The 10,000 Mile Diet

This article, Shop locally, eat globally? , appeared in today's edition of our university bulletin. I thought it was worth posting a link because, unfortunately, many of my relatives, friends, and colleagues think you can support a large city by only eating food grown within one hundred miles (161 kilometers).

Pierre Desrochers knows how to serve up controversy. When an acquaintance mentions she follows a 100-mile diet to help the environment, Desrochers calmly asks how much energy it takes to heat an Ontario greenhouse.

When a colleague lauds local food as more nutritious than products shipped thousands of miles, Desrochers politely points out that the diet of a 19th-century German peasant consisted of lentils and peas.

Now, the University of Toronto Mississauga geography professor has published a controversial new book that goes beyond polite mealtime conversation and pits what Desrochers calls the “romanticism” of local eating, or locavorism, against the realities of a global food-supply chain.

Desrochers is the co-author of The Locavore’s Dilemma: In Praise of the 10,000-mile Diet, in which he argues that we should stop obsessing about how many miles our food has travelled to get to our dinner plate.

“Three centuries ago most people were eating local food,” Desrochers says. “Why do we think the world moved away from that? There are significant benefits—particularly, environmental and economical—in collaborating to produce food in the best geographic locations.”

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Richard Harter 1935 - 2012

I just heard from Dave Greig that Richard Harter died over a month ago [Richard Harter 1935 - 2012]. He was a long time contributor to talk.origins having been there since it was called net.origins in the early 1980s. Richard was a staunch defender of science and evolution and a vocal opponent of stupidity (aka creationism). Here's how he describes the phenomenon that is talk.origns [Evolution, Creationism, and Crackpots].

I discovered the usenet news groups circa 1983. In those days there was no big 8 hierarchy; everything was net.this and net.that. One of the hot groups was net.origins, now talk.origins, the designated dumping grounds for creationism/evolution flame fests.

Some usenet newsgroups are models of decorum, where specialists in sundry topics urbanely discuss their specialties. Some are havens of nattering wherein recipes and small talk are exchanged. Such newsgroups represent usenet at its best as a civilized expression of the electronic personal free press. How boring.

There are newsgroups which are open cockpits wherein all and sundry engage in electonic eye-gouging, leaving bodies scattered about the floor, bodies which miraculously arise to gouge and rabbit punch in return. Much more entertaining. Unfortunately such entertainments pall after a while. The same things are said by the same people endlessly. When one flamer departs he or she is replaced by a clone, another mindless dweeb screaming invective into the electronic night air. There is no content, merely an exchange of prejudices and emotion.

The talk.origins group is, to my taste, a happy combination of meat and sauce. To be sure there are no end of flames. However there is much content also. It all has to do with the subject matter. Talk.origins is supposed to be the arena where creationism and evolution are debated. That happens. However it is a happy hunting grounds for cranks and crackpots who come to be told that they are idiots. They revel in it for, finally, someone is listening to them.

The nifty thing about talk.origins is that you can get a real education by reading the group -- the crackpots are not only told that they are idiots, people cite chapter and verse to show where they are in error. Biologists, archaeologists, paleontologists, and the like post there. There is also a good deal of offbeat humor. For your delectation I have prepared a potpourri of essays and materials drawn from talk.origins.

Richard was born in South Dakota and he moved back there in 2000. He never stopped reminding us that South Dakota actually exists and people actually live there. He died of complications from myelodysplastic syndrome (MDS) [Why couldn't I have something simple, like pneumonia].

There's lots more where that came from. Check out Richard Harter's World while it's still active. I especially like his detailed analysis of one of the most difficult problems in all of science: The Seat Stays Up. His summary of everything related to Piltdown Man is a classic.¹

The motto on his web page is appropriate ...

I don't worry about dying.
It's not going to happen in my lifetime.

UPDATE: talk.origins remembers Richard Harter

UPDATE: I'm told that Richard's website will be preserved at Richard Harter's World.

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1. I hope someone copies it before it disappears.

Visiting John Hawks

I'm in Madison Wisconsin. What in the world does one do In Madison? Well, there's the State Legislature (beautiful), the free zoo, and a boat ride on the lake.

But all those pale in comparison to the main attraction ... visiting John Hawks of John Hawks Weblog. I found him in a lab full of bones at the at the University of Wisconsin, Madison.

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Delusions

I know I shouldn't pick on David Klinghoffer and the other IDiots at Evolution News & Views but, believe it or not, this is the best the IDiots have to offer.

I just can't resist posting this quotation from his latest post at: The Stubbornness of Their Ignorance.

Forget for a moment about who, Darwinists or Design advocates, is actually right. If you took a sample of ID folks and a sample of Darwin people, specifically those who have felt confident enough in their views to write about them for publication, and then quizzed each group about what arguments their opponents offer, there's no question that those from the ID community would know better what their opposites in the debate say.

Just look at ENV as a convenient illustration. We strive to keep up with toughest challenges, such as they are, from evolutionists. Now look at the competing Darwin blogs. Guys like PZ Myers & Co. concentrate their fire on naïve young-earth creationists. Jerry Coyne and his colleagues in the Darwin-defending business are careful to stay unaware of the very serious challenges to Darwinism from ID.

Wrong!

As it turns out, most of us know more about Intelligent Design Creationism than the average IDiot. As for evolution, I've yet to meet an IDiot who even comes close to understanding it, although Michael Behe and Michael Denton come pretty close.

Klinghoffer and his friends are deluding themselves if they think we don't know what they are saying and they are even more delusional if they think they understand evolution. We've proven time and time again that they don't.

Are we surprised? No, because the one thing all IDiots have in common is the God delusion—the biggest one of all.

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What Do Aromatic Compounds Have to Do With DNA Stability?

Jacqueline of skepchick tells us at: 2D Molecules that Form Our 3D World.

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My Review of Shapiro's Book Is Finally Published!

I wrote a review of Evolution: A View from the 21st Century for NCSE (National Center for Science Education). It was finished last September but NCSE delayed publication until they fixed up the website for Reports of the National Center for Science Education.

Here's the Table of Contents of the latest issue. All articles are free!

Shapiro threatens to respond to my review if he doesn't like it. I'm certain he won't like it. I'm looking forward to seeing how he responds to my criticisms, especially concerning his lack of knowledge of the history of evolutionary theory and his confusion about the meaning of the Central Dogma of Molecular Biology.

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Carnival of Evolution #48

This month's Carnival of Evolution (48th version) is hosted by a developmental biologist at the University of Minnesota (Morris). He blogs at Pharyngula: Carnival of Evolution 48: The Icelandic Saga

I must begin by apologizing for my tardiness, especially since John Wilkins managed to post the last one on time. I was traveling in the 2½ weeks preceding the deadline for CoE, and the combination of spotty internet access, extreme jetlag (British Columbia to Germany to Iceland, where the sun hovered around the horizon all night long, just messed me up), and of course, the incredible distractions of exotic foreign lands, meant that I was disgracefully dilatory in putting it all together.

The next Carnival of Evolution (July) has no host. If you want to volunteer, contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before. Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution.

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Kirsty Duncan MP Objects to "Bias" in the Working Group on CIHR Funding of a Clinical Trial on "Liberation Therapy"

The previous post mentioned a recently published article on "liberation therapy" that referred to it as something akin to faith healing. It criticized the decision by Canada's CIHR to fund a clinical trial on the procedure. One of the authors of that article was Barry Rubin who served on the working group that recommended the trial.

This prompted a letter from Liberal MP Kirsty Duncan to Dr. Alain Beaudet, President of CIHR [MP lists concern with CIHR expert]. This is a blatant example of political interference and it should not be tolerated. Duncan should be reprimanded in Parliament.

Dear Alain,

Hello and warm wishes.

I am writing to you in order to bring an urgent issue to your attention. As you know, Dr. Barry Rubin is a member of CIHR's expert working group to study CCSVI. According to CIHR's website, the working group's mandate is: "The scientific expert working group will make recommendations on further studies including, if appropriate, a pan-Canadian interventional clinical trial that would evaluate the safety and efficacy of venous angioplasty in patients with MS, and will provide advice on the protocols to expedite such a trial (e.g. inclusion/exclusion criteria)."

Dr. Rubin is the fourth author on an article, 'The "Liberation Procedure" for Multiple Sclerosis: Sacrificing Science at the Altar of Consumer Demand', in the May, 2012 Journal of the American College of Radiology, Volume 9, Issue 5, Pages 305-308.

Alain, you and I have discussed conflict of interest numerous times before-both at committee and in correspondence. Surely, a member of the scientific expert working group publishing such a paper questioning clinical trials is in conflict with the group's mandate.

It is absolutely imperative that all members of the expert working group be independent, but equally important, be seen as independent, and not to have taken a position. Dr. Rubin can no longer be seen to be an independent judge of the scientific literature, as demonstrated by the conclusion of the paper.

Let me quote from the article, "Although some would agree that a randomized, blinded clinical trial is necessary to settle the issues raised in the controversy surrounding this procedure, others would agree that not all controversial procedures require such an expensive approach. Funding trials of a procedure that has minimal basis in rational, empirical knowledge seems questionable. At this point, the procedure rests in the same category of "medical" management as chelation therapy for atherosclerosis (which failed just such a trial), treatment of breast cancer with laser photodynamics, Laetrile for cancer, and other unproven therapeutics found in the retail sphere. When consumerism and patient advocacy groups pressure the scientific and political establishment, reasonable accommodation is warranted. The question is, What is reasonable? It may be that the operators believe in the therapy as much as the understandably desperate patients. The subsidiary question is, When is healing 'faith healing'?"

I will not comment on the science-or lack thereof-of the above.

It is extremely important to note that the first author of the paper, Dr. Michael Brant-Zawadzki of Hoag Memorial Hospital is being credited with prompting the FDA warning this past week.

There are important questions that need investigation. How did Dr. Brant-Zawadski and Dr. Rubin make contact? Were you apprised that Dr. Rubin was writing the article? Did you read the article pre-publication? When was the article accepted for publication? Were you or other officials at Health Canada and CIHR apprised of the FDA alert, and if so, when? Does CIHR support Dr. Rubin's behaviour? Are you concerned that the FDA alert-and this article-will prejudice/affect the ethical board reviews for CCSVI clinical trials? What action will be taken, as clearly this is a conflict of interest?

There is real concern amongst the CCSVI community that while the government fast-tracked Tysabri-a drug which was known to cause PML, and has now infected 232 people and killed 49 people-, and Gilenya, a drug which has now killed 11 people, and is currently under review in Canada (by the way, I am still waiting to hear from Paul Glover about the process for Health Canada's review of Gilenya)-, the government has been reticent about clinical trials for venous angioplasty, which is performed for Budd-Chiari syndrome, May-Thurner syndrome etc. across this country. Now a key panellist has not only come forward, but also published a paper with tremendous hyperbole, "sacrificing science at the altar", and members of the CCSVI community are concerned that a parallel process is being created-one in which the government says it will undertake clinical trials, while a key player appears to work actively to prevent this.

In closing, Dr. Haacke, Dr. McDonald, and Dr. Zamboni were not included in the August 26th, 2010 joint CIHR-MS Society meeting. The explanation given for their not being included in the meeting was that their work would be discussed, and including them might bias the discussion. Now, we have a member of CIHR's expert working group publishing and questioning clinical trials. Clearly, his position may bias the discussion.

Alain, this is extremely serious, and so, I look forward to hearing from you at the earliest time possible regarding Dr. Rubin's inclusion in the scientific expert working group.

Yours very truly,

Kirsty (Duncan)

Kirsty Duncan does not understand how science works and she does not understand that advocates of quack medicine are the ones who are "biased" against real science. It's not the scientists on the working group who caused the problem.

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Canadian Government Allocates Funds to Investigate "Liberation Treatment" for Multiple Sclerosis: Sacrificing Science at the Altar of Consumer Demand

The Canadian Institutes of Health Research (CIHR) is the main funding agency for health research in Canada. Most of the research in my department is funded by CIHR grants and the number and size of those grants has been shrinking, with disastrous consequences for my colleagues.

Chronic cerebrospinal venous insufficiency (CCSVI or CCVI) is the name of a condition invented by an Italian doctor named Paolo Zamboni. He claims that it is the cause of multiple sclerosis. He also claims to have developed a procedure called "liberation treatment" or "liberation therapy" that will alleviate the symptoms of MS. It involves opening up some of the veins in a patient's neck in order to improve blood flow. He has been treating patients from all over the world for the past few years.

As you might have guessed, the treatment at his clinic is not free.

There has been enormous pressure on the Canadian and provincial governments to fund this treatment for MS patients, who otherwise have no hope of a cure. So far, most provinces have refused to pay for the treatment. In August 2010, CIHR announced that it would not fund research into something that does not exist [CIHR makes recommendations on Canadian MS research priorities].

Ottawa (August 31, 2010) – On Thursday, August 26, the Canadian Institutes of Health Research (CIHR), in collaboration with the MS Society of Canada, convened a meeting of leading North American experts in multiple sclerosis (MS) to identify research priorities for Canada in this area. Today, at a press conference in Ottawa, CIHR President Dr. Alain Beaudet announced the outcomes of the discussions and shared the recommendations he has made to the Honourable Leona Aglukkaq, Minister of Health.

"There was unanimous agreement from the scientific experts that it is premature to support pan-Canadian clinical trials on the proposed "Liberation Procedure," said Dr. Beaudet. "There is an overwhelming lack of scientific evidence on the safety and efficacy of the procedure, or even that there is any link between blocked veins and MS."

This is the right decision. Money is scarce and it would be criminal to devote any of it to quackery at the expense of legitimate scientific research.

But there's a catch.

Casey Luskin "Explains" Intelligent Design Creationism

Casey Luskin is upset with a philosopher named Christopher Pynes. Paynes had the audacity to suggest that one of the key features of Intelligent Design Creationism is ... creationism. According to Paynes, "supernaturalism is a necessary component of ID: there must be a designer" [AD HOMINEM ARGUMENTS AND INTELLIGENT DESIGN: REPLY TO KOPERSKI].

Luskin wants to remind everyone that Intelligent Design Creationism has nothing to do with a creator/designer [Professor Pynes Rails Against the "Straw-Man Fallacy" while Attacking a Straw-Man Version of Intelligent Design]. According to Luskin (a lawyer), Intelligent Design Creationism is a purely scientific theory that relies on: (a) proving that evolution is wrong, (b) detecting the creator/designer by examining nature.

On the primary¹ grounds that it's always good to know your enemy, I present to you the best scientific grounds for Intelligent Design Creationism.

• Studies of physics and cosmology continue to uncover deeper and deeper levels of fine-tuning. Many examples could be given, but this one is striking: the initial entropy of the universe must have been fine-tuned to within 1 part in 10(10^123) to render the universe life-friendly. That blows other fine-tuning constants away. New cosmological theories like string theory or multiverse theories just push back questions about fine-tuning, and would, if true, simply exacerbate the need for fine-tuning. This points to high levels of complex and specified information (CSI) in the cosmid architecture of the universe--information which in our experieince only comes from intelligence.
• Mutational sensitivity tests increasingly show that DNA sequences are highly fine-tuned to generate functional proteins and perform other biological functions. Again, this is high CSI--which in our experience only comes from intelligence.
• Studies of epigenetics and systems biology are revealing more and more how integrated organisms are, from biochemistry to macrobiology, and showing incredible fine-tuned basic cellular functions. The integrated nature of organismal body plans shows CSI throughout biological systems--in our experience, only intelligence can generate tightly intregrated multi-component blueprints.
• Genetic knockout experiments are showing irreducible complexity, such as in the flagellum, or multi-mutation features where many simultaneous mutations would be necessary to gain an advantage. This is more fine-tuning--and in our experience, irreducibly complex machines arise only from intelligence.
• The fossil record shows that species often appear abruptly without similar precursors, which represents mass-explosions of high CSI--something which requires an intelligent cause.
• There have been numerous discoveries of functionality for "junk DNA." Examples include recently discovered functionality in some pseudogenes, microRNAs, introns, LINE and ALU elements. Intelligent design predicted this data.

If all of these things were true, then you'd predict that scientists would be flocking to church on Sundays. You'd also expect that the scientific literature would be full of papers proving the existence of God. It would be the most remarkable discovery in the history of humans.

A key part of Intelligent Design Creationism—the part that Casey Luskin is leaving out—is to explain why it has been so remarkably unsuccessful after 200 years of trying. That part has to do with the huge Darwinist conspiracy that forces scientists to tow the line and stick with atheistic Darwinism in spite of all the scientific evidence against it. If you read the blogs, you'll see that attacking scientists and Darwinism is the dominant theme. The "scientific" "evidence" for Intelligent Design Creationism is almost never mentioned.

Most of us scientists don't realize that we are part of such a conspiracy because we have been brainwashed into believing in evolution. However, a few god-fearing souls have seen the truth. Some of them are lawyers (Casey Luskin, Philip Johnson), some of them are philosophers, some of them claim to be mathematicians, and a few think they are scientists (Michael Behe, Jonathan Wells). The one thing they all have in common is that they are all IDiots.

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1. The secondary grounds are to keep a record of the June 2012 "facts" because they will change soon enough.

Graduation Day

June is graduation month at the University of Toronto. There are various classes graduating every morning and afternoon for several weeks. (We have more than 70,000 students on three campuses, counting undergraduates, graduates, and enrollment in professional faculties.)

Today it's the turn of medical students. About 215 students just received their M.D. degrees. I'll be glad when it's all over 'cause the lineups at Tim Horton's¹ are horrible.

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Starbucks too, but I don't care about them.

A Platypus Describes Humans

Ryan Gregory invents The Platypus Fallacy to illustrate an important concept in evolution. Here's how a platypus describes humans. See if you can spot the problem.

The lineage of which humans are a part is a very ancient offshoot of our mammalian family tree, so it was 166 million years ago that we last shared a common ancestor with humans, and that puts them somewhere between mammals and reptiles, because they lack a lot of specialized characters that we have gained but the ancestral amniote also lacked; for instance, they have no electroreception, no bills, no webbed feet, and no venom. So we can use them to trace the changes that have occurred as we went from being a reptile, to having fur to making milk to having our specialized features.

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Bruce Alberts Talks About Science Literacy

Bruce Alberts was president of the National Academy of Sciences (1993-2005), author of The Molecular Biology of the Cell, and winner of the Gairdner Award for his work on DNA replication. He was my Ph.D. supervisor. He is currently editor-in-chief of Science magazine. He has been interested in science education and science literacy for many decades so when he makes a comment about science education, it's worth listening to.

Here's a quote from a recent interview in PLoS Genetics [Scientist Citizen: An Interview with Bruce Alberts].

You look at the current political system in the US. It's incredibly depressing. These kinds of statements that “scientists only believe in climate change so that they can get a grant.” This kind of stuff couldn't be said if we actually had a population that understood what science is. We have a fantastic scientific community, and if we don't unleash them and give them credit for working on these things, then I don't think our country is going to prosper.

Every ten years the Academy publishes a booklet called “Science, Evolution and Creationism” [available online], and before the last one in 2008, the Academy hired one of the companies that put people behind a one-way mirror and interview them to see what they think about some new product. But this question was, “How do they think about science and creationism?”

And the staggering message from these college-educated adults is that they don't see any difference between science as a belief system and religion as a belief system. So basically, the preacher tells them what religious people believe, the scientists tell them what scientists believe, and [they think] “I can choose either one.” And the reason they can say that is that they don't understand what we call “science as a way of knowing”. That it is not a belief system, that it is an evidence-based community process.

This is just unbelievable, that our American public can determine our future without understanding the fundamental issues about scientific facts. If the population isn't prepared to deal with these kinds of issues, to think rationally and respect evidence, then I think the country is really in danger.

Like I say, science is a way of knowing that involves evidence and rationality. Now you know where I got that from.

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The photo was taken at Bruce's 70th birthday party. It shows him with his first three graduate students: Keith Yamamoto (left), me (second from right), and Glenn Herrick (right).

Monday's Molecule #173

This is an easy one. We talked about this molecule in our lunch time seminar just a few minutes ago. It binds to lots of proteins.

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 malonyl-ACP where ACP stands for acyl carrier protein. The winners are Bill Chaney and Matt McFarlane. One other person got it right but didn't specify what "ACP" stood for. The most common error among those who came close was to call it malonyl-CoA.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane

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Cornelius, Meet Johnnyb

Cornelius Hunter doesn't like anything about evolution. He especially doesn't like us to say that Evolution Is a Fact.

Here's the latest from Cornelius [When I Pointed Out the Evolutionary Tree Has Failed Two Professors Gave Me Pushback ].

If you are new to the evolution debate you might wonder why evolutionists do not simply acknowledge the painfully obvious fact that evolution is not a fact. It is not as sure gravity and in fact there are significant questions and problems with evolution. Why don’t evolutionists admit to the truth of how the science bears on their theory?

The answer is that evolution is not about the science. At issue here is not merely the status of another scientific theory. Evolutionists won’t be swayed by the evidence because doing so—and confessing that evolution is not overwhelmingly supported by the evidence—would immediately expose evolutionists to all kinds of possibilities which they simply cannot accept. An evolutionist can no more change his mind than could a cultist. Evolution is underwritten by a religious worldview—it is a metaphysical theory, not at scientific theory. As such it may lose every battle, but it cannot lose the war.

Contrast this with what Johnnyb said a few weeks ago on Uncommon Descent [see All IDiots Believe in Evolution! ].

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?”

Cornelius Hunter and Johnnyb really should get together and agree on the facts.

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Turn Right! Turn Left!

If you're driving on a two lane highway and a head-on collision seems imminent, you should turn right. This probably doesn't work in England.

Phil Plait of Bad Astronomy tells us that the Andromeda Galaxy is on a collision course with our Milky Way Galaxy [Hold on tight: in 4 billion years, we’re due for a galactic collision!]. What should we do? We don't know whether the Andromedons drive on the right side of the road or the left. Which way should we turn to avoid the collision?

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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.

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.”

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'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

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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.

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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 BurkeWe'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.

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[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.