DNA Replication in E. coli: The Problem

I've started reading microcosm by my favorite science writer, Carl Zimmer [Buy This Book!]. Watch for a review, coming soon.

I was mildly disappointed to see Carl repeat a common myth about DNA replication in E. coli on page 29. Since we often use this myth to teach critical thinking in our undergraduate classes, I thought it would be worthwhile to discuss it here.

Today I'm going to present the problem and let everyone think about a possible solution. On Sunday, I'll publish the answer. (If you know the solution, you are not allowed to post it in the comments—I'll delete those comments. You can ask for clarification or speculate.)

Here's what Carl says at the top of page 29.

E. coli faces a far bigger challenge to its order when it reproduces. To reproduce, it must create a copy of its DNA, pull those chromosomes to either end of its interior, and slice itself in half. Yet E. coli can do all of that with almost perfect accuracy in as little as twenty minutes.

Today, we're not concerned about the 20 minute generation time but I note, for the record, that the average generation time of E. coli, in vivo, is about one day. I also want to mention that the 20 minute generation time is an extreme example that's achieved only under the most extraordinary circumstances. Typical generation times in the lab are about 30 minutes.

However, that's not the problem. Let's assume a generation time of 20 minutes.

In the next paragraph Carl says ...

The first step in building a new E. coli—copying more than a million base pairs of DNA—begins when two dozen different kinds of enzymes swoop down on a single spot along E. coli's chromosome. Some of them pull the two strands of DNA apart while others grip the strands to prevent them from twisting away or collapsing back on each other. Two squadrons of enzymes begin marching down each strand, grabbing loose molecules to build it a partner. The squadrons can add a thousand new bases to a strand every second.

What Carl is referring to the the assembly of replication complexes (replisomes) at the origin of replication. Once those complexes are assembled, replication fires off and proceeds in opposite directions (bidirectionally) until the two fork meet at the opposite side of the chromosome.



Carl is correct when he says that the forks move at 1000 nucleotides per second. Later on in his book he mentions that the size of the E. coli chromosome is 4,600,000 base pairs or 4,600 kb (p. 116). At 1000 nucs per second it would take 4600 second to replicate this DNA if there was only one replication fork. Since there are two, it will take 2,300 seconds.

You can do the math. This is 38 minutes. It is a correct number—it takes at least 38 minutes to replicate the E. coli chromosome, not 20 minutes as stated earlier. It is true that the generation time of E. coli can be as short as 20 minutes under extraordinary circumstances.

Here's the problem. How can E. coli divide faster than it can replicate it's chromosome?

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Ben Stein's Dangerous Idea

 
Uncommon Descent is the Intelligent Design blog of Bill Dembski, Denyse O'Leary and their friends. It represent the best that the IDiots have to offer.

Yesterday's posting by DLH is an example of the best sort of creationist reasoning. The posting is an extensive quotation from an article by Robert Meyer originally posted in New Alliance Magazine [Ben Stein’s Dangerous Idea]. Here are the first three paragraphs quoted on the blog ...

Ben Stein has a dangerous idea. His idea is that professors and teachers who express skepticism about Darwinism are likely to find themselves not granted tenure, castigated and ridiculed, and disqualified from the opportunity to have research papers published.
. . .
Having reviewed the movie myself, it appeared that Stein was trying to make the case for academic freedom, not attempted to convert anyone to a particular ideological position.

Stein, in fact, never makes it known what particular beliefs he holds personally, he merely makes it known that he is disgusted by the idea that someone could lose their job over honest doubts about Darwinism.

No, your eyes are not deceiving you. Re-read that last paragraph. For all we know Stein may be a secret evolutionist. He's only interested in academic freedom. It's just a coincidence that the phrase "No Intelligence Allowed" uses the same word as Intelligent Design.

Jeesh. And you wonder why we call them IDiots?

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Make Englishe the Only Offal Language

 
I'm with Orac and Orcinus on this one. This is just too delicious to resist.¹

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1. Although, as a notoriously bad speller, I have made some pretty similar mistakes on Sandwalk.

Congratulations Jason Rosenhouse!!!

 
A big event just happened at Evolutionblog—Jason Rosenhouse got tenure [Tenure!]. Congratulations Jason.

I'll let him describe the process ....

I got tenure! Yay! By my count it's been about fifteen years getting to this point. I started studying mathematics seriously in my last two years of college (a rather late start in this profession). Then it was five years of graduate school, three years as a post-doc in Kansas, and now five years at JMU. Pretty satisfying. Suddenly that obnoxious and contentless rejection letter I received a month ago on a paper the journal should have been honored to publish doesn't seem to sting so much. (I'll just patch it up and send it off to the next journal, where it will languish for ten months to a year. What do I care? It's not like I'm in any great hurry to publish anymore!)

So there you go. Guess now I can tell you what I really think...

I guess this is when we discover that Jason is really a closet IDiot.

UPDATE: It didn't take long ...

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Nobel Laureates: Arvid Carlsson and Paul Greengard

 

The Nobel Prize in Physiology or Medicine 2000.

"for their discoveries concerning signal transduction in the nervous system"

Arvid Carlsson (1923 - ) and Paul Greengard (1953 - ) received the Nobel Prize in Physiology or Medicine for their work on identifying dopamine as a neurotransmitter. They also showed that L-dopa [Monday's Molecule #70], a precursor of dopamine, could relieve the symptoms of dopamine depletion and help control the symptoms of Parkinson's disease. They shared the prize that year with Eric R. Kandel.

THEME:Nobel LaureatesThe presentation speech was given by Professor Urban Ungerstedt of the Nobel Committee at Karolinska Institutet. (The date was, of course, December 10th as always. This is the anniversary of Alfred Nobel's death.)

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen,

This year's Nobel Prize in Physiology or Medicine concerns the most complex structure in the universe that we know of - the human brain. It consists of 100 billion nerve cells, which is the same number of cells as the total number of human beings that have ever lived on this earth.

We talk about the "Internet revolution"; 35 million Internet users who communicate now and then - what is that compared to the nerve cells we all carry within ourselves! 100 billion nerve cells that communicate continuously.

It is this communication, "signal transduction in the nervous system," which is the subject of this year's Nobel Prize. A single nerve cell forms thousands of contact points, so-called synapses, with other nerve cells. In these synapses the nerve cells communicate by chemistry; one cell releases a transmitter, which reaches the other cell.

Professor Arvid Carlsson proved that dopamine is such a transmitter. The general belief was that dopamine was a precursor of other transmitters and of little functional importance. However, Professor Carlsson was able to show that dopamine existed in specific parts of the brain and concluded that it was a transmitter in its own right.

He then used a naturally occurring substance, reserpine, which empties the dopamine from the nerves, and found that the animals lost their ability to move. He realized that it must be possible to restore the dopamine levels with L-DOPA, a precursor of dopamine. In a conclusive, dramatic experiment he showed that the animals regained their ability to move when he gave them L-DOPA.

Reserpine had depleted dopamine and had given the animals the symptoms of Parkinson's disease, that is, rigidity and inability to move and react to stimuli in the environment. When the animals were given L-DOPA, dopamine was produced again in their brains. In this way the idea of treating Parkinson patients with L-DOPA was born. This enables millions of patients around the world to live a normal life.

Professor Paul Greengard showed what happens when dopamine and other similar transmitters stimulate a nerve cell. Receptors on the cell surface activate enzymes in the cell wall, which starts the production of second messengers. These messengers travel into the cell and activate a protein kinase, which starts to bind phosphate groups to other proteins, in this way altering their function. This leads, for example, to the opening of ion channels in the cell membrane and a change in the electrical activity of the cell.

Professor Greengard then showed that dopamine and other transmitters affect a central regulatory protein, which has been called DARPP-32. Like the conductor of an orchestra, it tells other proteins when and how to be activated.

This so-called "slow synaptic transmission" controls our movements and also those processes in the brain that elicit emotions or react to addictive drugs such as cocaine, amphetamine and heroin.

Professor Eric Kandel showed that transmitters of the same type as studied by Arvid Carlsson, via the protein kinases characterized by Paul Greengard, are involved in the most advanced functions of the nervous system such as the ability to form memories.

Imagine how difficult or impossible it must be to study how memory is formed in a human brain with 100 billion nerve cells. Eric Kandel, therefore, did something which is classical in all natural science: He chose to study a simpler model system, a sea slug, Aplysia, which has 20,000 nerve cells. He did it with the conviction that even primitive animals must learn in order to survive.

The sea slug has a withdrawal reflex protecting its gills. If they are touched repeatedly, they react less and less - just as human beings do when subjected to an unexpected touch. If, on the other hand, the touch is forceful the reflex is amplified and becomes stronger and stronger.

The habituation or amplification effect lasts only for a few minutes. One may say that the sea slug exhibits a short-term memory. If the forceful stimulus is repeated several times, the sensitization may remain for weeks, that is, the sea slug develops a long-term memory.

Professor Kandel was able to show that habituation to touching was due to changes in the synapse, the contact point between the nerve cells. During habituation less and less transmitter was released.

The forceful stimulus that formed the long-term memory worked in a completely different way. Second messengers activated protein kinases that entered the cell nucleus and started the production of new proteins. This, in turn, brought about a change in the form and function of the synapse. What we call memory is, thus, elicited by direct changes in the billion of synapses that form the contact points between the nerve cells.

I am convinced that you and I will remember this Nobel ceremony for many years. This is because of the dopamine which Arvid Carlsson discovered, enabling the brain to react to what we see and hear; the second messengers that Paul Greengard described, carrying the signals into the nerve cell; and the memory functions that Eric Kandel found to be due to changes in the very form and function of the synapses.

Dear Arvid Carlsson, Paul Greengard and Eric Kandel. Your discoveries concerning "signal transduction in the nervous system" have truly changed our understanding of brain function. From Arvid Carlsson's research we now know that Parkinson's disease is due to failure in synaptic release of dopamine. We know that we can substitute the lost function by a simple molecule, L-DOPA, which replenishes the emptied stores of dopamine and in this way, give millions of humans a better life.

We know from Paul Greengard's work how this is brought about. How second messengers activate protein kinases leading to changes in cellular reactions. We begin to see how phosphorylation plays a central part in the very orchestration of the different transmitter inputs to the nerve cells.

Finally, Eric Kandel's work has shown us how these transmitters, through second transmitters and protein phosphorylation, create short- and long-term memory, forming the very basis for our ability to exist and interact meaningfully in our world.

On behalf of the Nobel Assembly at Karolinska Institutet, I wish to convey our warmest congratulations and I ask you to step forward to receive the Nobel Prize from the hands of His Majesty the King.

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[Photo Credits: The photo of Arvid Carlsson celebrating is from "The Nobel Prize did change my life!" . The photo of Paul Greengard with his wife Ursala von Rydingsvard is from The New York Times. Greengard used his prize money to fund an annual $50,000 award to an outstanding female medical researcher.

Healing Through Quantum Mechanics

 
Jeffrey Shallit at Recursivity posts about a chiropractor in Seattle who will heal you by using quantum mechanics [Your Daily Dose of Woo].

There's a comment on his blog that points to a quack right there in Kitchener/Waterloo who makes the same silly claims. Check it out. I've inserted a picture of the ECLOSION (Electro Physiological Feedback Xrroid) device from the Kuantum Power website. Wouldn't you just love to have one of those? It will even work on computers made by fruit companies.

These are more examples of the misuse of science. How can we combat this except by making sure we educate students properly? Judging by what I see at the University of Toronto, we aren't doing a very good job of teaching students how to think. I get the feeling that most of my colleagues aren't aware of the problem and those that are, don't care. I see lots of similar woo in the scientific literature.

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Misusing Science

 
Canadian Cynic has a new job that forces him to drive past a certain billboard every day [And now, two troublemakers that need no introduction ...].

CC links to the website of the billboard sponsor [Stop the Cover-up]. Here's what you see if you follow the link.


This is group of people who are opposed abortion. What they're saying is that women who choose abortion are more likely to get breast cancer. Specifically ...

It is a well established fact that abortion can increase a woman’s risk of developing breast cancer by denying her the protective effect of both a full-term pregnancy as well as breast-feeding. In addition, the abrupt, artificial termination of a healthy pregnancy leaves a woman with an increased number of vulnerable undifferentiated (immature) breast cells which are, in turn, exposed to the massive amounts of estrogen present during early normal pregnancy. Estrogen is a known cancer causing hormone.

Now, it doesn't take too much exposure to real science to recognize the problem with such claims. What they're doing is taking a little bit of truth and distorting it into something that's not the truth.

This sort of thing is very common these days. Everyone wants to bask in the glow of science even when they are doing their best to extinguish that glow. Everyone wants to have their cake and eat it too.

I hate to bring up the framing issue again but, at the risk of sounding like a broken record, this ad is exactly the sort of thing I fear when Nisbet and Mooney start preaching. There's no question in my mind that this ad is a good example of framing (=spin). I'm not sure how we distinguish between this approach and one were we all agree to use science to support certain policies on climate change, or certain approaches to dealing with creationism.

At what point do we draw the line between truth and lies? Who is going to be the judge of when that line is crossed?

UPDATE: Abortion and Breast Cancer: There Is no Link.

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You're Not Gonna Believe This ...

 

According to Bill Dembski [Who’s in it for the money?].

Darwinism has always been an upper-class movement. ID, by contrast, is strictly middle-class. That’s our base and that’s where we find our support.

You won't believe his evidence for such a statement unless you actually follow the link and read what he wrote.

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Atheists in the Media

 
Come to the Centre for Inquiry's lecture by Wodek Szemberg on the role of atheists in the media. [Why So Few Atheists in the Media?].

Email me if you'd like to attend. Maybe we could meet at my office and get together for something to eat before walking to the Centre for Inquiry on Beverley St.? I'm certainly going to ask him about the "Best Lecturer" series. That should be fun.

SPECIAL EVENT: Why So Few Atheists in the Media? with TVO The Agenda Producer

Starts
Friday, May 9th at 7:00 pm
Ends
Friday, May 9th at 9:00 pm
Location
Centre for Inquiry Ontario, 216 Beverley St., Toronto, ON M5T 1Z3, 1 minute south of College St. at St. George St.

Wonder why secular humanists aren't included on every media ethics panel which includes the perspectives of just about everyone else?

INFLUENTIAL TV PRODUCER DISCUSSES ATHEIST & HUMANIST MARGINALIZATION IN THE MEDIA AND SUGGEST NEW STRATEGIES

Special FREE Event!

Featuring Wodek Szemberg, TV Ontario Producer of The Agenda with Steve Paiken, Best Lecturer Competition and BIG IDEAS, and "out of the closet" atheist.

Everyone is welcome.

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Skepticast #145: Should Biology Students Pass the Course If They Don't Understand the Science?

 
Steven Novella (photo) is a skeptic and a neurologist at Yale University School of Medicine. He publishes a podcast called Skeptics Guide to the Universe. In the April 30th edition he discusses the proposed Florida Laws on "Academic Freedom" with Bob Novella, Evan Bernstein, and Jay Novella [Skepticast #145].

About one quarter of the way into the podcast they turn their attention to the issue of educating creationists at university. They discuss my views on the subject as described in Do Fundamentalist Christians Actively Resist Learning?. Here's what I said ...

Keeping all these cautions in mind, it is still quite remarkable that some significant percentage of fundamentalist Protestants can go to college and still reject the basic scientific fact that humans evolved. Note that in all of the other groups the college educated subset are more inclined to accept evolution. (Do most of those "college" educated fundamentalists go to some cheap reproduction of a college run by a religious organization?)

As we've seen time and time again on the blogs (and elsewhere), the Christian fundamentalists have erected very strong barriers against learning. It really doesn't matter how much they are exposed to rational thinking and basic scientific evidence. They still refuse to listen.

This is one of the reasons why I would flunk them if they took biology and still rejected the core scientific principles. It's not good enough to just be able to mouth the "acceptable" version of the truth that the Professor wants. You actually have to open your mind to the possibility that science is correct and get an education. That's what university is all about.

Of course, we all recognize the problem here. How do you distinguish between a good Christian who is lying for Jesus and one who has actually come to understand science? It seems really unfair to flunk the honest students who admit that they still reject science and pass the dishonest ones who hide their true beliefs.

I stand by this statement.

Let's take a simple example. Imagine that you are teaching a course in history and you assign readings about the holocaust. On the exam you ask students to describe the history of Nazi occupied areas of Europe from 1940-1945. Imagine that a student describes all of the historical facts that you have taught in class but then rejects them by denying that the holocaust ever happened. The student claims that belief in the holocaust goes against the student's religious convictions. Should the student be given a passing grade in order to avoid discriminating against religious beliefs?

What if you are a Professor of Medicine at Yale University? Imagine teaching a course on basic neurology and the treatment of, say, Parkinson's disease. What would you do about Scientology students who can recite correctly all of the data on effective drug treatment but then reject it all because it conflicts with their religion? Should they still get an M.D. degree? Is evidence based medicine a requirement or can it be sacrificed when it conflicts with sincerely held beliefs?

Imagine that you are teaching a geology class and as part of the exam you ask students to give the age of the Earth and explain the evidence supporting that age. Let's say a student describes the radiometic data correctly but then goes on to reject the 4.5 billion year old Earth because it conflicts with the Bible. This student insists that the Earth is less than 10,000 years old in spite of the scientific evidence. Should that student get a passing grade on the exam on the grounds that flunking them would be religious discrimination?

I'm sure you can make up similar scenarios involving the common ancestry of humans and other apes.

Here's the question. We flunk students who cannot demonstrate that they understand the material and the scientific facts. Should we make an exception for those students who claim that their ignorance is part of their religion?

Listen to the debate between Steven Novella and his friends. Part of the problem is their concept of what "understanding" the material really means. They think that as long as you can correctly regurgitate the words of the textbook then you have demonstrated understanding. That should be sufficient to pass the course. Do you agree with them?

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{Hat Tip: BigHeathenMike]

Reserpine

Reserpine is a powerful plant alkaloid that used to be used to control psychotic behavior and treat certain cancers. Unfortunately, it's severe side effects and unpredictable behavior has limited it's usefulness. The drug has been replaced by more reliable treatments.

Many plants contain mildly toxic alkaloids but in most cases the concentrations are not high enough to cause a problem.¹ Reserpine is concentrated in Rauwolfia serpentina (Indian snakeroot) and this plant has been used for several thousand years in treating a number of aliments. One of the main effects of reserpine is to block the action of dopamine. This blockage causes symptom's that resemble Parkinson's disease. They can be relieved by treating the patient with L-dopa [Monday's Molecule #70].

My first exposure to research was a summer job (1966) in the lab of George Setterfield at Carleton University in Ottawa (Canada). The project was to identify crystal-like inclusions in the cells of Rauwolfia serpentina. The hypothesis was that these inclusions were composed of alkaloids, especially reserpine. As I recall, I didn't make much progress. The inclusions weren't always visible and my suspicion was that they could have been an artifact of the fixation process.

I haven't been able to find any mentions of plant alkaloid inclusions in the literature. Does anyone know this field?

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1. It's much safer to eat meat.

Terms & Conditions on Nature Network

 
Eva Amsen has an interesting question about how you would fund research if you were in complete control of all the money in the world [see, Would you rather?].

I was all set to post a comment when I realized that I had to sign in to Nature Network in order to do so. That reminded me about the terms and conditions. That's way more hassle than I'm prepared to put up with. I prefer the rough and tumble of unrestricted blogs.

My question is, does anyone else feel this way? What's the future of science blogging? Is it the strictly controlled environment of Nature Networks where the fora are part of a for-profit venture? Or is it the free-for-all environment of some of the other science blogs? Or is it something in between like the relatively unrestricted environment of the blogs run by SEED magazine?

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Monday's Molecule #70

 
It's been a while since you had to identify a molecule and give it's correct IUPAC name so here's a molecule that will give you some practice. First, you should assume that this is the L- form of this molecule and not the D- form. (This isn't obvious from the chemical structure.)

Give the common name of the molecule and the complete IUPAC name.

Identify the two Nobel Laureates who were awarded a Nobel Prize, in the same year, for discovering the fundamental properties of this molecule.

The first person to correctly identify the molecule and name the Nobel Laureates wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are only two ineligible candidates for this week's reward.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureates. Note that I'm not going to repeat Nobel Laureates so you might want to check the list of previous Sandwalk postings.

Correct responses will be posted tomorrow. I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: This week's winner is Maria Altshuler from the University of Toronto. She identified the molecule as L-dopa ((S)-2-amino-3- (3,4-dihydroxyphenyl) propanoic acid) and the Nobel Laureates are Arvid Carlsson and Paul Greengard. Congratulations Maria, you beat out several others who came up with the correct answer. The University of Toronto is thumping all other schools in this contest!¹

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1. That might have something to do with the fact that you have to be in Toronto to collect the prize, ya think? Maybe I should have another prize for people who can't come to Toronto? How about a Tim Horton's gift certificate?

Evolution of Sex & Recombination

 
I've been wondering if John Logsdon was still alive. There have been very few postings on his blog Sex, Genes, & Evoluton. Now we know why. He has been organizing a meeting about Sex in Iowa. (Is that an oxymoron?)

This looks like a very interesting meeting. Most of the key players are going to be there. Looking over the list of speakers makes you realize that the problem of sex is still very complicated. We don't have a consensus on the evolutionary advantages of sex (if any). This is an important point since many on the evolutionist side think otherwise. They believe that the evolutionary advantages of sex have been proven and it's no longer an open question.

I hope we'll hear a summary of the talks once the meeting is over.

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Tangled Bank #104

 
The latest issue of Tangled Bank is #104. It's hosted at Dammit Jim! [Tangled Bank #104].

Welcome to the 104th edition of the Tangled Bank blog carnival (a biweekly showcase of good biology posts selected by the authors themselves). Rigorous calculations and archaelogical research have revealed that this is the Tangled Bank’s 4th birthday. In the birthday spirit, several people sent appropriately themed presents.

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If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

Effective Population Size of Our Ancestors in Africa

 
John Hawks has posted an interesting discussion of the effective population size of human ancestors. He concludes that N_e=34,000 during the late stone age (about one million years ago). According to Hawks, this means there were about 100,000 to 300,000 individuals spread throughout Africa at this time [Did humans face extinction 70,000 years ago?].

I don't understand the math, or the data. As a general rule, I'm skeptical of these calculations because so many papers seem to reach different conclusions. The really nice part of John's posting is that he tries to explain the assumptions and possible sources of error. It's worth a read just to get a feel for the kinds of things that are going on in population genetics.

There are no comments allowed on john hawks weblog. I'm sure if you post questions here he will answer.

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Atheism, Agnosticism and Religious Dissent in Ancient Western Civilization

 
Come to the Centre for Inquiry's lecture by David Hitchcock tomorrow night. I'm really looking forward to this 'cause I've often confronted theists who claim that atheism is a relatively new phenomenon. Many of them think it's caused by modern science.

Starts
Friday, May 2nd at 7:00 pm
Ends
Friday, May 2nd at 9:00 pm
Location
Centre for Inquiry Ontario, 216 Beverley St, Toronto ON (1 minute south of College St at St. George St)

Summary

Agnosticism, atheism and religious scepticism have a longer history in western thought than is often recognized. I survey the history of such thinking in the ancient Greek philosophical tradition from the 5th century BCE to the 2nd century CE. The views surveyed include arguments against the anthopomorphism of popular religion, explicit agnosticism, naturalistic explanations of the origin of religion, arguments that truly divine beings would be indifferent to human doings and sufferings, and sceptical attacks on the most common arguments for the existence of gods.

Brief biography of David Hitchcock

David Hitchcock is professor of philosophy at McMaster University in Hamilton, Canada. Born in 1942 in England, he was brought by his parents to Hamilton at the age of 5 and has lived there ever since, except for a year in England as a child and four years in California as a graduate student. His research falls into three main areas: the philosophy of argument, ancient philosophy, and the history of logic. He is the author of a textbook on critical thinking, as well as co-author of a textbook on logic and critical thinking in medicine. He has also co-edited a volume of original papers on the use of the "Toulmin model" for the analysis and evaluation of arguments. He is the author of dozens of book chapters, journal articles and conference proceedings papers. They deal with such topics as the evaluation of inferences, the concept of relevance, practical reasoning, the effectiveness of computer-assisted instruction in critical thinking, Plato's conception of the good, the relation between fallacies and formal logic in Aristotle's thought, Aristotle's theory of argument evaluation, the reconstruction of Stoic propositional logic, and the Polish version of Alfred Tarski's classic paper on the concept of logical consequence.

Dr. Hitchcock received his B.A. in Honours Philosophy in 1964 from McMaster University and his Ph.D. in philosophy in 1974 from Claremont Graduate School in Claremont, California. His Ph.D. dissertation dealt with the role of myth in Plato's dialogues and its relation to rational argument. He has been a full-time faculty member at McMaster since July 1968.

Dr. Hitchcock was the founding president (1983-85) of the Association for Informal Logic and Critical Thinking, an international scholarly association, and is currently serving a two-year term (2007-09) on its board.

Dr. Hitchcock has been a member of the New Democratic Party of Canada since 1963. He was the NDP candidate for Member of Parliament in the constituency of Hamilton -Wentworth in three federal elections, in 1979, 1980 and 1984. He is currently membership organizer in the Ancaster -Dundas -Flamborough -Westdale New Democratic Party Provincial Riding Association. He is also the official agent of Gordon Guyatt, who has been nominated as the NDP candidate in the constituency of Ancaster -Dundas -Flamborough -Westdale in the next federal election.

He is married and has two daughters, one stepson and four granddaughters.

$5 regular, $4 general, FREE for Friends of the Centre

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Sophisticated Religion

 
One of the arguments used against atheists is that they haven't studied religion. The theists maintain that there are very sophisticated arguments for the existence of God and that we atheists are just ignoring all those good argumnts in order to score points against the simplistic arguments of the hoi polloi.

I've been asking for examples of these "sophisticated" arguments for some time without success. Today, one of the Sandwalk readers posted an answer in the comments section. It's a talk given by Alvin Plantinga at Biola Unioversity [An Evolutionary Argument Against Naturalism].

This is old news [A Sophisticated Christian Philosopher Critiques The God Delusion]. If this is the best they can do then theism is in big trouble.

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Google and Blogger Screw Up Bigtime!

 
Starting about 10 days ago, a number of blogs on Blogger have been blocked because they are suspected of being spam. Apparently, the blogger/blogspot crew installed some new software to detect spam and the result was that many blogs were removed (blocked) without warning. You can imagine how upset some bloggers are about this.

The blogs are gradually being restored (unblocked) [e.g. ERV].

Here's the message at the help center. It looks like the Blogger employees have gotten the message ...

Hello Bloggers,

It seems that a few of you feel you aren't getting the proper TLC that you deserve when requesting a spam appeal. So to make sure that no one falls through the cracks, we have created a form where you can submit your locked URL for another manual review by a human being.

If you've already submitted a request from your dashboard and you have not heard back from us after four business days, please re-submit your blog's address at the form below:

https://spreadsheets.google.com/viewform?key=pZHHZdeYKeHjcTRpnBYV0Qw&...

Thanks,
Dana

PS If doing that doesn't work, then your blog has probably been determined to be spam :(

Some readers have noticed that posting comments has become a problem. I don't know exactly what Blogger has done to cause this problem. There were complaints about the new format for word verification so I've turned off that feature for now. Many people found it impossible to decipher the letters. (Blogger has since restored the old version.)

This isn't the only problem. Don't try to post a comment by clicking on "Publish this comment" under the comment that you are previewing. That doesn't seem to work. Click on the orange button "PUBLISH YOUR COMMENT" in the upper right-hand corner of the comment page. That seems to work most of the time.

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Ben Stein Is an IDiot

 
I know, I know, ... I'm not telling you something you don't already know. Ben Stein's role in Expelled: No Intelligence Allowed is more than sufficient to demonstrate that, indeed, intelligence is not permitted in that movie.

In case you didn't know how stupid Stein really is, there's even more proof in his various interviews. John Derbyshire has just posted an excerpt from an interview with Paul Crouch Jr. on the Trinity Broadcasting Network [see Science Equals Murder]. Stein's views need to be widely known. Here's what he said ...

Stein: When we just saw that man, I think it was Mr. Myers [i.e. biologist P.Z. Myers], talking about how great scientists were, I was thinking to myself the last time any of my relatives saw scientists telling them what to do they were telling them to go to the showers to get gassed … that was horrifying beyond words, and that’s where science — in my opinion, this is just an opinion — that’s where science leads you.

Crouch: That’s right.

Stein: …Love of God and compassion and empathy leads you to a very glorious place, and science leads you to killing people.

Crouch: Good word, good word.

Like the man says, when you're an IDiot, there's no intelligence allowed.

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Nobel Laureate: Bernardo Houssay

 

The Nobel Prize in Physiology or Medicine 1947.

"for his discovery of the part played by the hormone of the anterior pituitary lobe in the metabolism of sugar"

Bernardo Alberto Houssay (1887 - 1971) received the Nobel Prize in Physiology or Medicine for his work on pituitary gland hormones that affect carbohydrate metabolism. He shared the prize with Carl and Gerty Cori.

Houssay was mainly responsible for recognizing that the anterior lobe of the pituitary gland secreted a peptide hormone that antagonized insulin. We now know that this hormone is growth hormone [Monday's Molecule #69]. It has general effects on growth and development as well as regulating carbohydrate metabolism in adults.

Bernardo Houssay was a citizen of Argentina. He was known as an outspoken liberal and an advocate of democracy. Houssay was fired from his academic position when Juan Perón took over as dictator in 1945 but he remained in Argentina working in a private laboratory. The Nobel Prize award in 1947 was seen, quite rightly, as a repudiation of Juan Perón and his policies. This was very controversial in Argentina [see Bernardo Alberto Houssay for one of many biographies].

THEME:

Nobel Laureates
The presentation speech was given by Professor H. Theorell, Head of the Biochemical Nobel Department of the Royal Caroline Institute.

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

The teaching body of the Caroline Institute has decided to award one half of the 1947 Nobel Prize for Physiology or Medicine to Professor Carl Cori and Dr. Gerty Cori «for their discovery of the course of the catalytic conversion of glycogen», and the other half to Professor Bernardo Houssay «for his discovery of the part played by the hormone of the anterior pituitary lobe in the metabolism of sugar».

The work of these prize-winners is within the same centrally important sphere, namely the metabolism of sugar in the body. They have elucidated the enzymatic reactions between glucose and glycogen, and have shown how these reactions are controlled by physiological factors. Faulty sugar metabolism may lead to diabetes, with its universally known symptoms. Everyone now knows, too, that in the majority of cases it has been possible to keep this disease in check by insulin since its discovery by Banting and MacLeod, to whom the Nobel Prize was awarded in 1923. It would be a grave mistake, however, to believe that this brilliant discovery unravelled the immense complex of problems concerning sugar metabolism. Certainly it is long known that insulin decreases the blood sugar level, but until recently the mechanism of this effect was veiled in mystery.

The task of sugar metabolism is to supply energy for the activities of life. One cannot make the slightest muscular movement without the combustion of an appropriate amount of sugar. It is readily understandable that one of our most urgent tasks is to elucidate this branch of metabolism. A clear light has been thrown on previously obscure points in our knowledge, by the discoveries for which the prizes are awarded this year.

Ninety years ago the great French physiologist, Claude Bernard, discovered that the liver and muscles contain a starch-like substance, which he called glycogen, the «sugar former». Every molecule of glycogen consists of a large number of grape sugar molecules, which are united together to be stored up in that form until they are needed. When needed, the glycogen disintegrates again into grape sugar, or glucose, to use a more scientific name. In this way the glucose content of the blood can be kept fairly constant in spite of an uneven supply. The credit for having revealed how the interplay between the glucose and the glycogen takes place falls to Professor and Doctor Cori. From the works of Robison and Embden in the 1920's it was known that the sugar in living cells and tissues, e.g. in yeast and in muscle, appears under certain circumstances bound to phosphoric acid. Closer analysis showed that in these combinations the phosphoric acid was bound to the sixth in the chain of the six carbon atoms of the sugar molecule.

...

This latest work of the Cori's is directly connected with the discovery of the effect of the hypophysis on the utilization of sugar by Professor Bernardo A. Houssay, who has also been awarded a prize. The hypophysis, or the pituitary gland, is a small secreting gland at the base of the brain, where it lies sunk in a bony hollow in the most sheltered spot in the whole body. Its importance justifies its sheltered position, but its size is far from impressive: that of a bean in man, a pea in the dog, and a radish seed in the toad Bufo marinus.

People sometimes cite, more or less jokingly, the statement by Cartesius, the famous philosopher, that the soul lies in the pineal gland. Now it does so no more than in any other individual organ, but if Cartesius had chanced, instead, to guess at the hypophysis, which looks much the same and is situated immediately in front of the pineal gland, he would have been nearer the truth, for in spite of its diminutive size the hypophysis exercises a number of vital functions and occupies a commanding position in relation to the other endocrinous glands. By means of its hormones the hypophysis controls the thyroid, the sex glands and the cortex of the suprarenal glands; it regulates the formation of milk and the growth of the whole body. By means of extremely beautiful experiments Houssay has shown that it also plays a prominent role in the conversion of sugar.

It was the discovery of insulin which aroused Houssay's interest in the hypophysis. As early as in the 1880's the great French research worker, Pierre Marie, had found that the excretion of sugar in the urine was a regular symptom in acromegalia, which is due to a disturbance in the function of the hypophysis, and therefore a connection between the function of the hypophysis and the metabolism of sugar might be suspected.

Houssay has worked chiefly with dogs and a large kind of toad, Bufo marinus, which is plentiful in the Argentine. In many series of experiments the hypophysis, or sometimes only its anterior lobe, was removed by operation. In the case of dogs, especially, the operation calls for highly developed technical skill if the result is not to be «the operation was successful, but the patient died». Houssay then found that the animals which had been operated on were abnormally sensitive to insulin and died with symptoms of bloodsugar deficiency from doses which were quite harmless for normal animals. In conformity with this, the glycogen content in the liver was abnormally low. A corresponding pathological picture is met with in the case of Simmond's disease in man. Dogs and toads exhibited the same kind of reaction, as have all the rest of the vertebrates hitherto investigated. This proves that Houssay had discovered a universal biological mechanism.

The discovery that a daily implantation of anterior lobe of hypophysis from toads on the operated animals protected the latter from the dangerous effect of insulin, was also of immense importance.

Thus the hormone of the anterior lobe of the hypophysis was clearly antagonistic to the hormone of the pancreas, insulin. This was confirmed and illustrated by a further series of ingenious experiments. Davidoff and Cushing had observed already in 1927 that if diabetes was provoked in dogs by the removal of a part of the pancreas, the symptoms were moderated if part of the hypophysis was also taken away. However, these experiments were not entirely conclusive, since as a rule the diabetes provoked in this way may disappear spontaneously. Houssay and Biasotti obtained definite elucidation by means of a more radical procedure. The whole hypophysis was first removed and subsequently the pancreas. For three whole days after the latter operation no sugar appeared in the urine, which is always the case if the pancreas is removed from an animal which still has its hypophysis.

In 1931, in the course of their work on the growth hormone of the hypophysis, H. M. Evans and his co-workers in U.S.A. found that the extract which naturally was still impure - provoked diabetes if injected into animals. At the same time and independently of Evans, Houssay and his co-workers arrived at similar results. After injections of extract from the anterior lobe of the hypophysis, the diabetes persisted, in many cases for months, and this was found to be due to injury to the insulin-producing cells in the pancreas.

The active factor in the hypophysis is so extremely sensitive that all the preparations must be made at a low temperature, if they are not to be spoiled. Therefore a number of research workers, who were less careful than Houssay on this point, did not at first succeed in confirming his results. It may be added that the Cori's had to grapple with the same difficulties in the preparation of their extract of hypophysis, which to some extent confirms that both groups of workers were dealing with the same active substances.

A short description of the most important results of many years of scientific work can never give a complete idea of the days and nights of labour which is most frequently fruitless. Diligence and patience are indispensable components in the mental equipment of the research worker. These alone seldom or never lead to pioneer discoveries, however, because it is impossible to deal thoroughly and systematically with all the conceivable alternatives, at least in the case of biological problems. The possibilities are all too many. Intuition is the indispensable lode-star, promising new goals to be reached by a labyrinth of paths, the majority of which are blind alleys.

In work characterized by unremitting diligence, brilliant skill, and masterly acumen, today's prize-winners in physiology or medicine have shown themselves to possess all the qualities of the great research worker in natural sciences. They have thrown light on previously undreamt of connections between the inaccessible world of the enzymes and the hormones. The task of the doctor to prevent, heal or alleviate disease demands a knowledge of the functions of the body; this year's prize-winners have opened new fields in which Ernest Starling's happy expression «The physiology of today is the medicine of tomorrow» will prove its truth.

Professor Carl Cori and Doctor Gerty Cori. During the past decade the scientific world has followed your work on glycogen and glucose metabolism with an interest that has gradually increased to admiration. Since the discovery of glycogen by Claude Bernard ninety years ago, we have been almost totally ignorant of how this important constituent of the body is formed and broken down. Your magnificent work has now elucidated in great detail the extremely complicated enzymatic mechanism involved in the reversible reactions between glucose and glycogen. Your synthesis of glycogen in the test tube is beyond doubt one of the most brilliant achievements in modern biochemistry. Your discovery of the hormonal regulation of the hexokinase reaction would seem to lead to a new conception of how hormones and enzymes cooperate.

In the name of the Caroline Institute I extend to you hearty congratulations on your outstanding contribution to biochemistry and physiology.

Professor Houssay. That great philanthropist, Alfred Nobel, had a great personal interest in physiology. Few things gave him so great a pleasure as being able to witness the brilliant development of this science in the nineteenth century. In the development of physiology, Professor Houssay, you have played a very active part, particularly regarding the work which you have brought into prominence and which is now to be honoured by the Nobel Prize.

The hypophysis is a small gland, but its importance is not related to its size, since it regulates many of our most important functions. Amongst these functions, which you have studied and analysed in a clear and striking manner, is the dominant role the gland plays in our metabolic processes.

On behalf of the Caroline Institute I congratulate you on receiving the Nobel Prize which is presented to you today, and which is a sure sign that your name will ever remain engraved in the annals of physiology.

Professor Carl Cori and Doctor Gerty Cori; Professor Houssay. I now have the honour of asking you to accept the prize from the hands of His Majesty our gracious King.

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Richard Dawkins—polite and gracious to a fault

 
Some of you might remember Peter McKnight. He's a columnist for the Vancouver Sun (Canada) and he wrote a piece last year defending Marcu Ross and his Ph.D. degree [Peter McKnight on the Marcus Ross Issue].

My interactions with Peter McKnight have been quite enjoyable so it is with considerable satisfaction that I point you to his latest article on Richard Dawkins [How to reconcile Richard Dawkins?]. Peter puts his finger squarely on the discrepancy between what Dawkins says in public about religion and what he says in private.

I like the private Richard Dawkins when it comes to a position on religion as the root of all evil, and atheists as being free of violence.

Unlike the public Dawkins, I don't oppose superstitious beliefs because they lead to evil—I oppose them because there's no evidence that those beliefs are correct.

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[Hat Tip: RichardDawkins.net]

Should Undergraduate Programs Be Easier?

 
We have a biochemistry program for undergraduates. It would be called a major at most universities but at the University of Toronto we call it a Biochemistry Specialist Program. Here's an outline with the number of credits, where (1) is a standard two-semester course ...

1st year
Calculus (1), Biology (1), Physics (1), Chemistry (1)

2nd year
Biochemistry (1), Organic Chemistry (0.5), Physical Chemistry (0.5), Cell & Molecular Biology (1)

3rd year
Biochemistry Laboratory (0.5), Proteins (0.5), Nucleic Acids (0.5), Molecular Biology (1), 1.5 extra credits from a list of science courses

4th year
Advanced Biochemistry Laboratory (1), four (0.5) credit courses from a list of biochemistry and molecular biology courses

Here's the problem. Enrolment in this program is dropping because the students perceive it as being too hard. A number of easier, less rigorous, programs have recently become available in other departments. These other programs are being promoted as excellent choices for an undergraduate degree. Students are being told that these easy program will be just as acceptable as the more difficult ones when they apply to graduate school. (That won't be true in our department.)

Students believe that they will get higher grades in these other programs and that will make it easier to get into medical school or graduate school.

What should we do? There's a possibility that our program will disappear if we do nothing. On the other hand, making it a lot easier by dumbing down the material and giving higher grades goes against the principles that many of us believe in.

Have any other schools faced this situation? What did you do? What do the students think?

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Who Do You Know?

 
The Friendly Atheist asks ...

Who is the most famous person you know (who would admit to knowing you back)?

You can see my answer over there. Sandwalk readers might like to jump in and drop a few names.

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Monday's Molecule #69

 
This colorful molecule plays an important role in regulating carbohydrate metabolism, among other things. Your task for today is to identify the molecule. Be as specific as possible (what species?).

Identify the Nobel Laureate(s) who was/were awarded a Nobel Prize for discovering fundamental properties of this molecule without knowing the sequence or the structure. [Hint: The award was very controversial in the home country of the Nobel Laureate(s).]

Here's part of the PDB file to help you.

SEQRES 1 A 191 PHE PRO THR ILE PRO LEU SER ARG LEU PHE GLN ASN ALA
SEQRES 2 A 191 MET LEU ARG ALA HIS ARG LEU HIS GLN LEU ALA PHE ASP
SEQRES 3 A 191 THR TYR GLU GLU PHE GLU GLU ALA TYR ILE PRO LYS GLU
SEQRES 4 A 191 GLN LYS TYR SER PHE LEU GLN ALA PRO GLN ALA SER LEU
SEQRES 5 A 191 CYS PHE SER GLU SER ILE PRO THR PRO SER ASN ARG GLU
SEQRES 6 A 191 GLN ALA GLN GLN LYS SER ASN LEU GLN LEU LEU ARG ILE
SEQRES 7 A 191 SER LEU LEU LEU ILE GLN SER TRP LEU GLU PRO VAL GLY
SEQRES 8 A 191 PHE LEU ARG SER VAL PHE ALA ASN SER LEU VAL TYR GLY
SEQRES 9 A 191 ALA SER ASP SER ASP VAL TYR ASP LEU LEU LYS ASP LEU
SEQRES 10 A 191 GLU GLU GLY ILE GLN THR LEU MET GLY ARG LEU GLU ASP
SEQRES 11 A 191 GLY SER PRO ARG THR GLY GLN ALA PHE LYS GLN THR TYR
SEQRES 12 A 191 ALA LYS PHE ASP ALA ASN SER HIS ASN ASP ASP ALA LEU
SEQRES 13 A 191 LEU LYS ASN TYR GLY LEU LEU TYR CYS PHE ARG LYS ASP
SEQRES 14 A 191 MET ASP LYS VAL GLU THR PHE LEU ARG ILE VAL GLN CYS
SEQRES 15 A 191 ARG SER VAL GLU GLY SER CYS GLY PHE

The first person to correctly identify the specific molecule and name the Nobel Laureate(s) wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There is only one ineligible candidates for this week's reward.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureates so you might want to check the list of previous Sandwalk postings.

Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: This week's winner is David Schuller of Cornell University (again). He correctly identified the molecule as human growth hormone and the Nobel Laureate is Bernardo Houssay (1947). Thanks to all the others who sent in their guesses.

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Gene Genie #30

 

The 30th edition of Gene Genie has been posted at Gene Expression [Gene Genie #30].

Welcome to the 30th Gene Genie!

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

Here are all the previous editions .....

1. Scienceroll
2. Sciencesque
3. Genetics and Health
4. Sandwalk
5. Neurophilosophy
6. Scienceroll
7. Gene Sherpa
8. Eye on DNA
9. DNA Direct Talk
10. Genomicron
11. Med Journal Watch
12. My Biotech Life
13. The Genetic Genealogist
14. MicrobiologyBytes
15. Cancer Genetics
16. Neurophilosophy
17. The Gene Sherpa
18. Eye on DNA
19. Scienceroll
20. Bitesize Bio
21. BabyLab
22. Sandwalk
23. Scienceroll
24. biomarker-driven mental health 2.0
25. The Gene Sherpa
26. Sciencebase
27. DNA Direct Talk
28. Greg Laden’s Blog
29. My Biotech Life
30. Gene Expression

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Does science make belief in God obsolete?

 
The John Templeton Foundation has a website where "leading scientists and scholars" discuss the question "Does science make belief in God obsolete?" [A Templeton Conversation] One of these prominent intellectuals is Ken Miller and his answer is "Of course not."

One of our regular readers (Oldcola) left a comment on this site where he criticized the views of Ken Miller. His comment was initially posted intact but within a few days a heavily edited version replaced the original comment. The man responsible for editing the comment is Gary Rosen.

Apparently, the Templeton Foundation objected to the claim that they were soft on creationism, according to Oldcola. Oldcola requested that his edited comment be removed, and it was.

You can read an extended critique of Ken Miller's position on Oldcola's blog Coffee and Sci(ence) [Does science make belief in God obsolete?]. It's an excellent essay.

Incidentally, although it's not directly relevant to Miller's position, and it's not something that he clearly states, I find that theists of all sorts make the same false assumption when discussing the conflict between science and religion. They almost always assume that their atheist friends started life as theists and then lost their faith. Thus, they assume that there is something about science that disproves the default assumption; namely, that God exists.

While this might be true of many atheists, especially in the USA, it's not true of many others in Europe and elsewhere. Many atheists never bought into a belief in supernatural beings in the first place. This will be more and more likely as time goes on and the children of atheists have children of their own. When scientists like Ken Miller have to explain why science makes them go from being an atheist to a beleiver, it becomes much more difficult. Just look at the contortions that Francis Collins had to come up with.

Here's the point. It's up to theists to start making the case for the existence of God instead of just whining about those who have lost their faith. Let's say you've been raised in a home where superstitious beliefs are not valued. Then you start studying science seriously when you get to university. Is there anything about science that points to the existence of supernatural beings given that you haven't been brainwashed to believe in them as a child? I don't think so.

As Oldcola points out, many theists are simply afraid to abandon their comforting delusions. They believe science teaches us that the universe has no purpose—they are correct—and for them this depressing thought is sufficient to prove that science must be wrong. What they fail to understand is that the thought is only "depressing" if you've been brainwashed to to believe that there is a purpose in the first place.

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Is Anyone Stupid Enough to Fall for This?

 
I received this message today ...

Dear UTORONTO.CA Email Account Owner,

This message is from UTORONTO.CA messaging center¹ to all UTORONTO.CA email account owners. We are currently upgrading our data base and e-mail account center. We are deleting all unused UTORONTO.CA email account to create more space for new accounts.

To prevent your account from closing you will have to update it below so that we will know that it's a present used account.

CONFIRM YOUR EMAIL IDENTITY BELOW

Email Username :

EMAIL Password :

Address :

Department :

Attention!!! Account owner that refuses to update his or her account within ten days of receiving this Notification will lose his or her account permanently.

Thank you for using UTORONTO.CA!

Notification Code:VX2G99AAJ

Sandra Jacobson
ONLINE SERVICES

My question is serious. Is there any data out there to suggest that scams² like this actually succeed? Are there people who respond to these notices by sending off their email passwords?

Also, what's the purpose behind this attempt to get email passwords? What do they plan to do with them? Are they hoping that the email passwords will give them access to the user accounts or do they just like to read email messages?

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1. The sender is "Online Services (onlineservices@utoronto.edu)." A domain that does not exist. The reply-to address is "dataguards@instructor.net." I've often wondered how these scams work. How do the perps get the replies if the return address is bogus?

2. It's easier to recognize that this is a bogus message because of the language—obviously not written by someone whose native language is English—but even if it was grammatically correct most people would know that it's a scam, right?

Darwin's Garden

 
In order to walk on the sandwalk you have to pass through Darwin's garden behind Down House. Most visitors take advantage of the opportunity to pass through the greenhouses and the potting shed as well. Darwin was a passionate gardener and he did many experiments with plants. Some of his original varieties are still growing in the garden.

The New York Botanical Garden has mounted an exhibit of Darwin's experiments on plants [What Darwin Saw Out Back]. I'll have to see if Mrs. Sandwalk wants to take a trip to New York to see it with me.

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[Hat Tip: Don Henry]

Ben Stein Meets Charles Darwin

 
Do you remember this image from the Expelled trailer? [Expelled: The Movie] It's a picture of Ben Stein looking at the statue of Charles Darwin in the cafeteria of the Natural History Museum in London (UK).

The group over at the The Beagle Project ran a contest to come up with a funny caption for the photo and the result has just been announced [Caption (absolutely no) contest!]. It's excellent—very close to what I would have said if I had the wit and talent to enter the contest.

A fortnight ago we launched a caption contest for the provocative image below, originally taken from Time's negative review of Expelled. We received twenty-six highly humorous entries, but there was one that towered, marble head and shoulders, above the rest, both for its comic value and also for the amount of work involved in realising it.

I'm not going to give away the answer because you all need to scoot on over to The Beagle Project log and donate some money while you're there.

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Fibrin and Blood Clots

 
The formation of blood clots in mammals is an example of a complex pathway that does not seem to be very well "designed." This hasn't stopped the intelligent design creationists who often use it as an example of irreducible complexity. They conclude that the clotting pathway cannot possibly have evolved.

Last year I posted a bunch of articles on blood clotting because I needed to learn about it myself. Since then I've kept an eye on the literature but I've been too lazy to write up all the new information that comes out on a regular basis. Fortunately, André Brown has come to the rescue. He published a paper on the elastic properties of fibrinogen last year (Brown et al. 2007) and now he reviews a recent paper by his collaborator, John Weisel, that has just come out in Science. André's blog is Biocurious, a blog about biology written by two physics graduate students. The post url is New Perspective on Blood Clot Mechanics.

Theme

Blood Clotting
The image above shows blue strands of fibrin trapping red blood cells (red) and platelets (pink) to form a clot. It is from Yuri Veklich and John W. Weisel, University of Pennsylvania School of Medicine [Building better clots]. The structure of fibrinogen (below) hints at the complexity. Follow the link in the "Theme Box" to learn more.

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Brown, A.E.X., Litvinov, R.I. Discher, D.E. and Weisel, J.W. (2007) Forced Unfolding of Coiled-Coils in Fibrinogen by Single-Molecule AFM. Biophys J. 92: L39–L41. [doi: 10.1529/biophysj.106.101261]

Fun with Polls

 
The Expelled website has a poll asking "Do you think the theory of Intelligent Design should be taught in our education system?"

When PZ Myers discovered it, the "yes" voters were ahead three to one. Now that the Pharyngula readers have voted [Crash this poll], the results are very different. Eat your heat out Ben Stein!!

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Do We Need Genetic Counselors?

 
The blogs promoting genetic testing usually think that we don't need genetic counselors to interpret the results and advise on what to do. For the most part, they seem happy to leave it up to the individual to decide on a course of action if they discover they have a particular genetic trait. I don't agree. I think this is much more complicated and I'm pretty skeptical about the motives of the private, personal genetics, for-profit, companies.

The Sciphu Weblog has an interesting posting on this issue [Now this is why we need genetic counselors]. It's worth reading.

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Top 100 Public Intellectuals

 
The Foreign Policy website has a list of the top 100 public intellectuals from around the world [The Top 100 Public Intellectuals: Bios].

The Canadians are: Malcolm Gladwell, Michael Ignatieff, Steven Pinker, and Charles Taylor. I would have included Irshad Manji, Bob Rae, and Don Cherry.

I included Don Cherry because he would fit right in with David Petraeus who is listed as a top 100 public intellectual.

There are several scientists and people who write about science and religion: Pope Benedict XVI, Noam Chomsky, Richard Dawkins, Daniel Dennett, Jared Diamond, Christopher Hitchens, James Lovelock, Lee Smolin, Harold Varmus, J. Craig Venter, E.O. Wilson. It's interesting that Francis Collins and Ken Miller aren't on the list since the main criterion for inclusion seems to be that the person has written a book and they have Miller & Collins have both written books.

I would have included Richard Lewontin, Bruce Alberts, and David Suzuki. Are there any others who should be on the list? Who should be deleted to make room?

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[Hat Tip: Sean at Cosmic Variance]

Writing with Amino Acids

 
Eva has a picture of a bracelet that spells out "I am starstuff" using the structures of several amino acids and their single-letter identifier. Some of you may be wondering exactly how that phrase is written since there seems to be an unusual letter in there. Check out Etsy Wednesday - I Am Starstuff for the answer.

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