Was Charles Darwin an Agnostic Atheist?

 
Let me say, right at the start, that I really don't care whether Charles Darwin was a deist, an agnostic, an atheist, or something else entirely. He died on April 19, 1882. That was a very long time ago. And the truth of evolution does not depend on what Darwin may or may not have believed about God.

Still, it's of some historical interest to learn what Darwin thought of religion. My own opinion is that these speculations are never going to be satisfactorily answered because Darwin was not always candid about his beliefs, for Emma's sake.

It may come as a bit of a surprise to find me favorably recommending an article on Uncommon Descent but this article by Flannery deserves your attention: Theist, Agnostic, Atheist: Will the Real Charles Darwin Please Stand Up?.

It's not going to make my agnostic friends happy but I think it's a pretty good analysis of Darwin's beliefs. I especially like the emphasis on the fact that his grandfather wasn't religious and his father (Robert) was an atheist. I'm pretty sure that his brother, Erasmus, was a nonbeliever as well. It strains credibility to imagine that Darwin was ever a religious man.

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November 11, 2009

 
Today is Remembrance Day in Canada. It's a day to remember that war is evil and horrible. It's a day to remember that war represents the ultimate failure of a civilization.

War is not glorious. People who kill other people are not heroes. The people they kill are not heroes. We are shamed when we turn average citizens into murderers. We lament their deaths because it means we have failed in our responsibility to maintain peace. They paid the price of our failure.

Soldiers are a necessary evil, like prison guards. The long range goal of a humane society is to eliminate armies (and prisons). Once a year, on this day, we need to think about how far we are from achieving that goal and what we can do to make it a reality.

We need to remember our past—the dirty, ugly, face of death and destruction—and resolve never to repeat it. We need to apologize to those men and women we forced to endure those horrors. We need to promise our children that we won't make them go to war.

No war is necessary. Tanks, bombers, and battleships are not necessary. I dream of an eleventh day of the eleventh month when, at the eleventh hour, no cannons are fired, no soldiers are marching, and no fighter planes are flying overhead. That will be a day to remember.

The greatest generation will be the one that avoids war. Perhaps our children's children will be that generation.

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[Photo: Dresden, February 14, 1945]

[Poster by Lorraine Schneider (1925-1972), for the Los Angeles organization Another Mother for Peace, 1967.]

The Positive Argument for Intelligent Design Creationism

 
I've often been critical of the arguments made by IDiots Intelligent Design Creationists. They consist mostly of claims that evolution can't happen.

It's only fair that I point you to a rebuttal of this point of view by none other than Casey Luskin [Misrepresenting the Definition of Intelligent Design].

Scott Minnich and Stephen Meyer also explain the positive argument for design:

Molecular machines display a key signature or hallmark of design, namely, irreducible complexity. In all irreducibly complex systems in which the cause of the system is known by experience or observation, intelligent design or engineering played a role the origin of the system … in any other context we would immediately recognize such systems as the product of very intelligent engineering. Although some may argue this is a merely an argument from ignorance, we regard it as an inference to the best explanation, given what we know about the powers of intelligent as opposed to strictly natural or material causes. (“Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic Bacteria,” in Proceedings of the Second International Conference on Design & Nature, Rhodes Greece (2004).)

Let's see if I've got this right. We know about lots of irreducibly complex systems, such as the Krebs cycle and the bacterial flagella, that could easily have arisen by evolution. Nevertheless, according to the IDiots, we have to conclude that all such systems can only have been created by God.

That's what passes for a positive argument for Intelligent Design Creationism. I assume it's the best they've got.

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Monday's Molecule #143: Winner

 
The creature is a nematode, specifically a Soybean cyst nematode. The relevant Nobel Prize was to Johannes Fibiger who got for it "discovering" that the nematode Spiroptera carcinoma causes cancer. This species is now called Gongylonema neoplasticum and it doesn't cause cancer. Oops!

The first person to get it right was Linda Zhang, a former student at the University of Toronto who will soon be on her way to graduate school at the University of Hong Kong. The undergraduate winner is Kirill Zaslavsky, a Neuroscience student at the University of Toronto.

Many others got the right answer. It was easier than I thought it would be.

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Sometimes it's almost impossible to find an image of a specific molecule that honors a Nobel Laureate. This is another one of those times.

This spectacular photograph shows a particular kind of creature and its egg. You need to identify the phylum to which this species belongs and then use that as a clue to come up with an appropriate Nobel Laureate. Your answer should include the particular species that is associated with the Nobel Prize as well as the Nobel Laureate. Be careful, I want the modern name of the species—not the old name that was used when the Nobel Prize was announced.

Here's a clue. The Nobel Prize was awarded in the last century, not the current one. Here's another clue, outside of the Nobel Peace prize and the mini-Nobel Prize in Economics, this award is probably the biggest mistake that the prize committee has ever made.

The first person to identify the molecule and name the Nobel Laureate(s) wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are six ineligible candidates for this week's reward: Joshua Johnson of Victoria University in Australia, Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany, Jason Oakley a biochemistry student at the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Alex Ling of the University of Toronto, and Bill Chaney of the University of Nebraska.

Joshua, Dima, and Bill have all agreed to donate their free lunch to an undergraduate. Consequently, I have three extra free lunches for deserving undergraduates. I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.

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(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

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

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[Photo Credit: Wikipedia]

PZ Myers Gets It Wrong

 
Discover magazine sponsored a contest where you had to produce a two minute video explaining evolution. The judge was PZ Myers. Here's how PZ explains his choice [see The Winner: Evolution in Two Minutes].



Oh dear. Repeat after me, PZ, evolution is not natural selection!

This is, indeed, the 21st century, and not the Victorian England of Charles Darwin. We now know that evolution is any change in the frequency of alleles in a population. We know that for evolution to occur the change has to be genetic. We know that populations evolve, not individuals. We know that there are two main mechanisms of evolution: natural selection, and random genetic drift. It's a good idea to mention that variation within a species (population) arises from spontaneous mutations that create gene variants called alleles. That's what needs to be explained in two minutes.

Here's the winning video from Scott Hatfield, a high school biology teacher, and, more importantly, a blogger at Monkey Trials. Scott's a cool guy but it's not the video I would have chosen.

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2009 AAAS Kavli Science Journalism Awards

 
The American Association for the Advancement of Science has just announced the Kavli Science Journalism Awards for 2009. It's a very interesting group of winners. Among them is Carl Zimmer, who won in the category "Large Newspaper—Circulation of 100,000 or more."

Awards are nice, but the problem with science journalism awards is that they are decided by a panel of science journalists. What this means is that the awards are for good journalism and not necessarily for good science. As most Sandwalk readers know, I'm not happy with the way science is presented to the general public and my main complaint about science writers is that they don't do a very good job of getting the science right. (Many scientists aren't much better, but that's a different issue.)

If we are going to award good science journalism, don't you think that one of the main criteria should be whether the reporting is scientifically accurate? If you accept that premise, then the next question is who should make that call.

Take Carl Zimmer's articles for example. One of them was Now: The Rest of the Genome published in The New York Times in November 2008. This is an article about genes and genomes and the main point is that our concept of a gene is in trouble in light of recent discoveries in genomics.

Carl's article is better than most but it still misrepresents the modern status of a gene and the importance of phenomena like alternative splicing and epigenetics [Genes and Straw Men]. There's no doubt in my mind that Carl is the best of the science writers who could have written about this subject but I'm still troubled by the fact that the prize committee was probably incapable of evaluating the accuracy of the science in his article.

The award is sponsored by AAAS. What would be wrong with having a few scientists as judges?

From the press release ...

"The AAAS awards have long recognized the importance of high-quality science journalism across the board," said Cristine Russell, president of the nonprofit Council for the Advancement of Science Writing. "The Kavli Foundation’s decision to endow the awards is particularly important at a time when accurate, insightful writing about science is threatened by rapid changes in the media marketplace. The future of this program is now assured as a new generation of journalists tackles important science developments and their impact on society.

I don't know Cristine Russel but she's promoting these awards as examples of "accurate, insightful writing about science." I'd love to know who determines whether the reporting is accurate. How does she know they were scientifically accurate?

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Boycott Science.org

 
We all get spam in our mail box and usually there's nothing you can do about it. This time there is. I got this message today.

Subject: Award Acknowledgment for sharing great PHYSICS information to the public

Dear Blog Owner,

Our website Science.org is a informational databases and online news publication for anything and everything related to science and technology. We recently ran a poll asking our website users regarding what online informational resources they use to keep up to date or even to simply find great information. It seems many of our users have labeled your blog as an excellent source of Space information. We have reviewed your blog and must say, we absolutely love the information you have made available to the public and would love to make your blog a part of our top science blogs. After browsing your blog, our research team has decided to award you a Top science Blogs award banner.

It is a distinction we offer to the blogs that our team feels is ahead of the curve in terms of content.

Thanks again for the great information and we look forward to the great responses your blog will receive from our site. Your blog presence will be very effective for our users (top science blogs).

We have put great efforts in making this decision to give deserving with award acknowledgment. For listing please reply to request banner.

Sincerely,
--
William Lee
Research team
Science.org
1 international blvd
Mahwah NJ USA - 07430
201 247 8553
editor.science@gmx.com

It turns out that Science.org is an actual website. Mr. Lee apparently believes that by lying to Blog Owners he can enhance the reputation of his website.

That ain't gonna work. Any website that emails such lies does not even deserve a link.

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The Wreck of the Edmund Fitzgerald

 
Twenty-nine men died on November 10, 1975 when the S.S. Edmund Fitgerald sank in a storm on Lake Superior.

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Amazon's Top Ten Science Books for 2009

 
Check out the Best of 2009 for two lists of the top ten science books. One list was chosen by "editors" and the other list was chosen by "readers."

There are some interesting differences ... and it's not what you expect.

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[Hat Tip: Jason Rosenhouse whose book The Monty Hall Problem: The Remarkable Story of Math's Most Contentious Brainteaser made one of the lists.

Monday's Molecule #143

 
Sometimes it's almost impossible to find an image of a specific molecule that honors a Nobel Laureate. This is another one of those times.

This spectacular photograph shows a particular kind of creature and its egg. You need to identify the phylum to which this species belongs and then use that as a clue to come up with an appropriate Nobel Laureate. Your answer should include the particular species that is associated with the Nobel Prize as well as the Nobel Laureate. Be careful, I want the modern name of the species—not the old name that was used when the Nobel Prize was announced.

Here's a clue. The Nobel Prize was awarded in the last century, not the current one. Here's another clue, outside of the Nobel Peace prize and the mini-Nobel Prize in Economics, this award is probably the biggest mistake that the prize committee has ever made.

The first person to identify the molecule and name the Nobel Laureate(s) wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are six ineligible candidates for this week's reward: Joshua Johnson of Victoria University in Australia, Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany, Jason Oakley a biochemistry student at the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Alex Ling of the University of Toronto, and Bill Chaney of the University of Nebraska.

Joshua, Dima, and Bill have all agreed to donate their free lunch to an undergraduate. Consequently, I have three extra free lunches for deserving undergraduates. I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.

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(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

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

---

[Photo Credit: Wikipedia]

Ginkgo biloba

 
Ginko biloba is the only living species in the division (phylum?) Ginkgophyta. It is a species of deciduous tree that's only distantly related to to the other trees that we see around us. Some taxonomists classify it as a gymnosperm but that's not a universally recognized classification. It's certainly not an angiosperm (flowering plant).

Ginkgo is often called a "living fossil" because it resembles plants that date from 270 million years ago. The term is misleading because, like other "living fossils" Ginko biloba has evolved considerably since the time of its similar-looking ancestors.

The trees are either male or female. I recently visited a beautiful example of a female tree growing in the yard of Frank Lloyd Wright's house in Oak Park in the suburb's of Chicago. The tree was full of "berries" (technically not fruit), which were about to drop. I'm told that the berries are edible but not very pleasant. They smell like human feces. (The pun is obvious ... don't bother. )

I wish I'd been there a bit later 'cause ever since I learned about Ginkgo I've wanted to taste the berries.

All of the trees in North America have been deliberately planted by gardeners. The one in the yard of the Frank Lloyd Wright house was already there when Wright bought the property in 1889. It's estimated to be about 160 years old. They don't grow very well in most parts of Canada.

I was under the impression that the tree is native to some parts of China but recent genotyping of the trees suggests that even those trees may have been deliberately planted there by ancient monks.

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Charles and Camilla Are in Town

 
Charles and Camilla are visiting Toronto but you wouldn't know it if you didn't read the papers. Unless, of course, you just happen to be caught up in one of the mini traffic jams that are associated with such visits.

I witnessed one last night as several motorcycles and police cars with red and blue lights flashing, and sirens wailing, raced up University Avenue and around Queen's Park. They were escorting a convoy of half a dozen limos. I figure they were exceeding the speed limit by quite a bit.

Today, Charles is accompanying Camilla to Dundurn castle in Hamilton. The great house was built by Sir Allan Napier MacNab who happens to be Camilla's great-great-great grandfather. MacNab was Prime Minister of the Province of Ontario and was a member of the ruling elite that William Lyon Mackenzie opposed in the 1837 "rebellion."

This is Camilla's first visit to Canada. Charles has been here too often.

The couple will be opening the Royal Agricultural Winter's Fair before flying back to England.

For those of you interested in genealogy, here's how Camilla is related to MacNab.

Allen Napier MacNab (1798-1862)
m. Mary Stuart (1812-1846)
      Sophia Mary MacNab (1832-1917)
      m. William Coutts Keppel (1832-1894)
            Honourable George Keppel (1865-1947)
            m. Alice Frederica Edmonstone (1869-1947)
                  Sonia Rosemary Keppel (1900-1986)
                  m. Roland Calvert Cubbitt (1899-1962)
                        Honourable Rosalind Maud Cubbitt (1921-1994)
                        m. Bruce Middleton Hope Shand (1917- )
                              Camilla Rosemary Shand (1947- )
                              m. (1) Andrew Henry Parker-Bowles
                                    (2) Charles, Prince of Wales

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Nobel Laureate: Lee Hartwell

 

The Nobel Prize in Physiology or Medicine 2001

"for their discoveries of key regulators of the cell cycle"

Leland H. Hartwell (1939 - ) won the Nobel Prize for his contributions to understanding the cell cycle. His discovery of the regulatory molecule CDC28 led to the idea of "checkpoints"—steps in the cell cycle where specific action is needed to progress to the next stage.

Hartwell shared the 2001 Nobel Prize with Paul Nurse and Tim Hunt.

Some of you may think that elucidation of the cell cycle in yeast isn't such a big deal. You would be wrong. No only did this work stimulate a huge field of study in yeast, but the genes and the pathways uncovered in yeast are similar to those in other eukaryotic cells. This is a case where fundamental basic science has lead to a deep understanding of how life works at the molecular level.

THEME:
Nobel LaureatesI already posted the press release under Nobel Laureate: Sir Paul Nurse. It's a very good description of the work that was done by all three Nobel Laureates.

Here's an excerpt from the Presentation Speech.

This year's Nobel Laureates have discovered the key regulators of the cell cycle, cyclin dependent kinase (CDK) and cyclin. Together these two components form an enzyme, in which CDK is comparable to a "molecular engine" that drives the cell through the cell cycle by altering the structure and function of other proteins in the cell. Cyclin is the main switch that turns the "CDK engine" on and off. This cell cycle engine operates in the same way in such widely disparate organisms as yeast cells, plants, animals and humans.

How were the key regulators CDK and cyclin discovered?

Lee Hartwell realized the great potential of genetic methods for cell cycle studies. He chose baker's yeast as a model organism. In the microscope he could identify genetically altered cells - mutated cells - that stopped in the cell cycle when they were cultured at an elevated temperature. Using this method Hartwell discovered, in the early 1970s, dozens of genes specific to the cell division cycle, which he named CDC genes. One of these genes, CDC28, controls the initiation of each cell cycle, the "start" function. Hartwell also formulated the concept of "checkpoints," which ensure that cell cycle events occur in the correct order. Checkpoints are comparable to the program in a washing machine that checks if one step has been properly completed before the next can start. Checkpoint defects are considered to be one of the reasons behind the transformation of normal cells into cancer cells.

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[Photo Credit: Susie Fitzhugh and the Fred Hutchinson Cancer Research Center]

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

"Dr." Charlene Werner on Homeopathy

 
This video illustrates the extreme stupidity of those who believe in homeopathy.

The person who posted the video on YouTube recently received the following letter.

I thought you would like to know that you will be contacted by Dr Werner's Attorney shortly regarding her video. The posting of this video is in violation of copyright laws. We are aware that you have had this video up since March of '08 however I suggest you delete it immediately.

Jayson Patrick

This immediately triggers the Streisand Effect. Won't these people ever learn? No, of course not, that's because they are stupid.

Watch if you dare.

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Monday's Molecule #142: Winner

 
The diagram should remind you of the cell cycle and the 2001 Nobel Prize in Physiology and Medicine. Since I already covered Tim Hunt and Paul Nurse, this must be about Lee Hartwell. That means the molecule must be "start" or CDC28.

The winner is Bill Chaney of the University of Nebraska. He has agreed to donate his free lunch to an undergraduate. Unfortunately, there weren't any undergraduate who got the right answer this week so I still have three free lunches to give away.

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Sometimes it's almost impossible to find an image of a specific molecule that honors a Nobel Laureate. This is one of those times.

The diagram provides all the clues necessary to identify an important process and then to identify a particular molecule associated with this week's Nobel Laureate.

You must name the molecule and the Nobel Laureate. Be careful 'cause it's easy to make a mistake and name someone who has already been the subject of a Monday's Molecule.

The first person to identify the molecule and name the Nobel Laureate(s) wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only six ineligible candidates for this week's reward: Frank Schmidt of the University of Missouri, Joshua Johnson of Victoria University in Australia, Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany, Jason Oakley a biochemistry student at the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison and Alex Ling of the University of Toronto.

Joshua and Dima have agreed to donate their free lunch to an undergraduate. Consequently, I have two extra free lunches for deserving undergraduates so I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.

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(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

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

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