Party.

Friday, May 25, 2012

The Importance of the Null Hypothesis

Jonathan Eisen of The Tree of Life is hosting a series of guest postings by the authors of recetnly published papers. The latest is a guest post by Josh Weitz on their paper on BMC Genomics: A neutral theory of genome evolution and the frequency distribution of genes. The paper tries to explain the concept of a pan genome, where closely related species, or strains, each have a subset of the total number of genes in the entire collection of species/strains. Why do some strains and some genes and not others?

Josh Weitz makes a point that bears repeating because most people just don't understand it.
So, let me be clear: I do think that genes matter to the fitness of an organism and that if you delete/replace certain genes you will find this can have mild to severe to lethal costs (and occasional benefits). However, our point in developing this model was to try and create a baseline null model, in the spirit of neutral theories of population genetics, that would be able to reproduce as much of the data with as few parameters as possible. Doing so would then help identify what features of gene compositional variation could be used as a means to identify the signatures of adaptation and selection. Perhaps this point does not even need to be stated, but obviously not everyone sees it the same way. In fact, Eugene Koonin has made a similar argument in his nice paper, Are there laws of adaptive evolution: "the null hypothesis is that any observed pattern is first assumed to be the result of non-selective, stochastic processes, and only once this assumption is falsified, should one start to explore adaptive scenarios''. I really like this quote, even if I don't always follow this rule (perhaps I should). It's just so tempting to explore adaptive scenarios first, but it doesn't make it right.


Squirrels, Dawkins, and Evolution

Richard Dawkins doesn't like the new book by Edward O. Wilson [The Descent of Edward Wilson].

This shouldn't be a surprise to anyone since Wilson has become a supporter of group selection and—even more egregious—a critic of kin selection. Dawkins is a big fan of gene centric adaptation so group selection is heresy. Dawkins thinks that Hamilton's discovery of kin selection ranks right up there with Newton and Darwin, so anyone who casts doubt on kin selection is also a heretic.

I'm not an expert on the details of this debate although my instinct is to think that kin selection is vastly overblown1 and there's nothing obviously wrong with the concepts of group selection or species sorting. However, Dawkins mentions something that raises some important questions about evolution and I wonder what people think.

May 25, 1977

The first Star Wars movie was released on this day in 1977. I was living in Geneva, Switzerland at the time and I didn't get to see the movie until July or August.



Wednesday, May 23, 2012

Better Biochemistry: The Perfect Enzyme

The Biologic Institute is a "research" facility funded by The Discovery Institute of Seattle, WA (USA). From time to time they post articles on their website. A few years ago they posted the following article: Physicists Finding Perfection… in Biology.

I want to address one particular point in that article.
For decades enzymologists have recognized that certain enzymes are catalytically perfect—meaning that they process reactant molecules as rapidly as these molecules can reach them by diffusion. [1] That hinted at a principle of physical perfection in biology, but no one anticipated its breadth until recently.
The point of the article is that some things in biology are "perfect" but this presents a problem for "Darwinism." According to the "scientists" at the Biologic Institute. perfection is beyond the reach of a "Darwinian mechanism." The fact that we observe perfection in biology is evidence for design.

ERV picked up on this theme in a 2009 posting: Having your Ford Pinto and Crashing it Too. That posting seemed to concede the point that enzymes are perfect.

That's the issue I want to discuss.

Flunk the IDiots

Casey Luskin recently offered advice on the The Top Three Flaws in Darwinian Evolution. [see The Top Three Flaws In Evolutionary Theory ] At the end of that post he referred readers to The College Student's Back-to-School Guide to Intelligent Design. This is a remarkable document. It's designed to teach students how to debate their professors and/or disguise their true beliefs in order to pass a class.

Why do the IDiots need such advice? It's because Intelligent Design Creationism is under attack from dogmatic professors who can't think critically and who don't have open minds. The opening section lists examples, such as ...
A professor of biochemistry and leading biochemistry textbook author at the University of Toronto stated that a major public research university “should never have admitted” students who support ID, and should “just flunk the lot of them and make room for smart students.”

Tuesday, May 22, 2012

Free/Cheap Textbooks for Students

Sean Caroll, the physicist, has a blog called Cosmic Variance on the Discover Magazine website.1

Yesterday Sean posted an article by a guest blogger, Marc Sher, a physicist who teaches introductory physics at the College of William and Mary. Marc Sher is promoting something called the nonprofit textbook movement [Guest Post: Marc Sher on the Nonprofit Textbook Movement].

Here's what he says ...
The textbook publishers’ price-gouging monopoly may be ending.

For decades, college students have been exploited by publishers of introductory textbooks. The publishers charge about $200 for a textbook, and then every 3-4 years they make some minor cosmetic changes, reorder some of the problems, add a few new problems, and call it a “new edition”. They then take the previous edition out of print. The purpose, of course, is to destroy the used book market and to continue charging students exorbitant amounts of money.
Now, I usually think of myself as a socialist, so it's a little uncomfortable for me to be defending capitalism, but here goes.

Monday, May 21, 2012

Monday's Molecule #171

Today's molecule is four molecules. You need to correctly identify each one. Then you need to tell me whether each molecule (or a derivative) is found in living cells, and if so, where. That's a total of nine answers.

Post your answers as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answers wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch with a very famous person, or me.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE:The molecules are: N6-isopentyladenine, hypoxanthine, uridine, and 5-oxyacetic acid uridine. Uridine is found in all RNAs and the other three are found in various tRNA molecules.

There are no winners this week!!!

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



The Top Three Flaws In Evolutionary Theory

Casey Luskin is one of the leading IDiots of the Discovery Institute. He posts frequently on Evolution News & Views. Here's one of his recent posts where he lets us in one the The Top Three Flaws in Evolutionary Theory.

If you've ever wondered why I call them IDiots, this will help you understand.
Unfortunately most public schools do NOT teach about the flaws in evolutionary theory. Instead, they censor this information, hiding from students all of the science that challenges Darwinian evolution. But in a perfect world, if the evidence against Darwinian theory were taught, these would be my top three choices:
  1. Tell students that the fossil record often lacks transitional forms and that there are "explosions" of new life forms, a pattern of radiations that challenges Darwinian evolutionary theory.
  2. Tell students that many scientists have challenged the ability of random mutation and natural selection to produce complex biological features.
  3. Tell students that many lines of evidence for Darwinian evolution and common descent are weak:
    a. Vertebrate embryos start out developing very differently, in contrast with the drawings of embryos often found in textbooks which mostly appear similar.
    b. DNA evidence paints conflicting pictures of the "tree of life". There is no such single "tree."
    c. Evidence of small-scale changes, such as the modest changes in the size of finch-beaks or slight changes in the color frequencies in the wings of "peppered moths", shows microevolution, NOT macroevolution.


Sunday, May 20, 2012

Time to Re-write the Textbooks: RNA has a Fifth Base!!!

From Science Daily via a press release from NewYork-Presbyterian Hospital/Weill Cornell Medical Center/Weill Cornell Medical College: RNA Modification Influences Thousands of Genes: Revolutionizes Understanding of Gene Expression.
Over the past decade, research in the field of epigenetics has revealed that chemically modified bases are abundant components of the human genome and has forced us to abandon the notion we've had since high school genetics that DNA consists of only four bases.

Now, researchers at Weill Cornell Medical College have made a discovery that once again forces us to rewrite our textbooks. This time, however, the findings pertain to RNA, which like DNA carries information about our genes and how they are expressed. The researchers have identified a novel base modification in RNA which they say will revolutionize our understanding of gene expression.

Their report, published May 17 in the journal Cell, shows that messenger RNA (mRNA), long thought to be a simple blueprint for protein production, is often chemically modified by addition of a methyl group to one of its bases, adenine. Although mRNA was thought to contain only four nucleobases, their discovery shows that a fifth base, N6-methyladenosine (m6A), pervades the transcriptome.
Those who don't know history are destined to repeat it.

Edmund Burke
We've known about modified bases in DNA since the early 1970s so there aren't any modern textbooks that don't mention them. If your high school genetics course didn't mention modified bases it isn't because scientists didn't know of their existence—unless, of course, you graduated from high school more than forty years ago.

We've known about the presence of N6-methyladenosine in mRNA for several decades. Here's the introduction to a 1984 paper by Horowitz et al. (1984).
The most prevalent internal methylated nucleoside in eukaryotic mRNA is N6-methyladenosine (m6A). This modified nucleoside is found in RNAs of higher eukaryotic organisms (1-6), plants (7-9), and viruses (3, 10-12), and occurs at two specific sequences: Gpm6ApC and Apm6ApC (13-17).
Refereences 1-5 are from 1975 meaning that in the published scientific literature the presence of m6A dates back 37 years. That's more than enough time to make it into the textbooks. It's in the textbooks.

Not only that, textbooks also contain references to two other modified bases in mRNA. N7-methylguanylate is common in cap structures and several mRNAs are known to contain inosine (I), a modified form of adenylate.

I blame the science writers at Cornell Medical Center for writing something that is not true and I blame the authors of the paper for hype and exaggeration and for not correcting the press release before it was published. That's not how science is supposed to work.


[Hat Tip: Uncommon Descent: Is there a fifth base in RNA?]

Horowitz, S., Horowitz, A., Nilsen, T.W., Munns, T.W. and Rottman, F.M. (1984) Mapping of N6-methyladenosine residues in bovine prolactin mRNA. PNAS 81:5667-5671. [PDF]


Advice for High School Graduates

The Chicago Tribune has an opinion piece on Open letter to high school grads. You really should read the entire thing but here's part of it ...
If you haven't posted a good academic performance in high school, don't believe a university, its leadership, advertisements or admissions officers who co-sign your promissory note with no responsibility for its payment obligation. They need paying students.

Stoking a deceitful dream on life support — an underappreciated, overfinanced, media-hyped charade — is the real deception, and the weight falls on your back, not theirs.

A shameful, elaborate sham, when one out of two college graduates this year are unemployable in their chosen field.

Look carefully at the costs and benefits of a university education. University officials may not tell you the truth: Enrollments could drop. Bankers will not tell you the truth: Interest income will fall off. Elected officials will not tell you the truth: Elections will be lost. Listen to those really concerned for you carefully.
Who wrote this? It's Walter V. Wendler, who is listed as director of the School of Architecture and former chancellor at Southern Illinois University.

Thursday, May 17, 2012

All IDiots Believe in Evolution!

The title of this post may shock you but bear with me for a minute. I've been trying for years to educate creationists on the meaning of evolution and the strawman term "Darwinism." I've pointed out repeatedly that the the standard minimal definition of evolution ("Evolution is a process that results in heritable changes in a population spread over many generations") should be perfectly acceptable to any IDiot. They don't really reject all of evolution, just the part that causes particular problems for their religion.

Finally, we have an Intelligent Design Creationist who is willing to take the bull by the horns and point out the obvious. Johnnyb explains how his fellow IDiots should think about evolution [How to Talk to Your Professors About Your Darwin Doubts].
So what is one to do? Well, thankfully, our friends the evolutionists have given us a way out. In their zeal to claim consensus on the “fact of evolution,” they have had to steamroll together such a large diversity of opinion into the single term “evolution”, that the word “evolution” no longer has the grand meaning it used to. The only real meaning everyone can agree on is “change in allele frequency over time” – and that is a definition that literally everyone can agree with.

In other words, even if you are a young earth creationist, if your professor asks if you believe in evolution, the legitimate answer is “yes”. Given the common definition of “evolution,” the only thing they are really asking with that question is, “do you believe in genetics?”

Therefore, here is how you can, and, I say, should frame yourself – you believe in evolution. However, there are a few parts of the theory that you disagree with. Don’t be obnoxious, but don’t be overly shy either. Just be frank. Do you believe in evolution? “Yes, but I disagree that common ancestry is universal.” Do you believe in evolution? “Yes, but I don’t think that natural selection alone as a mechanism sufficiently explains life’s diversity.” You don’t even have to put the “yes” and the objection in the same sentence. What do you think about evolution? “The study of evolution is fascinating!” How do you think multicellularity evolved? “I think that multicellularity is a fundamental property of certain organisms, and can’t be evolved piecemeal from the presumed single-celled ancestors.” But you do believe in evolution? “Yes, of course.” Do you think multi-cellular organisms evolved? “Certainly!” From what? “Other multi-cellular organisms.”

If someone challenges you on the definition of evolution, simply challenge them back. What definition of evolution are you using? “I’m using the standard population genetics definition of evolution as the change in gene frequencies over time.” That’s not what evolution is. “What is your definition of evolution?” Evolution means natural selection and common ancestry! “Well, that’s a pretty narrow view of evolution in modern biology. So, while I agree with evolution in general, I don’t agree with your specific view of it.” What’s your specific view? “I’m still learning! But I do find it interesting that….[put your favorite evolutionary or non-evolutionary feature of biology here]”
Let's see how many of his fellow creationists take this advice to heart. Are you listening Denyse?

I'm willing to bet that the vast majority will still never admit that evolution, as defined, is a fact because we can directly observe it happening right before our eyes.


David Klinghoffer Will Bust Your Mark VIII Irony Meter

Back in the days of newsgroups (last century) the howlers in talk.origins developed a running joke about irony meters.

The lastest version (Mark VIII) is pretty sturdy but from time to time the IDiots come up with a real challenge. You might want to turn off your irony meter before reading any further and especially before following the link.

Here's David Klinghoffer's latest posting on the "prestigious" IDiot site, Evolution News & Views [What Is It about Professors and Reading Comprehension?].

How is it that many professors in the humanities and the sciences seem unable to read an opinion they don't like and then accurately relate the argument -- say it back to their interlocutor -- before trying to rebut it? This is a basic skill in communication that comes in handy in many areas of life, including personal relationships


The Problem with Psychology

Ed Yong of Not Exactly Rocket Science has just published a scathing criticism of the entire field of psychology [Replication studies: Bad copy]. The fact that this article appears in Nature should be of great concern to all psychologists. Here's the two opening paragraphs.
For many psychologists, the clearest sign that their field was in trouble came, ironically, from a study about premonition. Daryl Bem, a social psychologist at Cornell University in Ithaca, New York, showed student volunteers 48 words and then abruptly asked them to write down as many as they could remember. Next came a practice session: students were given a random subset of the test words and were asked to type them out. Bem found that some students were more likely to remember words in the test if they had later practised them. Effect preceded cause.

Bem published his findings in the Journal of Personality and Social Psychology (JPSP) along with eight other experiments1 providing evidence for what he refers to as “psi”, or psychic effects. There is, needless to say, no shortage of scientists sceptical about his claims. Three research teams independently tried to replicate the effect Bem had reported and, when they could not, they faced serious obstacles to publishing their results. The episode served as a wake-up call. “The realization that some proportion of the findings in the literature simply might not replicate was brought home by the fact that there are more and more of these counterintuitive findings in the literature,” says Eric-Jan Wagenmakers, a mathematical psychologist from the University of Amsterdam.
There's lots more where that comes from. Read the entire article.

One of the most remarkable things about Ed Yong's paper is that he doesn't even mention evolutionary psychology! I think that the absurdity of most evolutionary psychology papers is more than sufficient reason to question whether the entire field is fatally flawed [Boobies and Evolutionary Psychologists].

There's clearly something wrong. Can it be possible that an entire discipline has gone off the rails?1


1. Saying that there's a problem with a discipline is not the same as saying that there's a problem with every single psychologist. What I'm saying is that the good psychologists don't seem to have the same influence that good biochemists and good evolutionary biologist (mostly) have on their respective disciplines.

Wednesday, May 16, 2012

Cellphones in the Classroom

Here's an interesting video clip on the advantages (?) of encouraging students to use cellphones in the classroom.


Students have been using laptops in my classes for more than a dozen years. They were never using them for the sole purpose of taking notes, especially since the installation of WiFi. Smart phones don't change anything.

If you teach a class that engages students and gets them to debate and discuss the issues then they won't have time to live tweet or do anything else on their smart phones. If you are teaching difficult and challenging concepts and principles, then you are likely to keep their attention. If you teach a class that allows students to busy themselves with lots of other tasks during the lecture, and still get a good grade, then they will do that.

I pose the following question ... if your students can spend a considerable amount of time using their smart phones during class then they are not giving the class their full attention. Are you teaching effectively?

And whatever happened to note-taking? How can you take notes with a smart phone in your hand? Is taking notes an old fashioned concept that should be abandoned?


On Changing Education Because It's What the Students Want

In a previous post I mentioned an article by Sidneyeve Matrix who advocates changing the "traditional" form of undergraduate university education by incorporating more technology [Challenges, Opportunities, and New Expectations]. In that post, I concentrated on one of the arguments for online courses [On the Quality of Online Courses].

In this post I want to bring up one of the arguments for introducing new technology into a course. I'm going to pick a quote from Sidneyeve Matrix's article but she's not the only one who brings it up.
There’s a torrent of research demonstrating the costs and benefits of using social, mobile, and digital technology enhancements to teach; yet it’s inconclusive whether these result in higher student outcomes. Of course, there are multiple bottom lines to consider. What’s undeniable is that even though digital divides exist, today’s students expect to see some technology used in their classes. It follows that we can expect increased engagement and higher student satisfaction when profs power-up. In my experience, exceedingly positive end-of-term student surveys and reviews in my ed-tech enhanced courses document a beneficial halo effect.
The first statement is true, as far as I know. There are no sound pedagogical reasons for incorporating social media and other technologies into a course. That means there must be other, not-pedagogical, reasons for change.

The third statement says that it's "undeniable" that students expect to see some technology in their class. What does this mean? Will they be satisfied if they see a power point presentation and a website? Do they expect their professors to befriend them on facebook or follow their tweets? We don't know. The statement is devoid of meaning.

However, what seems to be "undeniable" is that there are some professors who think that it's important to give students whatever they want. These professors seem to think that it's the students, not them, who are the experts on undergraduate education. Is there any evidence for that?

Of course not. The reason for giving students what they want is clearly spelled out in the last sentence. If you give them what they want then you'll get good student evaluations.

In fairness, she also mentions "engagement." If student engagement is one of your goals—it's one of mine—then that's a reason for exploring technology options. That may, or may not, be associated with student satisfaction. My experience suggests that it's not. I first started an online discussion forum for students in 1987-88 using a usenet forum running on a VAX. Very few students used it but the ones who did liked it a lot.

Over the last 25 years, I've tried various ways of encouraging student engagement on the internet including, in the last iteration, trying to get students to read and comment on blogs. The result is always the same. A subset of the class has a great time "engaging" and a larger subset resists all attempts to draw them in. The most effective way to encourage, and reward, engagement is to do it in class with the students right there with you. The downside is that a good chunk of your class are miserable because they don't want to "engage" in their own learning. They would rather be passive learners.
In order for professors to engage in podcasting or online lectures or tweeting, or supporting their colleagues who opt to publish in open source journals or participate in online conferences, they must see real benefits and an immediate, significant return on investment. Perhaps for some profs evidence of increased student satisfaction and engagement will win them over.
I hope that "increased student satisfaction" will never be a primary motive for change. It may be a secondary benefit but that's not the same thing. Our job is to teach effectively. If the proper teaching methods don't "please" the students then our job is to convince them that they need to change their minds about what gives them pleasure. If they can't do that then they might have only two choices: (1) be miserable throughout their stay in university, or (2) drop out.

Option three: (3) make the professor change the course in order to cater to the student's view of how a course should be taught, is not a reasonable option.

Many of these debates and discussions about the use of new technology in the classroom assume that there's resistance from old professors who are uncomfortable with new technology and/or social media. That may be true of some professors but many of my mature colleagues have been computer literate since before many young professors were born. Many of my colleagues have been using email for thirty years. They have had webpages, including course webpages, since the web was created twenty years ago. In spite of the fact that they are not intimidated by technology—what science professor is intimidated by new technology?—they have not radically transformed their way of teaching in the past several decades. Why is that? Is it because they have the wisdom and experience to know that new technology is not the best way to improve undergraduate education?


Tuesday, May 15, 2012

On the Quality of Online Courses

Are online courses a good thing, a bad thing, or relatively neutral? There's much to debate.

The main issue, as far as I'm concerned, is pedagogical. Are online courses a good way to teach critical thinking—the primary goal of undergraduate education?

There are tangential issues that often get in the way of dealing with the important questions and I'd like to deal with one of them here.

In a previous post [Is Canada Lagging Behind in Online Education?] I criticized a newspaper article by Michael Geist because he made an incorrect assumption. He assumed that any online course from a "top-tier" university would be serious competition for the average Canadian school. I selected two courses from MIT and showed that the quality of their biochemistry teaching was not a threat.

This point needs to be emphasized. Just because an online undergraduate course comes from Harvard, MIT, or Stanford does not mean that it's a good quality course. In my own field of biochemistry I know of many, many teachers in small schools throughout North America who can teach biochemistry better than famous research professors at the so-called "top-tier" schools.

It still may be true that students will flock to the Harvard, MIT, and Stanford courses and pay those schools for biochemistry credits but let's not assume, without justification, that they are getting a better education.

Today I received a copy of Academic Matters: OCUFA's Journal of Higher Education, a magazine published by the Ontario Federation of University Faculty Associations (OCUFA). The articles are devoted to technology in the classroom ("Professor 2.0." ugh!). An article by Sidneyeve Matrix [Challenges, Opportunities, and New Expectations] caught my eye. She says,
When Stanford University offers massively open online courses (MOOCs) in science and engineering, in one case drawing over 150,000 participants, people take notice. When the Khan Academy wins significant Microsoft funding, posts 3,000 instructional videos online, and attracts massive traffic, stories proliferate about the future of self-directed, online, informal e-learning. ... Critics ask, what’s the value of having students attend a lecture in real time if essentially the same material is covered by world-renowned professors on professional-quality video courtesy of free services at TED-Ed or YouTube Education? ... Why pay enormous fees to learn from faculty in an accredited university program, when MITx offers free online courseware with options for students to get peer-to-peer and professor feedback, assessment and earn branded certificates of achievement? What is the return on investment for students (and perhaps their parents) opting to earn their credentials at a bricks-and-mortar university when they could join the 30,000 others enrolled at the London School of Business and Finance in their Global MBA program—delivered online via a Facebook app?
There's a myth here that needs exposing. The quality of undergraduate education in the sciences1 should be judged by the content of the course and not the prestige of the university that offers it. Let's not get bamboozled into thinking that just because Stanford and Khan University Academy offer an online course in biochemistry that it's necessarily a good course.

The MIT examples I highlighted in my previous post says that this is a a bad assumption. You can look at the Stanford University Courses and make up your own mind.

Here's the important point: don't just assume that because an online course exists, it is necessarily a good course. You may have legitimate reasons for thinking that online courses are good things, but that doesn't excuse you from actually looking at the quality of an online course before declaring that the producers of such a course did a good job. Putting a bad course online is worse than putting no course online no matter what you might think of online courses.


1. I restricted myself to the sciences because we are presumably judging quality by the ability to teach critical thinking and factually correct material. There may well be degrees and programs where this isn't important. For example, it may not be important who teaches MBA courses since the goal is just to get a degree to put on your CV. In that case the prestige of the London School of Business and Finance may be far more important than whether you are actually learning something useful, or correct.

Michael Richards on the Sandwalk

Technically, this isn't Michael Richards on the Sandwalk but I'm posting it anyway. He sent me this drawing from a recent visit. It's the same view as in the Steve Watson and Seanna Watson photos (links are below). Thanks Michael.


Larry Moran
PZ Myers
John Wilkins
Ryan Gregory
The God Delusion
Cody
John Hawks
Michael Barton
Seanna Watson
Steve Watson
Michael Richards


Monday, May 14, 2012

Next Generation Science Standards: Evolution

Next Generation Science Standards is an organization dedicated to developing new K12 science standards for schools in the United States. The partners are the American National Research Council, The American Association for the Advancement of Science (AAAS), The National Science Teachers Association (NSTA), and Achieve, a nonprofit education reform organization.

The draft standards are posted on the website and you are invited to make comments until June 1st. Let's see what the new standards have to say about teaching evolution.

Here's what should be taught in middle school.
LS4.A: Evidence of Common Ancestry and Diversity
  • Fossils are mineral replacements, preserved remains, or traces of organisms that lived in the past. Thousands of layers of sedimentary rock not only provide evidence of the history of the Earth itself but also of changes in organisms whose fossil remains have been found in those layers. (a)
  • The collection of fossils and their placement in chronological order (e.g., through the location of the sedimentary layers in which they are found or through radioactive dating) is known as the fossil record. It documents the existence, diversity, extinction, and change of many life forms throughout the history of life on Earth. Because of the conditions necessary for their preservation, not all types of organisms that existed in the past have left fossils that can be retrieved. (c)
  • Anatomical similarities and differences between various organisms living today, and between them and organisms in the fossil record, enable the reconstruction of evolutionary history and the inference of lines of evolutionary descent. (b)
  • Comparison of the embryological development of different species also reveals similarities that show relationships not evident in the fully-formed anatomy. (d)
LS4.B: Natural Selection
  • Genetic variations among individuals in a population give some individual an advantage in surviving and reproducing in their environment. This is known as natural selection. It leads to the predominance of certain traits in a population, and the suppression of others. (e),(f)
LS4.C: Adaptation
  • Adaptation by natural selection acting over generations is one important process by which species change over time in response to changes in environmental conditions. (g)
  • Traits that support successful survival and reproduction in the new environment become more common; those that do not become less common. Thus, the distribution of traits in a population changes. (f)
  • In separated populations with different conditions, the changes can be large enough that the populations, provided they remain separated (a process called reproductive isolation), evolve to be separate species. (g)
Not bad, all things considered. I'd like to add that some evolution occurs by the chance increase in certain traits in a population, a process known as random genetic drift. Drift is part of the standards in my province of Ontario.

I'd also like to delete "in response to changes in environmental conditions" and "in the new environment" from LS4.C. The idea that natural selection only occurs when the environment changes is a common misconception and there's no reason to perpetuate that misconception.

Here are the high school standards.
LS4.A: Evidence of Common Ancestry and Diversity
  • Genetic information, like the fossil record, also provides evidence of evolution. DNA sequences vary among species, but there are many overlaps; in fact, the ongoing branching that produces multiple lines of descent can be inferred by comparing the DNA sequences of different organisms. Such information is also derivable from the similarities and differences in amino acid sequences and from anatomical and embryological evidence. (e)
LS4.B: Natural Selection
  • Natural selection occurs only if there is both (1) variation in the genetic information between organisms in a population and (2) variation in the expression of that genetic information—that is, trait variation—that leads to differences in performance among individuals. (a),(c)
  • The traits that positively affect survival are more likely to be reproduced, and thus are more common in the population. (b),(c),(d),(f)
LS4.C: Adaptation
  • Natural selection is the result of four factors: (1) the potential for a species to increase in number, (2) the genetic variation of individuals in a species due to mutation and sexual reproduction, (3) competition for an environment’s limited supply of the resources that individuals need in order to survive and reproduce, and (4) the ensuing proliferation of those organisms that are better able to survive and reproduce in that environment. (a)
  • Natural selection leads to adaptation, that is, to a population dominated by organisms that are anatomically, behaviorally, and physiologically well suited to survive and reproduce in a specific environment. That is, the differential survival and reproduction of organisms in a population that have an advantageous heritable trait leads to an increase in the proportion of individuals in future generations that have the trait and to a decrease in the proportion of individuals that do not. (b),(c),(f)
  • Adaptation also means that the distribution of traits in a population can change when conditions change. (d)
  • Changes in the physical environment, whether naturally occurring or human induced, have thus contributed to the expansion of some species, the emergence of new distinct species as populations diverge under different conditions, and the decline–and sometimes the extinction–of some species. (d)
  • Species become extinct because they can no longer survive and reproduce in their altered environment. If members cannot adjust to change that is too fast or drastic, the opportunity for the species’ evolution is lost. (d)
I have more of a problem with the high school standards. High school students must learn about random genetic drift, especially if they are comparing sequences since most of the changes they will see are nearly neutral changes that have been fixed by drift.

I think the standards should specifically mention that selection can occur in a constant environment since no organisms are perfectly adapted.

I hope the standards include specific attention to the relationship between humans and other species as shown by the combination of sequence comparisons, anatomical similarities, and the fossil record.

The source of mutations is covered in another section (LS3.B).

It would be nice to describe the differences between the fact of evolution and evolutionary theory.


Monday's Molecule #170

This is a rather unusual molecule that I suspect most of you are unfamiliar with. You need to identify the molecule (correct trivial name will do). I also want you to identify the most important enzyme that uses this molecule as a substrate in the normal direction of flux. Describe the dominant symptom of patients who can't make this enzyme.

Post your answers as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answers 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.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is 4α-carbinolamine, one of the products of the phenylalanine hydroxylase reaction. 4α-Carbinolamine is transformed into 5,6,7,8-tetrahydrobiopterin in two steps. In the first step it is the substrate for 4α-carbinolamine dehydratase. Mutations in that enzyme cause a mild form of phenylketonuria that usually has no serious consequences for the patient.

There are no winners this week.

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


Sunday, May 13, 2012

Is Canada Lagging Behind in Online Education?

"Is Canada lagging behind in online education?" is the title of an article in today's Toronto Star. The title in the print edition is "Education not evenly distributed."

The author is Michael Geist who is described as follows ...
Michael Geist is a law professor at the University of Ottawa where he holds the Canada Research Chair of Internet and E-commerce Law. He has a Bachelor of Laws degree from Osgoode Hall Law School in Toronto, Master of Laws degrees from Cambridge University in the UK and Columbia Law School in New York, and a Doctorate in Law from Columbia.
Hmmm ... that's interesting. A lawyer with no obvious expertise in education is writing about education. Let's see what he has to say ...
... in recent weeks it has become increasingly clear that the future of education is here, though it is not evenly distributed. The emerging model flips the current approach of expensive textbooks, closed research, and limited access to classroom-based learning on its head, instead featuring open course materials, open access to scholarly research, and Internet-based courses that can simultaneously accommodate thousands of students. The concern is that other countries are becoming first adopters, while Canada lags behind.

Wednesday, May 09, 2012

Multi Faith Room Disappears!!

I forwarded a link to my blog post [Look What Just Appeared Right Beside My Office!!!] to the Dean of the Faculty of Medicine. Less than 24 hours later the sign has been removed, the furniture taken away, and the door is locked.

I'm pretty sure the Dean is behind this. As soon as she learned about it, she recognized that someone had done something inappropriate (i.e. stupid). We'll probably never learn who was responsible but I thank the Dean for taking care of the problem so quickly.

This is just one more in a long list of good things she has done recently. We are lucky to have her as Dean.

Now, if only she had a better staff in the Dean's Office ....




Non-Negotiables of Darwinism

For the sake of completeness, I thought I'd include the basic tenets of Darwinism as outlined by Bill Dembski in his BioLogos essay: Southern Baptist Voices: Is Darwinism Theologically Neutral?.
Non-Negotiables of Darwinism:
  • (D1) Common Descent: All organisms are related by descent with modification from a common ancestor.
  • (D2) Natural Selection: Natural selection operating on random variations is the principal mechanism responsible for biological adaptations.
  • (D3) Human Continuity: Humans are continuous with other animals, exhibiting no fundamental difference in kind but only differences in degree.
  • (D4) Methodological Naturalism: The physical world, for purposes of scientific inquiry, may be assumed to operate by unbroken natural law.
My question is for any scientist who defines themselves as a Darwinist. Do you agree with these non-negotiables? Are there any you would like to add or modify?


Non-Negotiables of Christianity

Many of us have been wondering what it means to be a Christian. Can Christianity be made compatible with science?

Bill Dembski has the answer on BioLogos at Southern Baptist Voices: Is Darwinism Theologically Neutral?.
Non-Negotiables of Christianity:
  • (C1) Divine Creation: God by wisdom created the world out of nothing.
  • (C2) Reflected Glory: The world reflects God’s glory, a fact that ought to be evident to humanity.
  • (C3) Human Exceptionalism: Humans alone among the creatures on earth are made in the image of God.
  • (C4) Christ’s Resurrection: God, in contravention of nature’s ordinary powers, raised Jesus bodily from the dead.
Decide for yourselves. Is Christianity compatible with science? Are there Christians who are prepared to abandon one of more of these "non-negotiable" in order to make science and Christianity compatible? Are there accommodationsts who think that Dembski's version of Christianity is compatible with science? with evolution?


On the Difference Between "Evolutionary Theory" and Scientific Fact

There's been a lot of discussion about Elliott Sober's talk at the University of Chicago. You can watch the entire talk and the questions & answers at [The Problem with Philosophy: Elliott Sober].

Most of the debate is taking place on Jerry Coyne's site [Can God create mutations? Elliott Sober says we can’t rule that out.] and on Jason Rosenhouse's blog [The Reason For the Ambivalence Towards the Philosophy of Science]. Things aren't going well for Elliott Sober and, by implication, for the philosophy of science.

I want to discuss another troubling aspect of Sober's talk. Throughout the talk he refers frequently to "evolutionary theory" or "the theory of evolution." This is consistent with the introduction by Robert Richards where he says they are considering "... the application of evolutionary theory to the humanities and social sciences" (27 sec). The title of Sober's talk is "Naturalism and Evolutionary Theory."

What do they mean by "evolutionary theory"? To me, evolutionary theory means the kinds of things that are discussed in Stephen Jay Gould book "The Structure of Evolutionary Theory." It includes things like population genetics and the potential influence of genome size on the fixation of alleles. It includes things like species sorting and punctuated equilibria. It even includes speculation about selfish genes and the level of selection.

Evolutionary theory does NOT include whether birds and dinosaurs share a recent common ancestor, the age of the Earth, the amount of junk DNA in our genome, or the causes of mutation. Those are interesting questions that bear on evolution but the answers to those questions are not a fundamental part of evolutionary theory. The are questions of scientific fact, in my opinion.

Do philosophers like Elliott Sober agree with this distinction? I don't think so. The main point of Sober's talk is whether evolutionary theory can show that mutations are random. He concludes that evolutionary theory cannot conclusively prove that all mutations arose by chance; therefore, there's room for God-directed mutations as long as their frequency is indistinguishable from randomness.

Sober has a paper that discusses this issue [Evolution without Naturalism]. Here's the part that describes "evolutionary theory" (page 5).
What is this thing called “evolutionary theory,” which theistic evolutionism is able to encompass consistently? It includes the origin of life from nonliving materials by physical processes, the branching genealogical process whose upshot is that current organisms are connected to each other by relations of common ancestry, the random origin of new mutations, and the processes that govern trait evolution within lineages, such as selection and drift. Among these several propositions, the idea that mutations are “random” may seem to be a sticking point.
This is not what I think of when I use the term "evolutionary theory." I don't think the origin of life is a part of evolutionary theory. I don't think that the random origin of new mutations is part of evolutionary theory. As far as I'm concerned, the discovery that mutations occurred preferentially in hotspots or that there was a base composition bias—which there is—would not refute evolutionary theory. I think my understanding of evolutionary theory is closer to that of the majority of evolutionary biologists and it's troubling to me that philosophers seem to use a different definition.

Here's another example from that same paper (page 4) ...
Although evolutionary theory is silent on the question of whether there is a God, it is not neutral with respect to logically stronger hypotheses about God. Consider, for example, the statement
Life appeared on earth about 10,000 years ago due to divine intervention.
This statement is inconsistent with evolutionary theory.
The Young Earth Creationist statement is inconsistent with all available scientific evidence on the age of the Earth. This evidence is so overwhelming that it is a scientific fact (sensu Gould) that the Earth is billions of years old. Why does Sober think that "evolutionary theory" plays a role here?

This is not just a semantic quibble. By confusing "evolutionary theory" with scientific facts Sober makes it much more difficult to follow his line of reasoning.

Is it true that the majority of philosophers of science use "evolutionary theory" when they should frequently be referring to scientific facts? Is it true that most philosophers think that the age of the Earth is a "theory"? Do they also think that evolution is only a theory?