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?

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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?

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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.

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[Hat Tip: RichardDawkins.net]

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?

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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.

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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?

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[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?

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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

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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.

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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.

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.

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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.

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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.