Saturday, January 31, 2009

My New York Ancestors

 
The January 24th issue of The New York Times has a article on what New york City must have looked like 400 years ago. The image is based on work by Eric W. Sanderson [Henry Hudson’s View of New York: When Trees Tipped the Sky].

The first Dutch North American Ancestors in my family were Hendrick Harmensen who was born about 1590 in Lent (Netherlands) near present day Nijmegen and his wife Catherine. They came to North America around 1638 with their daughter Grietje and her husband Abraham Rycken or (de Rycke) who was born about 1618, also in Lent (van Lent).

It is said that Harmenson was the first European to plant crops on Long Island. His farm was near the place where La Guardia airport is today. Harmenson was a blacksmith and he used to make tomahawks for the Indians. He was murdered in a local uprising in 1643. The cause of death was a blow to the head from one of his own tomahawks.

Arbraham Rycken and his wife owned a lot of property on Long Island, including a small island off the coast near their farms. Their children adopted several names including "van Lent" and "Riker." The small island remained in the family for several hundred years and it is still known as Rikers Island—now the site of a large prison.

Their daughter, Aeltje, married Captain Jan Harmse, a descendant of German/Dutch immigrants. Captain Harmse was born in New Amsterdam (New York) in 1657. Their son, Harmen Harmse (1684-1720), married Margaret Montras (1691-1739) thus uniting my French and Dutch ancestors. Harmen took his wife's last name. They moved to Tarrytown New York and joined the congregation of the Dutch Reformed Church of Sleepy Hollow.

The son of Harman and Margaret Montras is Peter Montras (1715-1790). He was my great6 grandfather.


Read More...

Intelligent Design Creationism

 
During the Kitzmiller v. Dover Area School District trial the question of whether Intelligent Design Creationism was really creationism was a hot issue. Professor Barbara Forrest's testimony put to rest any doubts on that score.

You can read the trial transcript on the TalkOrigins website. In this excerpt she is addressing the various editions of the creationist book that is now called Of Pandas and People.

You'll notice that the word "creation" has an ending, it has an "-is" ending. That is so that the counter will pick up any cognate of that word, creationist or creationism, that both will be counted, and here we're looking for the term "intelligent design" rather than just "design." What this indicates is that you see the same thing in these drafts. In the early drafts you see the use of the term "creationism" and its various cognates. Not very much use at all of the term "intelligent design." In fact, in Creation Biology it's zero times. And then subsequent to the version 1 of Pandas 1987 you see a steep decline in the use of the term "creation" and its various cognates, and you see a very sharp rise in the use of the term "intelligent design" in that second version of Pandas of 1987.


You can see that creationism morphed into Intelligent Design. The biggest shift occurred in 1987 when the US Supreme Court ruled, in Edwards v. Aguillard, that creationism was religious and couldn't be taught in public schools. The replacement of "creationism" with "intelligent design" was a political move designed to make belief in a creator sound less religious.

It's not a surprise that old-school creationism became Intelligent Design Creationism. After all, the same players were involved and 99.99% of those who advocate intelligent design also believe in a creator God. All this is old news to most of you but it bears repeating from time to time.

What's surprising is that there are Intelligent Design Creationists who deny that they are creationists. Usually they try and restrict the term "Creationist" to the Young Earth Creationism of the biblical literalists but the evidence in "Pandas" is conclusive. The Intelligent Design Creationism in Of Pandas and People is clearly derived from creationism.

Here's an example of our most famous Doctor IDiot (Michael Engor) bending over backwards to make a fool of himself in Reviewing Jerry Coyne. He's pushing the claim that there's no connection between "creationism" and "intelligent design."
Dr. Coyne misunderstands the history of this issue. Regardless of whether or not creationism has undergone an “evolutionary” process, ID isn’t on the historical continuum with creationism. Creationism is the opinion that Genesis is more or less literally true as science. Many Christians hold to that view, and they have my respect, but I (and the vast majority of I.D. advocates) disagree.

Intelligent design is the opinion that design is empirically detectable in biology, and that it is the best scientific inference to explain many aspects of biology, especially the genetic code and the complex molecular machinery inside cells. I wasn’t a creationist, ever. I was a Darwinist, for most of my life, until I looked closely at the evidence. Most ID advocates have had similar experiences. Most ID advocates were never creationists, and ID is not creationism nor is it derived from it. In fact, ID has been criticized by the creationist community. ID is an appeal to evidence in the natural world, not an appeal to Biblical revelation.
Hmmm ... "ID is not creationism nor is it derived from it." I guess Michael Engor has never read anything about that little episode in Dover only four years ago.

I believe that Michael Egnor is a creationist. I think he believes in a God who created the universe. I will continue to call him an Intelligent Design Creationist—as opposed to a Young Earth Creationist—unless he's willing to deny the existence of a Creator.1


1. Who, coincidentally, just happens to be the intelligent designer as well.

Read More...

Shame on The University of Vermont

 
The University of Vermont will be awarding an honorary degree to Ben Stein, the man behind the movie Expelled. Here's the press release from the University of Vermont [Ben Stein to Deliver Commencement Address]. Notice that they don't mention the movie. That's no excuse.

The multi-talented Ben Stein, actor/comedian/lawyer/economist/presidential speechwriter/filmmaker, will address the graduates and receive an honorary degree at the University of Vermont's 205th commencement ceremony on Sunday, May 17.

Popularly known as the host of Comedy Central's seven-time Emmy award winning game show, "Win Ben Stein's Money," and for an iconic classroom scene in the film Ferris Bueller's Day Off, Stein is also an accomplished writer who has published 30 books and written for publications ranging from the Wall Street Journal and The New York Times to E! Online and New York Magazine. Stein earned his undergraduate degree with honors in economics from Columbia University and went on to graduate as valedictorian of his class from Yale Law School. He has taught at American University, the University of California at Santa Cruz and Pepperdine University in subjects ranging from political and social content of mass culture to securities law. Along with his academic and entertainment achievements, Stein has as served as a trial lawyer for the Federal Trade Commission and as White House speechwriter for presidents Nixon and Ford.
The University of Vermont offers a Major in Biochemistry. Before enrolling, students need to check out the courses to see if they encourage critical thinking and to see how evolution is presented.

The University of Vermont has every right to award honorary degrees to anyone they want. That's what academic freedom is all about. The downside is that the University of Vermont will be judged by who they choose to get an honorary degree. That judgment is not going to be favorable.

UPDATE: Ben Stein has decided that he has another commitment that will prevent him from receiving the honorary degree from the University of Vermont [Stein backs out].

Having been involved in selecting honorary degree recipients, I can assure everyone that you don't make public announcements until the candidate has agreed. Thus, it looks very much like Ben Stein and the university have made a joint decision that inviting Stein to accept an honorary degree was a mistake.

I'm glad the University of Vermont came to its senses.


Read More...

Professor Alex Palazzo Is Coming to Toronto!!!

 
Alex Palazzo has been hired by my department as an Assistant Professor (tenure-stream). He'll be arriving in a few months to set up his lab.

Most of you know Alex from his blog The Daily Transcript. Pop on over there to congratulate him [The Deed is Done].

The Department of Biochemistry should also be congratulated for landing such an outstanding candidate. You can leave comments here and I'll make sure everyone sees them.

Alex's work on the targeting of messenger RNA is extremely impressive. Everyone in the Department wanted to offer him the job as soon as he finished his visit last summer. We all look forward to having him as our colleague. The fact that we will now have two blogging Professors is a nice bonus.

Palazzo, A.F., Springer, M., Shibata, Y., Lee, C.S., Dias, A.P., and Rapoport, T.A. (2007) The signal sequence coding region promotes nuclear export of mRNA. PLoS Biol. 5(12):e322 [doi:10.1371/journal.pbio.0050322]

In eukaryotic cells, most mRNAs are exported from the nucleus by the transcription export (TREX) complex, which is loaded onto mRNAs after their splicing and capping. We have studied in mammalian cells the nuclear export of mRNAs that code for secretory proteins, which are targeted to the endoplasmic reticulum membrane by hydrophobic signal sequences. The mRNAs were injected into the nucleus or synthesized from injected or transfected DNA, and their export was followed by fluorescent in situ hybridization. We made the surprising observation that the signal sequence coding region (SSCR) can serve as a nuclear export signal of an mRNA that lacks an intron or functional cap. Even the export of an intron-containing natural mRNA was enhanced by its SSCR. Like conventional export, the SSCR-dependent pathway required the factor TAP, but depletion of the TREX components had only moderate effects. The SSCR export signal appears to be characterized in vertebrates by a low content of adenines, as demonstrated by genome-wide sequence analysis and by the inhibitory effect of silent adenine mutations in SSCRs. The discovery of an SSCR-mediated pathway explains the previously noted amino acid bias in signal sequences and suggests a link between nuclear export and membrane targeting of mRNAs.

More papers are in the works.

I hope to see Alex very soon. I owe him a beer.


Read More...

Friday, January 30, 2009

Randolph Nesse on Darwinism

 
Randolph Nesse is the co-author of "Why We Get Sick: The New Science of Darwinian Medicine" (along with George C. Williams). This is the uncut version of an interview with Richard Dawkins. Thanks to RichardDawkins.net for posting the video.

The subject is evolutionary medicine.

It's interesting how one's perspective can be distorted by only thinking about animals. Nesse wonders how large multicellular species can survive when bacterial pathogens can evolve so rapidly. Part of his answer is the immune system but he also talks about pain and vomiting as adaptive responses to disease.

If you think about trees and tulips, you might come up with very different answers to the same questions. Plants survive very well without an immune system or pain. It makes you realize that there are different ways of solving a problem.




Read More...

Are You as Smart as a Second Year University Student? Q5

 
Are You as Smart as a Second Year University Student?

Question 1
Question 2
Question 3
Question 4
When you ask my students to remember some important facts about evolution and biochemistry, 98% of them get it right. This question was way too easy. How do Sandwalk readers do?

The evolutionary approach to biochemistry is often called “comparative biochemistry” because it involves comparing enzymes and pathways in different species. The objective is to recognize the fundamental principles that apply to all living organisms. Which of the following insights gained from such an approach is WRONG?

a) the enzymes of the gluconeogensis pathway evolved before
      those that are specific for the glycolytic pathway
b) not all species have a citric acid cycle
c) you can have membrane-associated electron transport
      without oxygen
d) the plant photosynthesis pathway arose from combining two
      different photosystems
e) the P/O ratio is the same in all species



Read More...

Are You as Smart as a Second Year University Student? Q4

 
Are You as Smart as a Second Year University Student?

Question 1
Question 2
Question 3
My students love doing problems. 91% of them got this one right.

In a typical bacterial cell the membrane potential across the inner membrane is –0.15 V. The protonmotive force is –21.2 kJ mol-1 at 25°C . If the pH in the periplasmic space is 6.35 what is the pH in the cytoplasm?

a) between 6.40 and 6.69
b) between 6.70 and 6.99
c) between 7.00 and 7.29
d) between 7.30 and 7.59
e) between 7.60 and 7.89



Read More...

Are You as Smart as a Second Year University Student? Q3

 
Are You as Smart as a Second Year University Student?
Question 1
Question 2
Biochemistry is a three-dimensional subject and one of the things we concentrate on in our introductory biochemistry course is understanding what molecules look like in three dimensions. In many cases we are forced to depict these molecules in two dimensions just for simplicity. There are rules about how to do this, especially when it comes to describing carbohydrates.

My students have copies of the names and structures of the standard aldohexoses (see below). I give them three views of an aldohexose and ask them to identify the sugar. On Tuesday's test 85% of my students got the right answer.

How would you do?




Are You as Smart as a Third Year University Student?
Question 1
Question 2
Question 3
Question 4
Question 5
Question 6
Some of them are a bit more difficult. In this case (below) you have to be much more specific in naming the structure. In these examples only about 50% of the students get them right. Can you name this molecule?




Read More...

Whatever Happened to Common Sense?

 
Steve Mirsky, writing in Scientific American, tells a story that we can all relate to [The Unkempt Results of Post-9/11 Airport Security Rules].

Lewis Carroll’s Alice would have had trouble distinguishing reality from Wonderland had she been with me on the Sunday after Thanksgiving as I watched a TSA officer confiscate my father’s aftershave at the airport in Burlington, Vt. It was a 3.25-ounce bottle, clearly in violation of the currently permissible three-ounce limit for liquids. Also clear was the bottle, which was obviously only about a quarter full. So even the members of some isolated human populations that have never developed sophisticated systems for counting could have determined that the total amount of liquid in the vessel was far less than the arbitrarily standardized three ounces. But the TSA guy took the aftershave, citing his responsibility to go by the volume listed on the label. (By the way, the three-ounce rule is expected to be phased out late in 2009. Why not tomorrow? Because of the 300-day-rules-change rule, which I just made up.)

Feeling curiouser, I did a gedankenexperiment: What if the bottle had been completely empty—would he have taken it then? No, I decided. When empty, the bottle becomes just some plastic in a rather mundane topological configuration. Not to mention that if you really banned everything with the potential to hold more than three ounces of liquid, you couldn’t let me have my shoes back. You also couldn’t allow me to bring my hands onboard. I kept these thoughts to myself, of course, because I wanted to fly home, not spend the rest of the day locked in a security office explaining what a gedankenexperiment was.

I first commented on what I used to call “the illusion of security” in this space in July 2003, after attending a conference on freedom and privacy. We heard the story of an airline pilot who had his nail clippers snatched away by the TSA just before boarding his plane. He then walked into a cockpit equipped with an ax.
Let's think a little more about the gedankenexperiment. If the bottle is really empty then you probably would have discarded it so the empty bottle isn't a good test. What if it only has a drop of aftershave in it? That will be barely visible to the airport security guys but it might give you one more day of smelling nice.

Would they confiscate that? Would they have to open the bottle to see if there was a drop of aftershave in it? What if the drop evaporated during the inspection? Then the bottle would be empty and you wouldn't want to keep it but the security guys won't confiscate an empty bottle. Can you make them confiscate the bottle if they empty it?

What if the bottle has about 2 ounces of aftershave and you pour it into your hands? You now have an empty bottle—which they won't confiscate—and no container with liquid in it, unless they count your hands. What will they do now?


Read More...

When Rationalism Trumps Superstition

 
Or maybe not ....



[Hat Tip: Canadian Cynic]

Read More...

Obama's Very Short Honeymoon

 
Canadian newspapers are headlining a recent decision by the US Congress to "buy American" [Obama's 'Buy American' plan blasted].

Both versions of the U.S. economic stimulus package block the use of foreign-made iron, steel, textiles and manufactured products according to the report in the Toronto Star. Canadians think that is an illegal example of protectionism but the US Vice-President disagrees, according to the report in The Toronto Star.

Liberal foreign affairs critic Bob Rae said bluntly the position taken by the U.S. Congress is illegal.

"A country cannot bring in a measure that restricts international commerce and international activity in this way," he said.

However, late yesterday, Obama's administration signalled a different view. In an interview with CNBC, U.S. Vice-President Joe Biden defended the "Buy America" steel provision.

"I don't view that as some of the pure free traders view it, as a harbinger of protectionism," Biden said.
Canada and the USA have signed a free trade agreement (NAFTA) that is legally binding in both countries (and Mexico). The USA has failed to live up to its commitments before but it has lost when the issues went to arbitration. Unfortunately, the legal proceedings take many years and during that time US protectionism benefits American countries at the expense of Canadian and Mexican companies. Meanwhile, America benefits by selling its goods and services in Canada and the Mexico.
As officials at Canada's embassy in Washington scramble to lobby U.S. senators to water down the language in the bill, Canada's trade and industry ministers suggested the measures could be challenged under the North American Free Trade Agreement or at the World Trade Organization.

"We are reminding the Americans that they have legal obligations under NAFTA, under WTO," said International Trade Minister Stockwell Day. "History shows clearly that you can't fall back into protectionist measures. That happened in the 1930s and what could have been a bad one- or two-year recession turned into, as we know, the Great Depression. So we want to curtail that."

But a NAFTA challenge will be neither easy nor a quick way to resolve anything.
Canadian policians were worried about Obama's commitment to international trade. So far it looks as though those fears were justified.

It was a very short honeymoon for Barack Obama. It will be interesting to see how he handles this problem. He has promised to work toward restoring America's stature in the international community. Setting up protectionist trade barriers in violation of international treaties isn't going to advance that cause.


Read More...

Thursday, January 29, 2009

Atheist Attack Ads

 
From today's Globe and Mail: Toronto church leader denounces atheist 'attack ads'.

A prominent evangelical leader says atheist ads suggesting there is no God - now headed for Toronto's transit system - are "attack ads" and should not be approved.

The Toronto-based Freethought Association of Canada won approval yesterday from the Toronto Transit Commission to place ads on buses and inside subway cars that read: "There is probably no God. Now stop worrying and enjoy your life."

Charles McVety, president of the Canada Family Action Coalition, which fought against the legalization of same-sex marriages, said his group has not decided whether it will formally complain about the ads once they appear.

"On the surface, I'm all for free speech. ... However, though, these are attack ads," Dr. McVety, president of Canada Christian College in Toronto, said in an interview yesterday.

"These ads are not saying what the atheists believe, they are attacking what other people believe," he said. "And if you look at the dictionary definition for ... bigot, that's exactly what it is, to be intolerant of someone else's belief system."
Hmmmm .... let's wander over to the Canadian Family Action Coalition website to see some examples of Christian love and tolerance. We certainly don't expect to see anyone attacking what other people believe, do we?
Your right to chose – your obligation to pay

Women who want the “right” to dispose of their baby in an abortion mill may be able to defend that position due to the lawlessness of Canada.But they cannot defend under any law or logic the position that tax payers must fund their abortions.

You want a right to chose then you have an obligation to pay.

If the Canadian government refuses to put any restriction on the killing of children in the womb, then it has at minimum a moral and legal obligation to stop allowing tax funded hospitals and taxpayer money to be used for such a purposes.

REAL Women has carefully documented, over the past few years, as reported in REALity, the relentless effort by the federal Liberal Party of Canada to push the homosexual agenda. Prominent Liberal Cabinet Ministers, especially a long line of Liberal Justice Ministers, starting with Allan Rock in 1996, working in tandem with the party hacks appointed to the Bench by a series of Liberal Prime Ministers, have brought about a homosexual revolution in Canada. Anything homosexual activists demanded was handed to them on a silver platter by the Liberals - sexual orientation protection in the Human Rights Act, same-sex benefits, same-sex marriage, immigration privileges, the subverting of religious rights, etc. During these monumental changes, the public's views were disregarded by the arrogant Liberals. After all, the Liberals were the party of power, in perpetuity they thought, and they knew what was good for us. The democratic process of consulting the public was irrelevant to the Liberal elites.

Have the Liberals learned their lesson by their defeat in 2006? Apparently not - judging by the new generation of Liberal elites, post Prime Minister Jean Chretien - who are also keen on pushing the homosexual agenda on the road to society's destruction. This was made apparent by their unabashedly marching in the so-called "Gay Pride" parade in Toronto on June 29, 2008.

They marched alongside drag queens, gyrating exhibitionists, nudes with their genitals totally exposed (but wearing sandals to avoid indecent exposure charges), sado-masochism specialists, "leather-men" etc. No doubt believing they were liberated forward-thinkers, these supporters of the Parade in fact, revealed themselves to be mindless followers of politically correct thought. The politicians in the parade included the following:

Former Leadership Candidate MP Bob Rae (Toronto Centre); Former Leadership Candidate and Liberal Deputy Leader Michael Ignatieff (Etobicoke - Lakeshore); Toronto Liberal MP Mario Silva (Davenport), a self-acknowledged homosexual; Toronto Liberal MP Carolyn Bennett (St. Paul - Trinity) happily escorted by transsexuals during the parade; Former Liberal Leadership Candidate Gerard Kennedy; Liberal MP Belinda Stronach (Aurora-Newmarket); Toronto Liberal MP Borys Wrzesnewskyi (Etobicoke Centre). The latter attended a morning church service conducted by the homosexual Metropolitan Community Church minister, the Rev. Brent Hawkes, who broke the law by officiating at an unlawful same-sex marriage ceremony in 2002; and Ontario Premier Dalton McGuinty and his homosexual cabinet minister George Smitherman, Minister of Energy and Infrastructure.

Sex ed coming to your 6 year old
Homosexual activists will stop at nothing. They will try to "educate " your 5 and 6 year old children that sodomizing another human being is normal - healthy - natural. It is none of these. This project in Great Britain is a forerunner to what is happening in Canada in various ways.

So you must demand information about what teachers intend to teach YOUR children in sex-ed, health and social classes.

Now any opposition to homosexual sex behavior is called heteronormativity, homophobia and transphobia. The phobia is that activists continue to fear any opposition to their sexual behaviors, respect for marriage and reality of monogamy's benefits. They now even have to invent meaningless words like homophobia and now heteronormativity. It is not even a word.

Protect your children's well being and health.
I'm convinced. Charles McVety, like many of his friends, is a hypocrite.

Who knew?


I took this photograph of Charles McVety last June in front of the ROM [Charles McVety Visits the ROM

Read More...

Should Atheists Have the Same Rights as Others?

 

From CP24. So far the correct answer is winning but 16% of the respondants think that atheists should not be allowed to buy ads because they might be offensive to some people. [PZ Myers probably affected the results of this poll: It's yet another atheist bus poll]

I wonder what those people think of the Conservative Party ads on the radio? I find them very offensive, and stupid.


[Hat Tip: Canadian Cynic]

Read More...

Harper Slashes Research in Canada

 
The Conservative Party under Stephen Harper has proposed drastic cuts in research funding. The new budget suggests that the major research councils will be able to "save" 87 million dollars over the next four years due to increased efficiency.

Read it at: Budget 2009 under "Granting Councils."

The Canadian Institutes of Health Research, the Natural Sciences and Engineering Research Council of Canada and the Social Sciences and Humanities Research Council of Canada are streamlining operations and aligning programs with the objectives of the Government’s Science and Technology Strategy and national research priorities. Through closer coordination, these agencies are improving the effectiveness of existing programs, aligning their programs with their core roles and fostering the development of innovative new programs.

These savings will be used in this budget to support repairs at post-secondary institutions, to upgrade key Arctic research facilities, to expand the Canada Graduate Scholarships program and graduate internships, and to support new world-class research facilities. This budget also sets aside $750 million to support the current and future activities of the Canada Foundation for Innovation.


Most enlightened countries are increasing funding for basic research but that's not what Conservatives have in mind in order to help Canada adjust to the 21st century. Instead, my government is going to reduce research grants at the same time they want to increase the number of graduate students. Where the heck are these graduate students going to carry out their studies? In the USA?

Genome Canada, a separate agency, isn't getting any money at all. But one thing the Conservative Party has learned from our neighbor to the south is that political parties can give money directly to their favorite causes. Even if it comes at the expense of all other scientists. In this case, the Institute for Quantum Computing gets $50 million in a special non-peer reviewed grant.

Canada adopts earmarks.

Disgusting.

The Liberal Party's Industry, Science & Technology Critic is Marc Garneau (Westmount-Ville Marie). You can send him a message here. Tell him that the Liberal Party should not support this budget.

Here's what Marc Garneau said today as reported by CBC: Critics question lack of new funding for Genome Canada.
Liberal party science and technology critic Marc Garneau told CBC News the funding of Genome Canada would be an issue the party would address with the government when it discusses amendments to the budget.

It will also raise cuts in the budget to Canada's three research councils. The cuts total close to $150 million and peak in 2011-12 at $87.2 million, Garneau said.

But he stopped short of saying these issues would be deal-breakers in ongoing budget talks.

"What we're going to do is continue to remind the government that they are not doing enough in that particular area," said Garneau. "I won't tell you whether or not this is a show-stopper because I'm not making those decisions, but I think our party will continue to point out the lack of real support in science by this government."
If the Liberals don't think this is a "show-stopper" then maybe it's time to vote NDP.


Read More...

Nobel Laureate: Osamu Shimomura

 

The Nobel Prize in Chemistry 2008.

"for the discovery and development of the green fluorescent protein, GFP"




Osamu Shimomura (1928 - ) was awarded the Nobel Prize for isolating and characterizing green fluorescent protein (GFP) from the jellyfish Aequorea victoria. Here's the Press Release describing his achievements.

Glowing proteins – a guiding star for biochemistry

The remarkable brightly glowing green fluorescent protein, GFP, was first observed in the beautiful jellyfish, Aequorea victoria in 1962. Since then, this protein has become one of the most important tools used in contemporary bioscience. With the aid of GFP, researchers have developed ways to watch processes that were previously invisible, such as the development of nerve cells in the brain or how cancer cells spread.

Osamu Shimomura first isolated GFP from the jellyfish Aequorea victoria, which drifts with the currents off the west coast of North America. He discovered that this protein glowed bright green under ultraviolet light.


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.

Read More...

Monday's Molecule #105: The winners

 
 
Monday's molecule is on Tuesday this week. Sorry for the delay, I've been busy with a mid-term test in my introductory biochemistry course.

You have to identify this molecule. The role of this molecule in a particular species was elucidated by a Nobel Laureate in the second half of the 20th century. We need the name of the Nobel Laureate who first isolated and characterized the protein.

Your task is to correctly identify the molecule and the species from which it was purified. You also need to name the Nobel Laureate. The first one to do so 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 five ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin, Bill Chaney of the University of Nebraska, Maria Altshuler of the university of Toronto, Ramon, address unknown, and Jason Oakley of the University of Toronto.

Dima and Bill have offered to donate their free lunch to a deserving undergraduate so the next two undergraduates to win and collect a free lunch can also invite a friend. Since undergraduates from the Toronto region are doing better in this contest, I'm going to continue to award an additional free lunch to the first undergraduate student who can accept a free lunch. Please indicate in your email message whether you are an undergraduate and whether you came make it for your free lunch (with a friend).

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 Laureate(s) 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. I reserve the right to select multiple winners if several people get it right.

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

UPDATE:The molecule is green fluorescent protein from the jellyfish Aequorea victoria. The Nobel Laureate is Osamu Shimomura (2008).

The winner is John Bothwell (again) from the Marine Biological Association of the UK, in Plymouth (UK). The local winner is Wesley Butt of the University of Toronto.


Read More...

Praise Darwin

 


This is a billboard that the Freedom from Religion Foundation is planning to put up in several American cities.

I'm totally opposed to this billboard for the same reason I objected to the New Scientist cover saying "Darwin Was Wrong."

Charles Darwin published his famous book in 1859. That's 150 years ago. Since then we have moved far beyond anything Darwin could have imagined while strolling on the Sandwalk. Modern scientists do not worship Darwin and they haven't been wedded to his ideas for over a century.

The editors of New Scientist don't get this, and neither does the Freedom from Religion Foundation.

John Pieret allerted me to this billboard [Praise Hymn]. His take is slightly different. He's more concerned with how the creationists will take advantage of these errors. I'm more worried about how the errors contribute to misunderstanding among sensible people.


Read More...

Mathematical Proof of God

 
Here's Kirk Durston explaining how mathematics can show that evolution is impossible and Intelligent Design Creationism is probable. Durston is a graduate student at the University of Guelph (Guelph Ontario, Canada). At some point he will have to describe his ideas to a group of scientists who will determine whether he should get a Ph.D. Good luck Kirk, you will need it. Unless, of course, if the committee is stacked with IDiots people who don't understand biology.

If this explanation forms any part of Durston's thesis then it would be extremely embarrassing if the University of Guelph awards him a Ph.D. But what if all this is left out of the thesis? Is it still fair game for the Ph.D. oral committee?




Read More...

Tuesday, January 27, 2009

Science Journalists and Junk DNA

 
The latest issue of SEED magazine concentrates on the idea that "Science Is Culture"—whatever that means.

One of the things it seems to mean is that good, accurate science reporting is not a high priority.

Junk DNA is one of those subjects that seem to bamboozle science journalists. They just can't seem to accept the possibility that much of our genome serves no purpose. One of the most extreme examples of this bias can be found in an article by Veronique Greenwood titled What We Lose.

The point of the article is that scientific models aren't perfect. They often over-simplify and, even more dangerous, they can exclude the very information required to refute the model. The example she uses is the software that will select what data to look at when the Large Hadron Collider (LHC) starts working. Greenwood's point is that the software might ignore the most interesting collisions because they aren't what scientists expect.

Here's how she explains the danger.

It wouldn't be the first time a standing model has excluded data that could revise it. In the 1980's, NASA analyses of the ozone layer flagged a great many data points as errors—values that seemed too low to be real, values that indicated a huge hole in the planet's protective layer. NASA scientists overlooked the possibility until an outside group published its discovery of the ozone hole in 1985. ....

Something similar happened in the 1990's when DNA that didn't code for proteins was labeled "junk." Noncoding DNA, biologist have since found, regulates protein-coding DNA.
THEME

Genomes & Junk DNA
No, Ms. Greenwood, that's not what happened. Junk DNA has been around for 35 years and it is well-established that much of our genome is composed of degenerate transposons and pseudogenes. There's good evidence that up to 90% of our genome may be junk, perhaps more.

Regulatory sequences have been known for over forty years. They cannot account for more than a small fraction of noncoding DNA. You are dead wrong when you claim that a function has been found for most junk DNA.





Read More...

Kirk Durston vs PZ Myers

 
PZ Myers has a brief account of his encounter with Kirk Durston in Edmonton (Alberta, Canada) last weekend [An ugly debate in Edmonton].

PZ discovered what many of us already knew about Kirk ...

He's a good debater, because he relies on a powerful tactic: he'll willingly make stuff up and mangle his sources to make his arguments. I'm at a disadvantage because I won't do that.
Exactly. It's hard to debate someone who lies with a straight face, especially if they act like a Christian while doing it.

Here's what I had to say last year about my encounter with Kirk Durston [Kirk Durston's Proof of God].
It was a very frustrating experience. Like most Intelligent Design Creationists, Durston was all over the map in terms of spreading lies and misconceptions about science. This scattergun approach seems to be very successful for them. I assume it's because no one person can address all of the problems with their presentation. Most people will catch one or two flaws but they'll assume that everything else has to be correct.
Sounds like nothing has changed.


Read More...

Does God Exist? A Debate

 
It's almost too late but here's an event you should attend it you live in Toronto.1 Jim Brown is an atheist philosopher and a very, very smart man. I almost feel sorry for William Lane Craig.

This event is co-sponsored by the University of Toronto Secular Alliance and the Campus for Christ at U of T.

Does God Exist? A Debate

Time: Tues Jan 27, 6:00pm
Location: Isabel Bader Theatre (BT), Victoria College, 93 Charles Street West
Tickets: $2 (Student) at the door (Tues) $10 (Non-Student)
Theist: Dr. William Lane Craig
Atheist: Dr. James Robert Brown

This will prove to be an exciting debate between two world-renowned philosophers, including a professor from here at U of T. After a formal debate structure, both debaters will take questions from the audience. We anticipate a full auditorium for this broad topic that appeals to many students, regardless of where they stand on the debate.

This event is co-sponsored by Campus for Christ at U of T and University of Toronto Secular Alliance.

We expect this debate to be full and will prioritize seating for university students. If you are not a student at this university, please attend the Thursday debate at York University as there will be more room there. Cost is $10 for non-students.


1. I can't make it. My mid-term is tonight. Please post a message telling us how it went.

Read More...

The Power of Darwin

 
Richard Dawkins has published an article in Free Enquiry titled The Power of Darwin. Here are the opening paragraphs.

Charles Darwin had a big idea, arguably the most powerful idea ever. A powerful idea assumes little to explain much. It does a lot of explanatory “heavy lifting” while expending little in the way of assumption or postulation. It gives you plenty of bang for your explanatory buck. Its Explanation Ratio—what it explains divided by what it needs to assume in order to do the explaining—is large.

Power of a theory = That which it explains/That which it needs to assume in order to do the explaining

If any reader knows of an idea that has a larger explanation ratio than Darwin’s, let’s hear it. Darwin’s big idea explains all of life and its consequences, and that means everything that possesses more than minimal complexity. That’s the numerator of the Explanation Ratio, and it is huge. Yet the denominator is spectacularly small and simple: natural selection, the non-random survival of genes in gene pools (to put it in neo-Darwinian terms rather than Darwin’s own).

Power of Darwin’s theory = The diverse complexity of life/Non-random survival

Natural selection is an improbability pump—a process that generates statistical improbability. It systematically seizes the minority of random changes that have what it takes to survive and accumulates them, step by tiny step over unimaginable timescales, until evolution eventually scales mountains of improbability and diversity whose height and range seem to know no limit.
Natural selection does NOT explain all of life and its consequences. A great deal of what we see in modern species is a consequence of accident and happenstance where contingency rules over natural selection. Natural selection does NOT explain diversity.

Darwin's big idea was to convince us that life has evolved rather than being created. That's a simple concept that explains a lot.

Natural selection explains adaptation. That's extremely important and extremely interesting but it's only a small part of evolution. Random genetic drift, which Darwin does not get credit for, explains much more because more of evolution is due to drift than to adaptation.

The contributions of Charles Darwin are enormous. That's why he gets credit for being the greatest scientist who ever lived. It does a disservice to his achievements to exaggerate them in celebration of the 150th anniversary of the publication of Origin of Species.


Read More...

Lower Animals and Higher Animals

 
Here's an article from ScienceDaily.

New Tree Of Life Divides All Lower Metazoans From Higher Animals, Molecular Research Confirms

ScienceDaily (Jan. 27, 2009) — A new and comprehensive analysis confirms that the evolutionary relationships among animals are not as simple as previously thought. The traditional idea that animal evolution has followed a trajectory from simple to complex—from sponge to chordate—meets a dramatic exception in the metazoan tree of life.

New work suggests that the so-called "lower" metazoans (including Placozoa, corals, and jellyfish) evolved in parallel to "higher" animals (all other metazoans, from flatworms to chordates). It also appears that Placozoans—large amoeba-shaped, multi-cellular animals—have passed over sponges and other organisms as an animal that most closely mirrors the root of this tree of life.
There's so much wrong with this description that one hardly knows where to begin. Ryan Gregory highlighted the worst parts at Lower and basal.

Do NOT use the words "higher" and "lower" to describe biological species. This is a mistake that many scientists make so we can't blame the journalists1 for this one.


1. I wonder what Graham Lawton thinks about this tree of life?

Read More...

Monday's Molecule #105

 
Monday's molecule is on Tuesday this week. Sorry for the delay, I've been busy with a mid-term test in my introductory biochemistry course.

You have to identify this molecule. The role of this molecule in a particular species was elucidated by a Nobel Laureate in the second half of the 20th century. We need the name of the Nobel Laureate who first isolated and characterized the protein.

Your task is to correctly identify the molecule and the species from which it was purified. You also need to name the Nobel Laureate. The first one to do so 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 five ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin, Bill Chaney of the University of Nebraska, Maria Altshuler of the university of Toronto, Ramon, address unknown, and Jason Oakley of the University of Toronto.

Dima and Bill have offered to donate their free lunch to a deserving undergraduate so the next two undergraduates to win and collect a free lunch can also invite a friend. Since undergraduates from the Toronto region are doing better in this contest, I'm going to continue to award an additional free lunch to the first undergraduate student who can accept a free lunch. Please indicate in your email message whether you are an undergraduate and whether you came make it for your free lunch (with a friend).

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 Laureate(s) 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. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours.





Read More...

Saturday, January 24, 2009

Good Science Writing

 

Good Science Writing
David Suzuki
Helena Curtis
David Raup
Niles Eldredge
Richard Lewontin
Steven Vogel
Jacques Monod
G. Brent Dalrymple
Eugenie Scott
Sean B. Carroll
Richard Dawkins
Albert Lehninger
Stephen J. Gould
Douglas Futuyma
Just to remind everyone that there is such a thing as a good science writer, here's a list.


Read More...

Saturday Morning Music

 
Ms. Sandwalk and I have facing desks in our basement study. Many of her blog postings involve music. For the past hour I've been listening to her singing along to all kinds of songs. Some good, and some not so good.

Here's the result. The best ones made it to her blog [Music this week].


Read More...

Jerry Coyne on Science vs. Religion

 
Many people have written about the conflict between science and religion but most get it wrong, especially the apologists for religion. Jerry Coyne is an exception. I don't always agree with his views about evolution but when it comes to the conflict between science and religion he has hit the nail on the head.

Read his article in The New Republic—it's disguised as a review of Ken Miller's book Only a Theory and Karl Giberson's book Saving Darwin: How to be a Christian and Believe in Evolution [Seeing and Believing].

Coyne exposes the fallacy of theistic evolution, a theme close to my own views [Theistic Evolution: The Fallacy of the Middle Ground], ... only Coyne says it so much better ...

True, there are religious scientists and Darwinian churchgoers. But this does not mean that faith and science are compatible, except in the trivial sense that both attitudes can be simultaneously embraced by a single human mind. (It is like saying that marriage and adultery are compatible because some married people are adulterers. ) It is also true that some of the tensions disappear when the literal reading of the Bible is renounced, as it is by all but the most primitive of JudeoChristian sensibilities. But tension remains. The real question is whether there is a philosophical incompatibility between religion and science. Does the empirical nature of science contradict the revelatory nature of faith? Are the gaps between them so great that the two institutions must be considered essentially antagonistic? The incessant stream of books dealing with this question suggests that the answer is not straightforward.

The easiest way to harmonize science and religion is simply to re-define one so that it includes the other. We may claim, for example, that "God" is simply the name we give to the order and harmony of the universe, the laws of physics and chemistry, the beauty of nature, and so on. This is the naturalistic pantheism of Spinoza. Its most famous advocate was Einstein, often (and wrongly) described as believing in a personal God ...

But the big problem with this "reconciliation," in which science does not marry religion so much as digest it, is that it leaves out God completely--or at least the God of the monotheistic faiths, who has an interest in the universe. And this is unacceptable to most religious people. Look at the numbers: 90 percent of Americans believe in a personal God who interacts with the world, 79 percent believe in miracles, 75 percent in heaven, and 72 percent in the divinity of Jesus. In his first popular book, Finding Darwin's God, Kenneth Miller attacked pantheism because it "dilutes religion to the point of meaninglessness." He was right.

A meaningful effort to reconcile science and faith must start by recognizing them as they are actually understood and practiced by human beings. You cannot re-define science so that it includes the supernatural, as Kansas's board of education did in 2005. Nor can you take "religion" to be the philosophy of liberal theologians, which, frowning on a personal God, is often just a hairsbreadth away from pantheism. After all, the goal is not to turn the faithful into liberal theologians, but to show them a way to align their actual beliefs with scientific truths. Theologians sometimes suggest a reconciliation by means of naturalistic deism, the idea that the creation of the universe--and perhaps the laws of physics--was the direct handiwork of a deity who then left things alone as they unfolded, never interfering in nature or history again. For the faithful, this has been even more problematic than pantheism: it not only denies miracles, virgin births, answered prayers, and the entire cosmological apparatus of Christianity, Judaism, Islam, Hinduism, and much of Buddhism, but also raises the question of where God came from in the first place
I've met many "liberal theologians" who claim to believe in some version of "process theology"— a wishy-washy concept that, as Coyne correctly points out, is just a hairsbreadth away from pantheism. The catch is that when you follow these so-called "liberal theologians" back to the safety of their church you'll find that they quickly revert to another form of religion altogether. The "sophisticated" version of Christianity that they proclaim in public is just a sham designed to make them look as though they accept science and all its implications.

The real value of Coyne's review is the dismantling of Ken Miller's version of theistic evolution. Miller, like most theists, wants to have his cake and eat it too. He wants to accept science and evolution but, at the same time, he wants to sneak God into the picture so that humans are special. This is a recognition of the fundamental conflict between science and religion; namely, that according to what we know about the natural world, humans are not special in any way and life does not have a purpose. There are very few believers who can stomach those ideas, hence their science and their religion are in conflict.
Miller opts for theology. Although his new book does not say how God ensured the arrival of Homo sapiens, Miller was more explicit in Finding Darwin's God. There he suggested that the indeterminacy of quantum mechanics allows God to intervene at the level of atoms, influencing events on a larger scale:
"The indeterminate nature of quantum events would allow a clever and subtle God to influence events in ways that are profound, but scientifically undetectable to us. Those events could include the appearance of mutations, the activation of individual neurons in the brain, and even the survival of individual cells and organisms affected by the chance processes of radioactive decay."
In other words, God is a Mover of Electrons, deliberately keeping his incursions into nature so subtle that they're invisible. It is baffling that Miller, who comes up with the most technically astute arguments against irreducible complexity, can in the end wind up touting God's micro-editing of DNA. This argument is in fact identical to that of Michael Behe, the ID advocate against whom Miller testified in the Harrisburg trial. It is another God-of-the-gaps argument, except that this time the gaps are tiny.
Exactly. The difference between Ken Miller and Michael Behe is trivial compared to the difference between Ken Miller and Richard Dawkins. Coyne is not the only one who has trouble seeing why Behe isn't a theistic evolutionist and Miller isn't an intelligent design creationist.

Coyne has written a great article and you must read all of it. Here are two more teasers that I hope will entice you to learn more ...
Giberson and Miller are thoughtful men of good will. Reading them, you get a sense of conviction and sincerity absent from the writings of many creationists, who blatantly deny the most obvious facts about nature in the cause of their faith. Both of their books are worth reading: Giberson for the history of the creation/ evolution debate, and Miller for his lucid arguments against intelligent design. Yet in the end they fail to achieve their longed-for union between faith and evolution. And they fail for the same reason that people always fail: a true harmony between science and religion requires either doing away with most people's religion and replacing it with a watered-down deism, or polluting science with unnecessary, untestable, and unreasonable spiritual claims.

Although Giberson and Miller see themselves as opponents of creationism, in devising a compatibility between science and religion they finally converge with their opponents. In fact, they exhibit at least three of the four distinguishing traits of creationists: belief in God, the intervention of God in nature, and a special role for God in the evolution of humans. They may even show the fourth trait, a belief in irreducible complexity, by proposing that a soul could not have evolved, but was inserted by God.

This disharmony is a dirty little secret in scientific circles. It is in our personal and professional interest to proclaim that science and religion are perfectly harmonious. After all, we want our grants funded by the government, and our schoolchildren exposed to real science instead of creationism. Liberal religious people have been important allies in our struggle against creationism, and it is not pleasant to alienate them by declaring how we feel. This is why, as a tactical matter, groups such as the National Academy of Sciences claim that religion and science do not conflict. But their main evidence--the existence of religious scientists--is wearing thin as scientists grow ever more vociferous about their lack of faith. Now Darwin Year is upon us, and we can expect more books like those by Kenneth Miller and Karl Giberson. Attempts to reconcile God and evolution keep rolling off the intellectual assembly line. It never stops, because the reconciliation never works.
Visit The Edge to see how otherwise intelligent men and women respond to Coyne's argument. Some of them make the kindergarten error of confusing disagreement with intolerance.

Read More...

Friday, January 23, 2009

It took Ricky Gervais only one hour to become an atheist

 
Watch the full story in this clip from Inside the Actors Studio, which, incidentally, is one of my favorite shows.

The good bit comes at four and a half minutes.



[Hat Tip: Friendly Atheist]

Read More...

Explaining the New Scientist Cover

 
Yesterday I criticized the cover of the latest issue of New Scientist [Darwin Was Wrong?]. There's a good discussion going on at EvolutionBlog [The Trouble With Science Journalism].

I pointed out that the cover was, "an egregious example of journalistic hype and it's unacceptable in a magazine like New Scientist." I also mentioned that the article itself, written by Graham Lawton, contained some interesting—and mostly correct—information about the early history of life.

Graham Lawton posted a comment to my earlier posting where he critized Sandwalk readers because they (we?), "lack a fundamental understanding of how the media works." He was asked to explain. This is how Graham Lawton replied.

The way we work here is that the writer of the piece generally has almost no say over the headline, standfirst and other bits of "page furniture". These are the resonsibility of the copy editor and the sub-editors. The online version often has its own headline, which again is out of the control of the writer (in this case the magazine headline is "Uprooting Darwin's Tree").

Coverlines, similarly, are written not by the writer but by senior editors with the express purpose of selling the magazine (the line between marketing and journalism blurs a little here).

As I'm a senior editor too, however, I can't and won't claim that the coverline was entirely beyond my control. Not my ultimate decision, but I was in on the discussions. We knew we were courting controversy but the feeling was that the story was solid enough to allow us to be provocative and, in any case, the statement is true.

So I feel very strong ownership of the article itself, particularly the print version (and I totally stand by the story, which is the product of weeks of hard work, extensive interviews with scientists, a stack of journal papers and much thought, despite what some bloggers are saying). I feel some ownership of the front cover "sell", though as always I'm acutely aware that it is 50% journalism, 50% sales pitch.
I, for one, am not surprised by this "revelation." I have known for some time that decisions on titles and covers are not made by authors. I've known for some time that decisions about titles and covers can be based on "sales pitch" and "hype" and that scientific accuracy can play a minor role in those decisions.

I'd like to thank Graham Lawton for explaining the process in case there are some people who still don't understand the basics.

The fact that I knew how covers were selected does not affect my criticism of the decision in spite of what Lawton might think. As a matter of fact, now that I know how he was involved as senior editor I can put some of the blame on him. The fact that he defends the cover title ("Darwin Was Wrong") by saying that, "... in any case, the statement is true" is revealing.

It's unusual for a science journalist to be so candid about the trade-off between scientific accuracy and "sales pitch."

As for the article itself, Graham Lawton is quite proud of it. He seems to be implying that the title of the article was not his fault, thereby shifting the blame somewhat to other editors. That position is not going to stand up to close examination of the article.

The first four paragraphs talk about Darwin and what he thought in 1837 and 1859 [Why Darwin was wrong about the tree of life. It will be clear to every reader that this is not just ancient history, the strong implication is that up until recently most evolutionary biologists thought just like Darwin must have thought 150 years ago. They were stuck in the late nineteenth century Victorian mindset. That's why Lawton begins the next paragraph with, "For much of the past 150 years, biology has largely concerned itself with filling in the details of the tree."

That's nonsense, of course. There's a lot more that's been happening in evolutionary biology than just filling in the details of trees. Is it any wonder that the editors picked up on this false notion and created the headline "Darwin Was Wrong"? Graham Lawton, as author of the article, seems to be making exactly that point.

The article would have been much better if Darwin's name had never been mentioned. Darwin knew nothing about molecular evolution and he knew almost nothing about bacteria or the last common ancestor. Dragging Darwin's name into the article serves only to confuse the readers. It's probably another example of "sales pitch" designed to sell the magazine. It may not be only editors who are guilty.


Read More...

Thursday, January 22, 2009

44 Presidents?

 
This video is very popular these days. The title is "44 US Presidents from George Washington to Barack Obama." There's only one small problem .... there are only 43 different Presidents shown in the video. Can you spot the "missing" President?



How many can you name without watching the video? Please indicate whether you are American or a "foreigner."

Do Americans agree on who the best President was, and on who was the worst President? It seems to me that there are several excellent choices in each category.


Read More...

Advice for Prospective Graduate Students: Letters of Recommendation

 
Mark, of Cosmic Variance has some advice about Letters of Recommendation. There's lots of useful information in the posting but here's something that bears repeating.

Perhaps the most important thing for prospective graduate students in particular to keep in mind is that admissions committees, while certainly holding great power over individuals’ futures, are in fact desperately seeking good candidates, and are willing to overlook all kinds of blemishes, indiscretions, and specific weaknesses if they feel that they’re getting a fundamentally good candidate. A single specific fact about an application is very unlikely to ruin a person’s chances (you’d be amazed at the GRE scores of some students admitted to even the top programs). Rather, the committee tries to get an overall picture of the candidate, and then to rank them relative to other candidates (also taking into account the department’s research needs at a given time). Only then are admissions decision taken.

I have certainly missed some issues and subtleties here. But the basic idea should be clear and, if my own experience is anything like typical, then it should help some of you, particularly prospective graduate students, to understand what really goes on with letters. It is quite terrifying to ask people for letters and not to know precisely what’s said in them. Hopefully it helps to know that mostly, by far, you can rely on people to do what they can for you, without being dishonest (and this is important - you can’t expect them to write that you’re one of the best students they’ve ever seen if they don’t think that is the case).


Read More...

Darwin Was Wrong?

 
The cover is this week's issue of New Scientist is sure to get your attention.

I happen to believe that the science of evolutionary biology has moved on since 1859, and I happen to be a proponent of evolutionary processes that Darwin new nothing about. Nevertheless, proclaiming that "Darwin was wrong" is a different story. That's an egregious example of journalistic hype and it's unacceptable in a magazine like New Scientist.

The main article is Why Darwin was wrong about the tree of life. The author is science journalist Graham Lawton.

The essence of the story is that the early history of evolution is probably characterized by a net of life and not a traditional tree. The "net" metaphor is due to many example of lateral gene transfer.

Ever since Darwin the tree has been the unifying principle for understanding the history of life on Earth. At its base is LUCA, the Last Universal Common Ancestor of all living things, and out of LUCA grows a trunk, which splits again and again to create a vast, bifurcating tree. Each branch represents a single species; branching points are where one species becomes two. Most branches eventually come to a dead end as species go extinct, but some reach right to the top - these are living species. The tree is thus a record of how every species that ever lived is related to all others right back to the origin of life.

For much of the past 150 years, biology has largely concerned itself with filling in the details of the tree. "For a long time the holy grail was to build a tree of life," says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. "We have no evidence at all that the tree of life is a reality," says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.
As it happens, I was at a function last night with Jan Sapp of York University (Toronto, Canada). Loyal Sandwalk readers might recall a series of articles on the Three Domain Hypothesis. The articles were based on a book edited by Jan Sapp. Sapp is a supporter, as am I, of the scheme advocated by Ford Doolittle (see below).


This net, or web, of life is characteristic of the earliest stages of evolution when all organisms were single cells and the distinction between eukaryotes and prokaryotes was barely discernible. Once the main groups rose out of the web, they evolved pretty much as you light expect by binary speciation events. This gives rise to a traditional tree-like pattern.

As Jan and I discussed, for the last three billion years of evolution the tree of life is a very good metaphor for evolution. Darwin was mostly right about that. On the other hand, the New Scientist article discusses some problems with the tree of life that extend beyond the early history. It makes several valid points that should make everyone skeptical of claims about evolution that are too simple. The tree isn't perfect.

The bottom line is that it's unfair to say that Darwin was wrong. It's as unfair as saying the Newton was wrong because of Einstein. We need to recognize that modern evolutionary biology is an improvement over the view of the Victorian founder of the field, but a cover saying that Darwin was wrong conveys the wrong message. It suggests that up until recently scientists believed that Darwin was right about everything.

A better headline might be: "More evidence that Charles Darwin didn't know everything there is to be known about evolution when he published his book in 1859."

UPDATE: In a surprising development, the IDiots at Uncommon Descent have picked up on these recent (sic) developments in evolutionary theory. Paul Nelson, a Young Earth Creationist philosopher, writes: “The tree of life is being politely buried”.

Read More...

Wednesday, January 21, 2009

Nobel Laureates: Ulf von Euler and Julius Axelrod

 

The Nobel Prize in Physiology or Medicine 1970.


"for their discoveries concerning the humoral transmittors in the nerve terminals and the mechanism for their storage, release and inactivation"

Ulf von Euler (1905 - 1983) and Julius Axelrod (1912 - 2004) won the Noble Prize in 1970 for elucidating the role of noradrenaline (norepinephrine) in transmitting nerve impulses. Axelrad and von Euler shared the prize with Sir Bernard Katz who worked on the role of acetylcholine.

Here's the Press Release.

THEME:
Nobel Laureates
Professor Ulf von Euler has discovered that the substance noradrenaline serves as neurotransmitter at the nerve terminals of the sympathetic nervous system. He has also shown how this substance is stored in small nerve granules within the nerve fibres of this system.

Dr. Julius Axelrod's discoveries concern the mechanisms which regulate the formation of this important transmitter in the nerve cells and the mechanisms which are involved in the inactivation of noradrenaline, partly under the influence of an enzyme discovered by himself.

von Euler's and Axelrod's discoveries have not only increased our knowledge about the transmission in the sympathetic nervous system, they also form the basis for the understanding of the transmission in the central nervous system and its pharmacology. Thus in a very significant way, the laureates have presented basic data about the physical and chemical mechanisms of the synaptic transmission and thus given us basic information about how the messages are mediated between nerve cells. Their discoveries concerning these regulatory mechanisms in the nervous system are fundamental in neurophysiology and neuropharmacology and have greatly stimulated the search for remedies against nervous and mental disturbances.


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.

Read More...

Tuesday, January 20, 2009

Gene Genie #42

 
The 42nd edition of Gene Genie has been posted at Genetic Future [Gene Genie #42 - focus on personalised genetics].

Welcome to the 42nd edition of Gene Genie, the blog carnival of clinical genetics and personalised medicine.

Most of the entries in this edition fall under the broad umbrella of personalised genetics, with posts emphasising both the pros and cons of the emerging consumer genetic testing industry.
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
  31. Adaptive Complexity
  32. Highlight Health
  33. Neurophilosophy
  34. ScienceRoll
  35. Microbiology Bytes
  36. Human Genetic Disordrs
  37. The Genetic Genealogist
  38. ScienceRoll
  39. Genetics & Health
  40. Human Genetics Disorders
  41. ScienceRoll
  42. Genetic Future


Read More...

Wealthy men give women more orgasms

 
A reader directed me to this article on The Sunday Times (UK) website: Wealthy men give women more orgasms.

Scientists have found that the pleasure women get from making love is directly linked to the size of their partner’s bank balance.

They found that the wealthier a man is, the more frequently his partner has orgasms.

“Women’s orgasm frequency increases with the income of their partner,” said Dr Thomas Pollet, the Newcastle University psychologist behind the research.

He believes the phenomenon is an “evolutionary adaptation” that is hard-wired into women, driving them to select men on the basis of their perceived quality.

The study is certain to prove controversial, suggesting that women are inherently programmed to be gold-diggers.

However, it fits into a wider body of research known as evolutionary psychology which suggests that both men and women are genetically predisposed to ruthlessly exploit each other to achieve the best chances of survival for their genes.
This explains why some women like being "trophy" wives.

I wonder if very rich women ever have orgasms?

The entire field of evolutionary psychology is becoming a farce. It's about as scientific as creationism. There must be some intelligent psychologists out there. Why aren't they speaking out?


Read More...

Monday, January 19, 2009

Darwin and Gradualism

 
From DaveScot on Uncommon Descent comes this remarkable example of stupidity: Darwin’s Big Mistake - Gradualism.

The big mistake in Origin that Darwinists won’t admit is gradualism. Darwin explained that according to his theory we should expect to observe a continuum of living species each with only the slightest of variations between them. He postulated that we don’t observe this because the fittest species take over and the insensibly slight variants die off leaving species that are fully characteristic of their kind which then makes possible taxonomic classification by those characters. It’s in the full title in the latter half “The Preservation of Favored Races”.

That left Darwin with explaining the fossil record which is indisputably a record of saltation.
Bzzzzz!!!! Wrong!

Thanks for playing, DaveScot. Unfortunately, there are no consolation prizes for IDiots.


Read More...

Princeton Professor denies global warming theory

 
This is embarrassing. I'm an alumnus of Princeton (GS '74) and it pains me to read this in The Daily Princetonian: Professor denies global warming theory.

Physics professor William Happer GS ’64 has some tough words for scientists who believe that carbon dioxide is causing global warming.

“This is George Orwell. This is the ‘Germans are the master race. The Jews are the scum of the earth.’ It’s that kind of propaganda,” Happer, the Cyrus Fogg Brackett Professor of Physics, said in an interview. “Carbon dioxide is not a pollutant. Every time you exhale, you exhale air that has 4 percent carbon dioxide. To say that that’s a pollutant just boggles my mind. What used to be science has turned into a cult.”

Happer served as director of the Office of Energy Research in the U.S. Department of Energy under President George H.W. Bush and was subsequently fired by Vice President Al Gore, reportedly for his refusal to support Gore’s views on climate change.
More proof, if it's needed, that Al Gore is smarter than George Bush (either one).
He asked last month to be added to a list of global warming dissenters in a Senate Environment and Public Works Committee report. The list includes more than 650 experts who challenge the belief that human activity is contributing to global warming

Though Happer has promulgated his skepticism in the past, he requested to be named a skeptic in light of the inauguration of President-elect Barack Obama, whose administration has, as Happer notes, “stated that carbon dioxide is a pollutant” and that humans are “poisoning the atmosphere.”
I've been watching the excitement build in Washington as the inauguration approaches. Who knew that one of the unintended consequences would be to flush out the kooks?1


1. For the record, I don't think it's helpful to call CO2 a "pollutant." That doesn't mean there isn't an optimal concentration; after all, there's also an optimal concentration of N2 (100% is too much) and O2 (more than 50% and fires become a really serious problem. I'd also like to go on record as one of those who think that human activity is an important part of global warming but it's probably not the only cause of the current trend.

Read More...

Liberals won't back tax cuts

 
The Harper government will present its budget next week. The NDP and the Bloc have announced that Stephen Harper has lost the confidence of the House and they will vote against the budget. The Liberal Party under Michael Ignatieff hasn't made up its mind about whether Harper can continue to govern even if all the other parties don't trust him. But the Liberals seem to be clear on one thing; according to today's Toronto Star, Liberals won't back tax cuts.

The Liberals are opposed to making tax cuts the centrepiece of the budget, and new leader Michael Ignatieff signalled yesterday the party is prepared to dump the Conservative minority if the budget is inadequate.

...

As they position themselves in advance of the budget, the Liberals argue that, while they generally favour income-tax cuts, it's the wrong approach during the recession.

"We don't want to see the Prime Minister come up with the kind of broad-based tax cuts that put Canada in a permanent, structural deficit once we recover from this (recession)," Liberal finance critic Scott Brison (Kings-Hants) told CTV yesterday as his party gathered in Ottawa for the caucus meeting.

Liberal MP John McCallum said such cuts are fiscally irresponsible at a time when the Tories have already put Ottawa's books in a deficit position and there's no way to ensure tax cuts benefit those who have lost their jobs or otherwise need help during the recession.

"There's a very good argument to be made that this is not the right time for across-the-board tax reductions," said McCallum, MP for Markham-Unionville and chair of a party advisory committee on the economy.
This could get interesting. I would support the Liberals if they vote against the budget because it contains significant tax cuts. Cutting taxes is typical conservative dogma so we may be headed for an election.


Read More...

Monday's Molecule #104

 
Name this molecule. We need a biochemically accurate name and the formal IUPAC name. The role of this molecule in biological systems was elucidated by one or more Nobel Laureate(s) in the second half of the 20th century.

Your task is to correctly identify the molecule and name the Nobel Laureate(s). The first one to do so 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 four ineligible candidates for this week's reward: John Bothwell of the Marine Biological Association of the UK in Plymouth, UK, Dima Klenchin of the University of Wisconsin, Bill Chaney of the University of Nebraska, and Maria Altshuler of the university of Toronto.

John, Dale, Bill, and a previous winner (Ms. Sandwalk) have offered to donate their free lunch to a deserving undergraduate so the next two undergraduates to win and collect a free lunch can also invite a friend. Since undergraduates from the Toronto region are doing so poorly in this contest, I'm going to make a special award this week. In addition to the normal winner, the first undergraduate student who can accept a free lunch will win a second prize. Please indicate in your email message whether you are an undergraduate and whether you came make it for your free lunch (with a friend).

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 Laureate(s) 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. I reserve the right to select multiple winners if several people get it right.

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


UPDATE: The molecule is norepinephrine (noradrenaline) [4-[(1R)-2-amino-1-hydroxy-ethyl]benzene-1,2-diol]. The Nobel Laureates are Ulf von Euler and Julius Axelrod.

The first person to get it correct was Ramon, address unknown. The first undergraduate who can collect a free lunch is Jason Oakley of the University of Toronto. Jason can bring a friend.


Read More...

Like this is going to happen

 
Normally A.C. Grayling makes a lot of sense and I enjoy reading his columns in New Scientist. Today's column is an exception: Universities should flag up which websites to trust.

Graying rightly points out that the internet is a mixed bag of mostly crap interspersed with the occasional website that makes sense at a level beyond kindergarten. His solution?

The lesson is that to make best use of the internet as an educational resource, its content has to be audited for reliability, and a system of classification introduced. Given that the internet is already the main resource for students, the need is urgent. I suggest that an international consortium of universities should set up panels to audit the worth of websites, endorsing those that are reliable. They should not censor, nor comment on matters of opinion - the price we pay for the internet's open democracy is the rubbish it contains. But they should authoritatively identify worthwhile sites, and warn of factual error when it occurs. Without such expert monitoring, the internet will increasingly be a problem rather than a boon, and limited in educational value.
Can you imagine a panel of Professors from different universities agreeing on which websites are reliable and accurate?

It might work for blogs. We all know which blogs to select, don't we?


Read More...

John Hawks doesn't like random genetic drift

 
The human MYBPC3 gene encodes a muscle protein. A 25 bp deletion in that gene is associated with a large increase the risk of cardiomyopathy ("heart muscle disease"). The most severe problems appear when carriers reach the age of 40.

According to a recent paper by Dhandapany et al. (2009), the overall frequency of the deletion allele is about 4% in India but it ranges from 0% to 7% in different parts of the country. The allele is not present in most other populations outside of India.

The authors conclude that the allele has reached this frequency by random genetic drift beginning with an initial mutation about 30,000 years ago. This increase has occurred in spite of the fact that the allele is deleterious and should decrease overall fitness.

John Hawks disagrees: Could genetic drift really break your heart?.

The issue is not really whether a gene could go from 1 copy to 4 percent in 1200 generations by chance. That wouldn't be so terribly unlikely in Pleistocene humans -- in fact, the mean time for a mutation to go from 1 copy to 4 percent by drift in a population of effective size 10,000 individuals is not 30,000 years, but only around 20,000 years. On the other hand, mtDNA variation today suggests that South Asia experienced early and rapid population growth -- so we're not likely talking about a population of 10,000, but more like a minimum of 100,000 effective individuals through the past 30,000 years at least. It would take genetic drift at least 10 times longer to accomplish the requisite frequency change given that demographic history. Still, a single allele at a single gene locus might be exceptional.

But that scenario, however unlikely, is simply not the situation we have here. Here we have a deletion that must have some disadvantage, because it gives people a fatal disease. This disadvantage is apparently dominant in effect, based on the case-control study. Yet the deletion has managed to persist within the large South Asian populations of the last 10,000 years so that today it is still around 4 percent.
John is an expert on evolution within human populations but he seems to be basing all of his calculations on the idea that the mutation arose in a population of 100,000 individuals and that this population was the effective population (e.g. they all freely interbred). I don't think this is very likely.

The fact that the allele frequency varies within India suggests that there are many subpopulations. Some of them might have been as small as 1000 individuals at vary time over the course of the last 30,000 years. As I'm sure John knows, the populations dynamics of human groups is extremely complex. We only have to think about the allele frequency differences in the Pennsylvania Amish communities or French Canadians to recognize this fact.

And let's not forget that the frequency of Huntington's disease is high around Lake Maracaibo in Venezuela. Over a period of 200 years a single individual with the Huntington's disease allele has left 18,000 descendants.

When we look at modern allele frequencies we don't only think about average rates of change due to random genetic drift in panmitic populations. We also have to consider the unusual events that occur from time to time. These include founder effects, natural disasters, etc. etc. The MYBPC3 is a lottery winner. You can't dismiss evolution by accident just because the probability of any one event is low.

This is why John says that, "Still, a single allele at a single gene locus might be exceptional." But John seems to think that in this case the result is not just "exceptional" but extraordinarily exceptional. He suggests that the deleterious effects of the allele are a recent phenomenon and that explains why it survived in early populations.
I would hypothesize that the disadvantages of the deletion have actually increased over time. The average lifespan increased into the Upper Paleolithic and probably later as well. Meanwhile, as the population grew, larger completed family sizes became more important to fitness. As people became more sedentary, the accumulation and inheritance of possessions and land became an important means of investing in children. The increasing importance of later survival and investment in children should have raised the fitness cost of chronic disease. That would explain a pattern of evolution in which this deletion increased in frequency early in its history, but later remained static or declined.

So, I don't suppose I can say people are crazy for thinking genetic drift could explain this deletion's current high frequency. But considering the powerful effect of weak selection over the many generations involved here, and the very large size of the South Asian population during most of that time, genetic drift seems pretty unlikely.
This makes sense to me. It's consistent with John's idea that the rate of human evolution has changed substantially over the past 30,000 years but I don't see why he objects so much to a random genetic drift explanation. Why does he suggest the the authors of the paper are crazy to suggest drift as an explanation?

It seems to me that his explanation is consistent with an increase in allele frequency due to random genetic drift just as the authors claim.


Dhandapany, P.S., Sadayappan, S., Xue, Y., Powell, G.T., Rani, D.S., Nallari, P., Rai, T.S., Khullar, M., Soares, P., Bahl, A., Tharkan, J.M., Vaideeswar, P., Rathinavel, A., Narasimhan, C., Ayapati, D.R., Ayub, Q., Mehdi, S.Q., Oppenheimer1, S., Richards, M.B., Price, A.L., Patterson, N., Reich, D., Singh, L., Tyler-Smith, C., and Thangaraj, K. (2009) A common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia. Nature Genetics, Published online: 18 January 2009 [doi:10.1038/ng.309]

Read More...

When TAs Go on Strike

 
York University is the "other" large university in Toronto. The university has been closed since November 5th when members of the Canadian Union of Public Employees Local 3903 (CUPE Local 3903) went on strike.

The situation is a bit complicated because the union has three different groups and there are separate contracts for each group, even though the contracts are all part of the same negotiation package. The three groups are:

Unit 1 if they have a teaching contract (note - teaching includes demonstrating, tutoring, and marking) and they are a full-time graduate student.

Unit 2 if they have a teaching contract and are not a full-time graduate student.

Unit 3 if they have a graduate assistantship or research assistantship and are a full-time graduate student.
What I'm mostly interested in is the graduate students in Units 1 & 3.

After several months of fruitless negotiations, the university exerted its legal right to call for a ratification vote when the union negotiators turned down the latest offer. The vote will take place later this week and, as you might have guessed, the CUPE 3903 leaders are urging their members to "Kill the Rat."

What is the role of a faculty union in situations like this? It's really not complicated. Sister unions will invariably support the right to collective bargaining and demand that both sides negotiate in good faith. Faculty unions tend to tilt in favor of the TA union simply out of solidarity but also because both groups often have common grievances against the administration.

Here's where things get messy. As reported in several newspapers, a group of 300 faculty members recently signed a letter urging CUPE 3903 members to ratify the latest offer by the university administration. Here's how it was reported in the National Post.
Another group urging the union to vote yes is nearly 300 faculty members who signed their names to a letter urging CUPE to accept the current contract proposal.

The signees of the letter are also members of the York University Faculty Association (YUFA).

YUFA president Arthur Hilliker said while he does not endorse the letter, he does not condemn it or believe it to be illegal either, according to Eric Lawee, a York humanities professor and one of the letter’s signees. YUFA maintains it wants a fair and equitable offer for CUPE.

“We, the undersigned retirees and full-time faculty members of York University, urge our colleagues in CUPE 3903 who have been on strike since November 6, 2008, to end their labour action by accepting the current contract offer of the York University administration,” the letter begins.

The letter addresses specific concerns if the strike were to drag on, including the potential loss of the summer term, which not only would hurt the school’s undergraduate students, but would affect CUPE as well, with possible job losses due to the elimination of the summer term.

“In their own interest and that of the entire university community, we urge CUPE members to end their labour action and help the university resume expeditiously the provision of its full academic programs,” the letter concludes.

Mr. Lawee said that there were two main reasons behind the letter. The first was due to “a strong sense that the strike has dragged on too long and that the rights and needs of students must now take priority over all else,” he said. “And ... that this should be an easy settlement to endorse because the offer is very fair.”
Why is this a problem? Well, for one thing, it's a problem because these 300 faculty members are going against the advice of their own union.

The York University Faculty Association (YUFA) issued a press release today in which they reiterated their position.
Press Release

These are our principles with respect to the CUPE 3903 forced ratification vote. They are motions passed unanimously at the YUFA Executive meeting of 12 January 2009:
  1. YUFA Executive re-affirms its support of free collective bargaining and does not endorse a ratification vote of CUPE 3903 members as forced by the Employer.

  2. YUFA Executive strongly urges all YUFA members to respect individual CUPE 3903 members’ rights in the forced ratification vote to vote freely and according to their conscience. We urge all YUFA members to respect CUPE members’ rights to vote freely.

  3. YUFA Executive, recognizing the power relations implicit in the roles of YUFA members and CUPE 3903 members, does not endorse any YUFA member attempting to influence how a CUPE 3903 member might vote in the forced ratification vote.
We recognize the serious problems the strike is causing for the students and for York. We also recognize that the issues of this strike need to be resolved for the future of York University.
The second and third points are very important. Faculty members are often the bosses of teaching assistants and they need to be very careful to remain neutral in situations like this. Because they are in a position of authority over graduate students they should not be urging these students to vote one way or the other. You can see why this is a problem. If Professors tell their graduate student to vote for ratification when the student wants to vote the other way, then this sets up a dangerous conflict for the student. What can be gained by doing that?

This is not a new problem. It's been around for decades and faculty unions in dozens of countries have learned to deal with it by urging individual members to avoid taking sides. I'm surprised that there are nearly 300 retired and active Professors at York University who don't get it.

Some of these faculty members have been writing letters to the editors of various newspapers in defense of their position. Here's one from Bernard Lightman, a Professor of Humanities. It appeared in today's Toronto Star.
Professor Berland has claimed that the open letter by full-time faculty and retirees to striking members of CUPE 3903 is in direct defiance of motions passed by the faculty union's executive. The signees have never claimed to speak on behalf of, or to represent, the faculty union.

Professor Berland interprets the motions of the faculty union's executive as saying that faculty are not free to express their opinions on the strike. I do not believe that that is the correct interpretation. However, if Professor Berland's interpretation were correct, then I would have to defy the faculty union.

It is not the business of a faculty union to gag its own members. One of the most important priorities of a university is to encourage free discussion and expression. That priority is not suspended during a strike, especially when the fate of more than 50,000 students hangs in the balance.
Let's be clear about one thing. YUFA was offering advice to its members based on decades of experience. The advice was to keep your mouth shut because you are in a position of authority over your graduate student TAs.

Every Professor has the right to ignore that advice and try to influence the decision of their graduate students. That's what academic freedom is all about. Whether it's a smart thing to do is another question.1 I don't think it is.

Graduate students are smart enough, and mature enough, to make up their own minds. They don't need advice from their supervisors and bosses.


1. It may be illegal as well, but that's another thing entirely. I doubt that any Professor would be prosecuted for pressuring their graduate students unless that Professor holds a prominent administrative position where the potential for retaliation against a student is much more likely.

Read More...

Saturday, January 17, 2009

Evolution News & Views

 
From time to time I mention the Disco site called Evolution News & Views. It has a lofty purpose that's prominently displayed on every posting.

The misreporting of the evolution issue is one key reason for this site. Unfortunately, much of the news coverage has been sloppy, inaccurate, and in some cases, overtly biased. Evolution News & Views presents analysis of that coverage, as well as original reporting that accurately delivers information about the current state of the debate over Darwinian evolution.
Here's a posting from Robert Crowther dated yesterday afternoon.
So, Darwinists are admitting that up until Friday, Jan. 16 2009 @ 4:10PM, evolution was “mostly theory.” Interesting. I am now certain that dogs adapt to their environment, too. Last night my dog kept barking and I shook my finger and spoke very firmly to her and made her sit on her bed. She stopped barking. So, at 7:10 pm I had a perfect example of evolution. Or was it adaptation? Or was it bad parenting? Whatever, we now see that dogs evolve, which previously had been believed to be “mostly theory.” My peers, who were there reviewing the moment, are skeptical because they think my dog is asexual. Regardless, this is all speculation — except for poor Kali. She still lacks an opposable thumb.
We may need a better word than IDiot to describe these people.

Is there an atheist bus campaign in Seattle? I'd like to donate.


Read More...

Canadian Atheist Bus Campaign

 

Donate to The Canadian Atheist Bus Campaign and get those atheists signs on Toronto buses and subways.

The campaign is sponsored by the Freethought Association of Canada. They've raised over $10,000 in just a few days.


Read More...

BioGPS

 
BioGPS is billed as a "Biology Gene Portal System." It's another database. You can read the review on genomeweb but you will have to register [GNF Team Rolls Out BioGPS Gene Portal for Users and Contributors].

The brains behind BioGPS is Andrew Su at the Genomics Institute of the Novartis Research Foundation (GNF) in San Diego (USA). According to the genomeweb article ...

As scientists move forward in analyzing experimental results, they generally consult up to a dozen "standard web sites" Su said, such as Entrez Gene, Ensembl, UniProt, or the Mouse Genome Informatics site. Each site delivers "partially overlapping gene annotation," so users must visit each, enter their search, learn the interface, and learn how to find each of the genes of interest on that site, he said. "Often that is a quite daunting process."

The idea behind BioGPS, Su said, is to avoid that process as well as reveal to researchers smaller and less-known gene portals that scientists might have missed.
Call me skeptical. The author of the article, Vivian Marx, contacted me and asked me to check out BioGPS. I have a long-standing interest in biological databases dating back to an early attempt to improve and update GenBank by adding annotation. That attempt was a failure—for very sound reasons [Errors in Sequence Databases].

I looked at my favorite genes on BioGPS. Here's the link to their homepage: BioGPS. The first thing you notice is that that database is restricted to rat, mouse, and human genes. The second thing you notice is that there's no value added. The data appears to be copied from other databases. This includes all of the errors, omissions, and misinterpretations found at each site. The emphasis is on expression data—that's what overwhelms the visible record of each gene.

Here's an example. This is the human HSPA1L gene. It happens to be a member of the HSP70 gene family. HSP70 proteins are the major chaperones of the cell. The HSP1AL version is specifically expressed in testes.


The expression data is correct but none of the databases mention that this gene is a developmentally regulated member of the HSP70 gene family even though that information has been in the literature for almost twenty years. You don't learn anything from visiting BioGPS that you wouldn't learn from visiting most other databases and, more importantly, you don't learn the information that might be most important to your research because it isn't in any of the databases. Anyone looking at this record would be puzzled by the lack of connection between the correct expression profile and all of the other information.

It gets worse. If you check out the rat HSPA1L gene you won't even learn that it is developmentally regulated because the expression profile doesn't include testes. The links to this genes suggest that it responds to stress, but it doesn't.

This is just one example of the problems with biological databases. Collecting together links from a variety of databases doesn't help. It just ensures that the errors from each database will be combined, creating maximum confusion.

I'm quoted correctly in the article ...
Larry Moran, a biochemist at the University of Toronto, told BioInform by e-mail that he had looked at a few of his "favorite genes" in the portal. "I don't think it's a very useful database," he said, since it is a summary of information gleaned from other databases with "no attempt at annotation."

In addition, he said, "much of the information is wrong or misleading," such as some of the expression profiles, which "seem to be incorrect; probably because the data is for another gene and not the one in the database record."

Users "who would rely on that sort of expression data would be making a very serious mistake," he said."

Reacting to these comments, Su said, "I think it is a good thing, in terms of making those errors more widely seen. The more eyes that see it, the more likely that that error will be fixed."

Being able to detect errors, however, has to be connected to the ability to fix it, he said. "This is the wiki principle, everybody can edit it, everybody can fix it, everybody has the responsibility and the power to make sure it's correct."
In an ideal world, researchers will fix errors in the databases and a Wiki-like system seems like a good idea. The experiment is already underway [A Gene Wiki]. But, as it turns out, this approach is incredibly naive as I discovered from attempts to fix GenBank a few decades ago. Nobody's going to do it. It's way too much work and there's no motivation to share information on public databases.

I received an email message from one of the authors of the expression data. As you might expect, the expression data profiles that are so prominently featured in the BioGPS database records are from the team at The Genomics Institute of the Novartis Research Foundation (e.g. Su et al., 2004). Much of it may be correct—it certainly succeeded with the HSP1Al gene—but I think it's wrong for HSPA1A.

My correspondent pointed out that his expression data has been widely used by hundreds of researchers and the papers have tons of citations.1 He described several studies that have made important discoveries based on the expression profiles that have been published. I don't doubt that this is true. That's not the point. The point is whether taking the expression data and adding links from other sources makes BioGPS a valuable resource.

Not as far as I can see.


1. The idea that just because a paper is widely quoted means that it must be correct is something that troubles me greatly. It seems to be part of the new way of doing science.

Su, A.I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K.A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., Cooke, M.P., Walker, J.R. and Hogenesch, J.B. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. (USA) 101:6062-6067. [PubMed]

Read More...

Apple Software Update

 
Every few weeks I have to sit patiently and watch while Apple updates my iTunes and QuickTime software.1 Since I use three different computers (home, work, laptop), this becomes quite a pain and it gives me plenty of time to think about Apple software and it's update policy. They are not happy thoughts.

Maybe someone can answer the questions? Why are the update files so big and why does it take so long to install them? It seems as though I am reinstalling the entire suite of programs each time. Why are there so many updates? Is the software so bad that it needs constant fixing?

Is there any way to turn off the notices? I don't use iTunes but I don't want to uninstall it. Can't I just update it when I want to use it? Same for QuickTime; how important. really, are the updates? Does anyone know?


1. To be honest, I can do other things as long as I don't mind a very slow internet connection. The updates are huge and the installation takes up a lot of RAM.

Read More...

Friday, January 16, 2009

What Homeschooling Can Do for your Children

 
Normally I don't make fun of spelling mistakes because I make lots of them myself and I don't think they're funny. However, from time to time the irony is just too delicious.

Leonard has a blog called Stand Your Ground. Who's Leonard, you might ask? Here's the answer ...

A Socially Conservative Don Quixote from Moncton. Strongly pro-life. Strongly pro-family. Strongly opposed to any attempts to turn my nation into something shapeless, cultureless, childless, gender-neutral and politically correct.
Here's the heading from Leonard's post on homeschooling [Homeschooling Is On The Raise].

More and more parents prefer to take control over their children's education, rather than trusting them to a public school system. ....

Sounds much better than a system which has become more about indoctrination (or at the very least - about merely keeping the kids busy from 9 to 3) than about education, doesn't it? Back in 1999, the CBC aired a short report on homeschooling in the National. I don't recall the exact number they mentioned, but there were between 20,000 and 25,000 homeschooled children in Canada back then. Since then we had the courts ruling that excluding books about homosexual cohabition from elementary school libraries is "discriminatory"; that a perverse graduate should be allowed to bring his partner in perversity to the high-school prom - even if it's a Catholic school.

Since then we had the BC government allowing militant homosexuals to monitor all the school curriculum to ensure it's "gay friendly". We had Quebec government introducing a mandatory "Chinese buffet" course in "world religions" which is nothing but a virtual indoctrination into social and moral relativism. How many parents have since resorted to homeschooling as the only way to save the children from becoming guinea-pigs in lefty's social experiments? I dare to assume it's in the 6 digits now.



Read More...

Mississippi Act

 
Here's how separation of church and state works in America. There's a bill before the legislature in Mississippi that requires the following disclaimer in public school textbooks [House Bill 25].

The word 'theory' has many meanings, including: systematically organized knowledge; abstract reasoning; a speculative idea or plan; or a systematic statement of principles. Scientific theories are based on both observations of the natural world and assumptions about the natural world. They are always subject to change in view of new and confirmed observations.

This textbook discusses evolution, a controversial theory some scientists present as a scientific explanation for the origin of living things. No one was present when life first appeared on earth. Therefore, any statement about life's origins should be considered a theory.

Evolution refers to the unproven belief that random, undirected forces produced living things. There are many topics with unanswered questions about the origin of life which are not mentioned in your textbook, including: the sudden appearance of the major groups of animals in the fossil record (known as the Cambrian Explosion); the lack of new major groups of other living things appearing in the fossil record; the lack of transitional forms of major groups of plants and animals in the fossil record; and the complete and complex set of instructions for building a living body possessed by all living things.

Study hard and keep an open mind.
This is similar to the language in Cobb country Georgia. Their sticker was ruled unconstitutional in 2005 (Selman v. Cobb County School District).

It's bad enough that there are elected officials in Mississippi who oppose evolution but even worse is the fact that they propose legislation that is unconstitutional. Isn't that treason?

They don't see it that way. They don't really believe that the public schools should be free of religion and they'll keep fighting to put it back in the schools in spite of what any court might say. It's one thing to have something written down in a constitution and it's quite another to get people to live by it. This fight between science and superstition isn't going to be won in the courtroom. It requires changing hearts and minds.

For the time being, let's ignore the fact that the disclaimer contains lies and misrepresentations of science. The main issue is the idea that evolution suggests, "... that random, undirected forces produced living things." This is where science and religion conflict and people who believe in God are quite right to be fearful of what critical thinking and an open mind might do to the faith of their children.1


1. The disclaimer pretends to support open-mindedness but in fact it's the exact opposite. It's a form of censorship.

Read More...

Why Michael Ignatieff Is better than Stephen Harper

 
Here's Michael Ignatieff, leader of the Liberal Party of Canada, speaking to young liberals in a Vancouver pub. He may not have been my first choice as leader but he's a lot better than Stephen Harper.

This is a man who can get along with, and be respected by, Barack Obama.




[Hat Tip: Jennifer Smith]

Read More...

Thursday, January 15, 2009

Take a Stand Without Taking Sides

 
On Tuesday night I went to a meeting of Liberals in my riding and heard Michael Ignatieff speak.

It was a small gathering (250) so there was plenty of opportunity to get to know the new Liberal leader. Many of the questions were challenges to his statements about the Gaza conflict. Ignatieff is careful to blame Hamas and defend Israel and this did not sit well with many of the constituents in my riding who are from the Middle East and South Asia.

There has to be a way to stand up for principles without taking sides. Today's column by James Travers in the Toronto Star makes a good case [Don't take sides but do take a stand].

Canada, with its polyglot population and its military fighting fundamentalism in Afghanistan, is more interested in Middle East conflicts than it is able to influence them. At best it can exert pressure on all sides not to reduce future peace prospects by making the immediate situation worse.

What's possible is relatively straightforward. Canada should be as forceful in holding Israel accountable for its actions as Hamas. And when the shooting stops it should invigorate honest-broker efforts to address the inequities and injustices that inevitably spawn violence.

While no panacea for a conflict layered in complexity, it would at least reaffirm values and principles that in the past informed Canadian Middle East policy. Beyond Israel's security, they include its legitimate expectation to live without fear and the countervailing requirement that Palestinians be released from decades of bondage in their own land.

Not taking sides does not mean not taking a stand. Unequivocal support for Israelis and their safety does not require equivocation on Palestinian human rights and political freedom.

Canada can best serve Israelis and Palestinians by finding its voice when it's time to say "enough."
Sounds good to me.

Jennifer Smith of Runesmith's Canadain Content makes the same point in her letter to Ignatieff [Dear Mr. Ignatieff].


Read More...

What Is Science?

 
This video does an excellent job of explaining the difference between science and superstition. The world would be a much better place if everyone took the advice shown here.




Read More...

Arlo Guthrie: City of New Orleans

 
While poking around on YouTube I stumbled across this performance by Arlo Guthrie of one of the best songs ever. I just had to share it with the one or two other people who might agree with me. The song was written by Steve Goodman in 1970.




Read More...

Meat Loaf: Would you let your daughter listen to "Paradise by the dashboard light?"

 
I have a confession to make. I've been fan of Meat Loaf ever since Rocky Horror Picture Show.1

It was fun watching Meat Loaf on this FOX news clip—thanks to Greg Laden for posting it.


At six minutes and ten seconds into the video the moderator says that he doesn't want his daughter, when she become 14, listening to "Paradise by the dashboard light." Them's fighting words.

Would you let your daughter see this video and listen to the lyrics? If not, what are you afraid of? Do you think that 14 year old girls (and boys) don't know about sex?


Here's one of my favorites ("I Would Do Anything for Love"). I seem to recall that it was my daughter—when she wasn't much older than 14—who first started playing it on our car trips. Incidentally, Ms. Sandwalk isn't a big fan of Meat Loaf. She has a stack of 20 or 30 CDs that we play on our car trips and I don't think there's a single song by Meat Loaf. There are lots of songs by dudes I never heard of, like Tchaikovsky and The Rolling Stones.




1. I'm also a fan of Susan Sarandon

Read More...

Wednesday, January 14, 2009

Nobel Laureates: Sir Henry Hallett Dale and Otto Loewi

 

The Nobel Prize in Physiology or Medicine 1936.


"for their discoveries relating to chemical transmission of nerve impulses"


Sir Henry Hallett Dale (1875 - 1968) and Otto Loewi (1873 - 1961) won the Noble Prize in 1936 for discovering the role of chemicals, especially acetycholine, in transmitting nerve impulses.

Today we take it for granted that chemicals are involved at the synapses but in the beginning of the 20th century this wasn't obvious. The impact of this work is apparent from the Presentation Speech.
THEME:
Nobel Laureates
It was generally thought that impulses in the nerves act directly on the muscles or glands bringing about a change in their activity. But as early as 1904, Elliott presented a different interpretation. From the medulla of the adrenal glands, which, as embryonic development shows, is related with the sympathetic nervous system, a substance can be produced, i.e. adrenaline, the effect of which is remarkably similar to that produced by increased activity in the sympathetic system. Elliott therefore supposed that the impulses in the sympathetic nerves produced a release of adrenaline in the nerve endings which would then be the real vehicles of the stimulation effect. Ten years later, Dale published a comprehensive investigation of another substance, acetylcholine, for which he found a corresponding conformity with the effect of the parasympathetic stimulation. As, however, at that time acetylcholine had not been met with in the body, there was not sufficient basis for a discussion as to whether it normally transmitted impulses.


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.

[Photo Credits: Henry Hallett Dale: Jamd; Otto Loewi: ©Copyright Encyclopedia of Austria]

Read More...

Dr. Larry Moran Flunks Philosophy

 
It wouldn't be fair for me to ignore Michael Egnor's devastating put-down demonstrating my ignorance and bigotry [Dr. Larry Moran Flunks Philosophy].

I especially like being called a Darwinian fundamentalist.

The "discussion" is all about Mary's Room. Here's the synopsis from the Wikipedia site.

Mary is a brilliant scientist who is, for whatever reason, forced to investigate the world from a black and white room via a black and white television monitor. She specializes in the neurophysiology of vision and acquires, let us suppose, all the physical information there is to obtain about what goes on when we see ripe tomatoes, or the sky, and use terms like ‘red’, ‘blue’, and so on. She discovers, for example, just which wavelength combinations from the sky stimulate the retina, and exactly how this produces via the central nervous system the contraction of the vocal cords and expulsion of air from the lungs that results in the uttering of the sentence ‘The sky is blue’. [...] What will happen when Mary is released from her black and white room or is given a color television monitor? Will she learn anything or not?
The answer, by the way, is "yes." Mary will learn something when she actually experiences how photons of different wavelengths impinge upon her retina and are interpreted by her brain.

Isn't that profound?


Read More...

Falling into a pit

 
Falling into a pit may be a much better analogy for evolution than adaptive peaks and climbing Mt. Improbable. To find out why read Chris Nedin's blog Ediacaran [Climbing Pit Improbable].


Read More...

Atheist Buses in Genoa

 
"The bad news is that God does not exist. The good news is that you do not need him."

I wonder how long it will take until these signs show up on buses in the major cities of North America? Anyone want to takes bets on when we'll see an atheist bus sign in Vancouver, Toronto, Montreal, or Calgary?


[Hat Tip: Friendly Atheist]

Read More...

The taste of MSG

 
Discount Thoughts has posted a wonderful description of how we taste the glutamate in monosodium glutamate [How we taste umami]. The taste is called "umami" and it's distinct from the four standard tastes of sweet, sour, salty, and bitter.

The figure shows a glutamate molecule (yellow) bound to the umami receptor with inosine monophosphate (IMP) (green). You need both glutamate and IMP in order to get the umami taste.

Theme
A Sense of Smell
I know lots of people who can taste MSG but that's not the problem. There appear to be some other effects of this chemical that are much less pleasant.

The umami flavor is common in meats, cheese, seafood, and lots of other foods that are rich in protein. Vegetarians don't know what they're missing!


Read More...

Do you know what this is?

 
If you can't identify the organism in the photograph then read The Beautiful Angel of Death on Catalogue of Organisms.

Life is stranger than most of us realize.


Read More...

Tuesday, January 13, 2009

ScieneOnline '09: Things to do in Durham

 
ScienceOnline '09 is being held in the Research Triangle, North Carolina (USA) this weekend. For those of you who aren't familiar with the region, the "triangle" consist of Chapel Hill, Raleigh, and Durham. I've spent a lot of time there over the past 25 years but unfortunately I can't make it this weekend.

Chapel Hill is one of the best places in America for all kinds of reasons. Raleigh is a pretty decent city.

Abel Pharmboy has the unenviable task of promoting Durham. You can read his attempt at: General cool stuff to do in Durham, NC, during ScienceOnline'09.

He did about as good a job as someone from Durham could possibly do.


Read More...

2008 Weblog Awards

 
Voting for the best science blog will close tonight. Pharyngula is in the running and so is Bad Astronomy.

The current leader in the voting is a climate change denialist blog called Watt's Up with That?.

Do NOT, repeat DO NOT, rush over and vote for Pharyngula or Bad Astronomy, or any other real science blog. PZ is not asking you to do that. Many science bloggers (including me) want the anti-science blog to win in order to completely discredit the whole notion of online voting for best blog.

It's about time we put an end to this nonsense and letting an anti-science blog win for "Best Science Blog" is an excellent way to send a message.


Read More...

Paleobet and Cambrian Fossils

 
PZ has discovered palaeobet1 so, naturally, I had to post my initials as well.


Some of you may not recognize "laggania." It's Laggania cambria, one of several species related to Anomalocaris. Collectively they are known as Anomalocarids.

Here's a fossil of Laggania cambria from the Burgess Shale (right). It just so happens that I was looking at this very fossil on Saturday during our visit the the Royal Ontario Museum. The Burgess Shale fossils are stuck in a corner of the museum where they can easily be missed by people entering the dinosaur rooms. That's a shame since these are unique fossils and very few museums have such a wonderful collection of Cambrian fossils.

Most of you are probably more familiar with Anomalocaris canadensis, a much more fierce-looking cousin of L. cambria (see below). A comparision of the two species can be found on The Anomalocaris Homepage.

Anomalocaris and Laggania were among the species made famous by Stephen Jay Gould in his excellent book Wonderful Life. Gould pointed out that these species so not fit neatly into any of the existing phyla, although they have some of the characteristics of arthropods and onychophora (velvet worms).

Lumpers will now include them in Arthropoda and splitters assign them to a separate, extinct, phylum called Dinocaridida. What's clear is that there are no modern species that can trace their ancestry directly to the anomalocarids. They represent a body plan that has not survived and this lends support to Gould's idea that there were more fundamentally different kinds of animals in the past that we see today. As he put it on page 208 ...

The Burgess Shale includes a range of disparity in anatomical design never again equaled, and not matched today by all the creatures in the world's oceans. The history of multicellular life has been dominated by decimation of a large initial stock, quickly generated by the Cambrian explosion. The story of the last 500 million years has featured restriction following by proliferation within a few stereotyped designs, not general expansion of range and increase in complexity as our favored iconography, the cone of increasing diversity, implies. Moreover, the new iconography of rapid establishment and later decimation dominates all scales, and seems to have the generality of a fractal pattern.
Scientists have been chipping away at Gould's thesis over the years since the publication of Wonderful Life in 1989. Several problematic species have been reliably assigned to existing phyla and others have been tentatively squeezed into the standard animal phyla. The goal is to discredit the idea that life was more diverse (disparate) during the Cambrian and the conclusion that the evolution of animals is characterized by the extinction of major lines.

I think Gould's main point is still valid and I don't understand why so many people find it troubling. It may have something to do with people's perception of evolution as progress.


1. Fossil animals for each letter of the alphabet.

[Hat Tip: P (pteraspis) Z (zalambalestis) Myers]

Read More...

Monday, January 12, 2009

Trouble with Blogger Is Over

 
Blogger has finally fixed the problems with RSS feeds. As I mentioned earlier [Trouble with Blogger] this is a problem that the blogger team seem to have created back on December 19th. It was fixed on January 9th—21 days later.

The most obvious change is in the recent comments in the left sidebar. You can now actually see recent comments instead of comments from June 2007.

I suppose we shouldn't complain, after all Blogger is free and it's pretty good most of the time.

I'm sorry if I missed any of your comments during the outage. I was able to keep up with all comments on recent postings but if you commented on an old posting chances are I missed it.


Read More...

Drift vs. Selection

 
Daniel MacArthur of Genetic Future weighs in on the ongoing debate over the important of random genetic drift vs natural selection during human evolution [Genetic differences between human populations: more drift than selection?].

Daniel MacArthur seems to be a smart guy. Here's a teaser ....

I should emphasise that there's little doubt that at least some recent population-specific selection has occurred in humans (the signal around the lactase gene in Europeans is about as unambiguous as it gets) - but perhaps it has not been anywhere near as pervasive as some researchers (e.g. John Hawks) have argued.


Read More...

Monday's Molecule #103

 
Name this molecule. We need a biochemically accurate name and the formal IUPAC name. The role of this molecule in biological systems was discovered by one or more Nobel Laureate(s) almost one hundred years ago.

Your task is to correctly identify the molecule and name the Nobel Laureate(s). The first one to do so 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 three ineligible candidates for this week's reward: Timothy Evans of the University of Pennsylvania, John Bothwell of the Marine Biological Association of the UK in Plymouth, UK and Dima Klenchin of the University of Wisconsin.

John, Dale (twice), and a previous winner (Ms. Sandwalk) have offered to donate their free lunch to a deserving undergraduate so the next two undergraduates to win and collect a free lunch can also invite a friend. Since undergraduates from the Toronto region are doing so poorly in this contest, I'm going to make a special award this week. In addition to the normal winner, the first undergraduate student who can accept a free lunch will win a second prize. Please indicate in your email message whether you are an undergraduate and whether you came make it for your free lunch (with a friend).

Mmmmmm .... poutine. Good luck.

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 Laureate(s) 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. I reserve the right to select multiple winners if several people get it right.

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

UPDATE: The molecule is acetylcholine (2-acetoxy-N,N,N-trimethylethanaminium). The Nobel Laureates are Sir Henry Hallett Dale and Otto Loewi.

The winner is Bill Chaney of the University of Nebraska who was the first one to correctly identify the molecule and the Nobel Laureates. The undergraduate winner is Maria Altshuler of the University of Toronto. She can bring a friend to lunch.


Read More...

Postdoc Salaries: Foreigners vs Americans

 
Check out Biocurious for a discussion stimulated by Lou Dobbs on CNN. Watch the YouTube video.

A typical graduate student in our department gets $25,000 per year. A typical post-doc gets $40,000 per year (range 36-45) and a typical Assistant Professor is hired at about $80,000 per year (range 70-100, depending on the university).

What should a post-doc earn? Would salaries be higher if you couldn't hire any foreigners as post-docs?


Read More...

Sunday, January 11, 2009

Homeschooling and Creationism

 
Not all homeschoolers are Creationists but for strong Biblical literalists homeschooling does offer an easy way of "protecting" children from evil ideas in the real world. Such ideas may cause them to doubt their religion.

If you are a Young Earth Creationist there are some problems associated with the anti-science approach to education. If would be nice to have some helpful advice in case your children ever have to deal with the real world outside the home.

The current issue of Home School Enrichment magazine comes to the rescue. They have an article called Creation and You that's available for free download. (You have to give them an email address.)

The main part of the article extols the virtues of the Answers in Genesis Creation Museum; "600,000 visitors have gone through its doors into an amazing experience demonstrating the power, creativity, and love of the Creator God." I suppose this is a good thing if you're into brainwashing. We just spent yesterday with two young girls in the Royal Ontario Museum in Toronto and there was very little evidence of the "power, creativity, and love of a Creator God." On the other hand, there was quite a bit of good science. Our two friends might have got a bad impression of Biblical literalism. If their parents had been Young Earth Creationists we would have been in big trouble for leading them astray.

Anti-science homeschoolers are right to keep their children away from real museums.

But that's not the only problem they face. What to do if your kids want to have a career in Creation Science? Hmmm ... that's a tough one, isn't it? Here's the answer ....

Preparing for a Career in Creation Science

Answers in Genesis content developers Gary Vaterlaus and Roger Patterson agree that more researchers are needed in Creation Science, but warn that the path may not be easy. Several Christian colleges across the country offer science courses taught from a Young-Earth Creationist perspective, but few research positions are available to those with anything less than a Master’s degree in their field; more likely a Ph.D. And, Roger says, getting those degrees will likely require spending some time in a secular university.

Furthermore, Gary explains that the evolutionary teachings at these secular universities are only part of the problem—there is also a very real prejudice against Creationists who attempt to embark upon a career in any of the relevant branches of science. Aside from the strong possibility of a known-Creationist student receiving failing grades merely for believing God created the universe, Gary cited a case where evolutionists actually petitioned a university to revoke a graduate’s Ph.D. when it was discovered he was a Creationist.

There is a need for young, up-and-coming students to enter the realm of Creation Science, but Gary and Roger emphasize that a student must have an unshakable foundation on the reliability and truthfulness of the Bible, and then be ready, willing, and able to face unbelievably strong opposition while pursuing a degree that will qualify them for the research positions they wish to obtain.

While none of this should dissuade students from choosing such a career, it is important for students and their parents to recognize the potential difficulties and take steps early to ensure a successful and victorious outcome.

For students wishing to be involved in the area of Creation Evangelism, such as speaking at churches or writing about creation related topics, Roger believes a Bachelor’s degree in some branch of science is important for establishing credibility. Several Christian colleges offer science programs, taught from a Young-Earth Creationist perspective, in which students can earn their Bachelor’s degrees. However, many Christian colleges have compromised in the area of origins and evolution, so this is something that should be carefully investigated when researching options for collegebound Creationist students.
Life is tough if you are anti-science but want a career in science. Not only are the secular universities trying to persuade you that truth is important in science but even some of the Christian colleges are "compromised."

But you can succeed if you resist education and maintain "unshakable foundation on the reliability and truthfulness of the Bible." Incredible.

What about average students who venture out into the secular world? What happens if they happen to pick up a book written by a (gasp!) real scientist, or if they mistakenly enter a real museum?

Roger Patterson of Answers in Genesis has some advice.
Homeschool parents often wonder how to protect their children from evolutionary ideas. We brought this up to Roger Patterson, a former biology teacher in a public school who is now one of the main content-developers at Answers in Genesis, and were impressed by his answer:

“As a ministry in general,” Roger explains, “we don’t say, ‘keep your kids isolated from evolutionary ideas.’We think that’s kind of a bad philosophy because when they do go out on their own, they’re going to face those things every day. Case in point: [my wife and I recently] got this space-age ant colony gel material. Flip open the book, and you’re reading through the instructions and all these fun facts about ants, [then] ‘Fossil ants have been found a hundred million years old.’ What we would hope parents can do through homeschooling is teach their kids how to spot those things, and then what the biblical response is for those things. Not to isolate them from those things, but to insulate them to some degree and then help them understand what the problems are there.

“Okay, this is a fun ant gel colony, [but] they didn’t need to throw that little tidbit [about millions of years] in there; it adds nothing to the product or your ability to enjoy and watch the ants. And when you look at it from the perspective that God created these creatures to do what they do, and it’s an amazing thing, it even gives an opportunity to give praise to God when you run across the idea of evolution. [We can say] ‘We know that’s not true. Praise God He did create us, that He is the one who’s sustaining all this.’ Rather than running away and hiding from all those things, let’s face up to it. And then if you’re with your friend, you can tell them about it if they don’t understand those things.

“So my encouragement is not to be afraid of going and getting the dinosaur book from the library, but [be sure to] teach your children as they go through it to understand that some parts [evolutionary statements] are made up, based on the idea of rejecting God in science, and other parts are facts—such as when it tells us what shape the egg was, what size it was, what food they probably ate. Those types of things, we can trust those; those are solid scientific ideas. It’s when we start adding our own assumptions into those things, and telling stories, that we run into trouble.”

Roger explains that there are certain “code words” that parents can teach their children to watch out for. Among these would be “millions or billions of years,” statements about kinds of animals changing into other kinds of animals, and questionable statements of what scientists “know.” Above all, Roger says, it’s important to make sure our children have a solid biblical foundation for
their education, and to help them stand firm on the full authority of scripture.
I can't imagine what it must be like to be constantly on the lookout for sneaky remarks about evolution and other scientific facts that challenge your religion. I can't imagine what it must be like to brainwash your kids into responding with, "We know that’s not true. Praise God He did create us, that He is the one who’s sustaining all this."

I not a huge fan of the idea that teaching your children to be Young Earth Creationists is a form of child abuse but there are times, like today, when Dennet and Dawkins seem to have a strong case.

Home schooling isn't always a good thing for children.


Read More...

Friday, January 09, 2009

A Shocking Discovery

 
Almost all proteins in Escherichia coli begin with the amino acid N-formylmethionine (f-met), a modified version of methionine.

N-formylmethionine is inserted at AUG codons at the beginning of the open reading frame in mRNA. The initiation mechanism requires a specific initiator tRNA called f-Met-tRNA (right).

Internal AUG codons are recognized by another tRNA and normal methionine is inserted at these positions. The observation that a single codon (AUG) can serve as the codeword for two different amino acids depending on their position was made over thirty-five years ago and it has been incorporated into the textbooks for decades.

You can imagine how surprised I was to read this in a press release written by Haley Stephenson of ScienceNOW Daily News. You can read it yourself on the Science website: Genetic Code Sees Double.

Call it the genetic version of a double-entendre. Scientific dogma dictates that various three-letter combinations of our genetic sequence each "mean" exactly one thing--each codes for a particular amino acid, the building block of proteins. But a protozoan named Euplotes crassus appears to be more versatile: One of its three-letter combinations has two meanings, coding for two different amino acids. Although the find may seem trivial, it poses a major challenge to more than 4 decades of scientific thinking.
The idea that a protozoan might use UGA to encode both cysteine and a modified form of serine called selenocysteine is quite interesting. It has long been known that UGA is a normal stop codon that is also used to encode selenocysteine. It has also been known for a long time that some organisms can use UGA to encode cysteine.

But the idea that scientific dogma has been overturned by the discovery of a single codon that can encode two different amino acids is just plain silly. It doesn't pose a "major challenge to more than 4 decades of scientific thinking" unless your scientific thinking is flawed to begin with.

This must be an example of hyperbole. Such a claim would never make it into a scientific publication, especially in a prestigious journal like Science. Or so I thought.

Here's the opening sentence in the paper by Turanov et al. (2009).
Although codons can be recoded to specify other amino acids or to have ambiguous meanings (1, 2), and stop codons can be suppressed to insert amino acids (3), insertion of different amino acids into separate positions within nascent polypeptides by the same codeword is believed to be inconsistent with ribosome-based protein synthesis.
It's enough to make me give up writing biochemistry textbooks. Apparently nobody reads them.

We seem to be producing a generation of scientists who don't know about the fundamentals of biochemistry and molecular biology that were elucidated in bacteria and bacteriophage in the mid-20th century. Doesn't anyone teach this stuff any more?


Turanov, A.A., Lobanov, A.V., Fomenko, D.E., Morrison, H.G., Sogin, M.L., Klobutcher, L.A., Hatfield, D.L., and Gladyshev. V.N. (2009) Genetic Code Supports Targeted Insertion of Two Amino Acids by One Codon. Science 323:259-261. [DOI: 10.1126/science.1164748]

Read More...

John Pieret Issues a Challenge

 
John Pieret took the American Civil Liberties Literacy Quiz.

In his posting, Flunking At Being American, he reports that he scored 32/33 or 96.97%. Impressive.

He then asks, "I would be interested to know how non-US citizens score on the test."

Ask, and you shall receive. Here's my result.

You answered 30 out of 33 correctly — 90.91 %

Average score for this quiz during January: 74.2%
Average score: 74.2%

You can take the quiz as often as you like, however, your score will only count once toward the monthly average.
I didn't know which amendment was which, and what the Bill of Rights specifically prohibited. I'm too embarrassed to reveal the third question I got wrong.

Here's one I got right.
27) Free markets typically secure more economic prosperity than government’s centralized planning because:

A. the price system utilizes more local knowledge of means and ends
B. markets rely upon coercion, whereas government relies upon voluntary compliance with the law
C. more tax revenue can be generated from free enterprise
D. property rights and contracts are best enforced by the market system
E. government planners are too cautious in spending taxpayers’ money
I got it right by thinking like an American! (Ouch!)     ;-)

It's a very strange "civil liberties literacy" question. Is it un-American to advocate socialist policies?



Read More...

What Could Be More Scary than the Flying Spaghetti Monster?

 
From the BBC News: Church removes 'scary crucifix'.

A large sculpture of Christ on the cross has been removed from outside a church in West Sussex after its vicar said it was "scaring young children".

The Reverend Ewen Souter said the 10ft crucifix was "a horrifying depiction of pain and suffering" which was also "putting people off".

The sculpture, located at the side of St John's Church in Broadbridge Heath, has now been given to Horsham Museum.

It will be replaced with a new stainless steel cross.
Stainless steel crosses are also pretty scary.


[Hat Tip: RichardDawkins.net]

Read More...

Africans Need Jesus?

 
From RichardDawkins.net: Matthew Parris: As an atheist, I truly believe Africa needs God.

Now a confirmed atheist, I've become convinced of the enormous contribution that Christian evangelism makes in Africa: sharply distinct from the work of secular NGOs, government projects and international aid efforts. These alone will not do. Education and training alone will not do. In Africa Christianity changes people's hearts. It brings a spiritual transformation. The rebirth is real. The change is good.
Read the comments. Some people aren't convinced that Christianity is the only way to change people's hearts for the better. Some people think it might be a wee bit condescending to imply that rationalism might be fine among Caucasians but Africans need superstition.


Read More...

Changing Your Mind About Evolutionary Psychology

 
Every year John Brockman collects essay from his friends (I want to be one) and published them on his website and in a little book [The Edge Annual Question - 2009].

This year's question was, "What game-changing scientific ideas and developments do you expect to live to see?" Last year's question was, "What Have You Changed Your Mind About? Why?" The book is now out.

There are far too many answers to these questions. I usually look at a few of them but it soon becomes boring.

Sharon Begley feels the same way but she has picked out a few interesting mind changes from the 2008 question. She writes in the Jan. 3, 2009 issue of Newsweek [On Second Thought ...].

The most fascinating backpedaling is by scientists who have long pushed evolutionary psychology. This field holds that we all carry genes that led to reproductive success in the Stone Age, and that as a result men are genetically driven to be promiscuous and women to be coy, that men have a biological disposition to rape and to kill mates who cheat on them, and that every human behavior is "adaptive"—that is, helpful to reproduction. But as Harvard biologist Marc Hauser now concedes, evidence is "sorely missing" that language, morals and many other human behaviors exist because they help us mate and reproduce. And Steven Pinker, one of evo-psych's most prominent popularizers, now admits that many human genes are changing more quickly than anyone imagined. If genes that affect brain function and therefore behavior are also evolving quickly, then we do not have the Stone Age brains that evo-psych supposes, and the field "may have to reconsider the simplifying assumption that biological evolution was pretty much over" 50,000 years ago, Pinker says. How has the view that reproduction is all, and that humans are just cavemen with better haircuts, hung on so long? "Even in science," says neuroscientist Roger Bingham of the University of California, San Diego, "a seductive story will sometimes … outpace the data." And withstand it, too.
There are many reasons for changing your mind about the validity of evolutionary psychology but the idea that "human genes are changing more quickly than anyone imagined" isn't one of them.

As you might have guessed, John Hawks is really happy to encourage that kind of thinking. Hawks is a proponent of the idea that genes can be fixed in the entire human population by natural selection in only a few thousand years [Recent evolution in Newsweek].


Read More...

An Unnecessary War?

 
Read what Jimmy Carter has to say about the current situation in Gaza [An Unnecessary War].

I wish Canadian politicians would be as rational as Carter and appreciate that this is a complex situation where nobody is totally right.

The one thing we can be sure about is that war is wrong.1


1. Firing rockets at your neighbors is war.

[Hat Tip: Runesmith's Canadian Content]

Read More...

Thursday, January 08, 2009

Testing Natural Selection: Part 2

 
There are several interesting articles about evolution in the Januray 2009 issue of Scientific American. One of the most interesting is an article by H. Allen Orr of the University of Rochester (NY, USA). The magazine title is "Testing Natural Selection"1 and, as the title implies, the focus is on evolution by natural selection.

Orr's article gives us an opportunity to compare and contrast the views of an adaptationist (Orr) and a pluralistic approach to evolution.

In Testing Natural Selection: Part 1 we discussed two of Orr's opinions: (1) random genetic drift is not as common as most people think, and (2) most (if not all) visible phenotypic change is driven by natural selection.

Here, we discuss Orr's ideas about speciation.

When we say "speciation" we're talking about the biological species concept. Speciation occurs when two formerly compatible populations evolve to the point at which they can no longer interbreed. The key question is what causes this reproductive isolation and how does it evolve?

To contemporary biologists, then, the question of whether natural selection drives the origin of species reduces to the question of whether natural selection drives the origin of reproductive isolation.

For much of the 20th century, many evolutionists thought the answer was no. Instead they believed that genetic drift was the critical factor in speciation. One of the most intriguing findings from recent research on the origin of species is that the genetic drift hypothesis about the origin of species is probably wrong. Rather natural selection plays a major role in speciation.
Orr is correct to point out that random genetic drift is important in speciation. It's the mechanism described in many evolutionary biology textbooks, though it's not the mechanism that most people think about when they think about speciation.

Many biologists have always believed that natural selection plays a much more important role in speciation than random genetic drift. They aren't happy with the textbook description. Orr is one of these biologists. He now claims that the drift explanation is "probably wrong."

Let's think about what has to happen when two species become reproductively isolated. We'll use allopatric speciation as an example.2

We begin with a situation where two populations (races, subspecies) are geographically separated. There is very little gene flow between them so they evolve independently of each other. Over time, they may come to be different because each is adapting to different environments or they may just drift apart by accident. With respect to the actual speciation event, these differences don't matter.

From time to time, individuals from the two subspecies will interbreed to produce fertile offspring. This is responsible for limited gene flow between the subspecies and it proves that speciation has not occurred. If the barrier between the two populations breaks down they will merge back into a single population.

But if the two species have been separated for a long period of time, mutations that prevent interbreeding will accumulate and hybrids will become less and less viable until eventually no fertile hybrids are produced and speciation is complete. There are many ways that this can happen but a common hypothesis involves the build-up of post-zygotic genetic incompatibilities called Dobzhansky-Muller (D-M) incompatibilities.

How are D-M incompatibilites fixed in the population? If they interfere with the matings of individuals from the two populations then how come they don't contribute to infertility when individuals from the same population mate with each other? When the mutation first arises it seems to have a very strange property. It doesn't affect matings between an individual carrying the D-M allele and an individual not carrying that allele from the same population but it does affect matings between the individual carrying the new D-M allele and and an individual from the other population.

In order for this to happen there must already be some genetic differences between the two populations in terms of mating and reproduction. Those differences have accumulated in each of the populations but they must not have an effect on hybrid crosses. Presumably, the new D-M allele is not harmful in one genetic background but it is in the other.

Are these pre-existing potentiators neutral within a population, in which case they become fixed by random genetic drift? Or, are they beneficial in one of the populations, and not in the other, in which case they are fixed by natural selection? The general consensus has been that they are neutral within a population and they accumulate by accident. When enough of them become fixed the cumulative effect is to prevent hybridization. The last allele to arise, the D-M incompatibility allele, is the straw that breaks the camel's back.

Orr believes that the alleles are beneficial in one of the populations. Thus, according to him, reproductive isolation is driven by natural selection. He gives two examples.

The first one is the incomplete speciation in monkeyflower subspecies. I described this in an earlier posting [Speciation in Monkeyflowers], where I pointed out that the role of natural selection was not clear. The differences in flower color and pollinators could have arisen by selection if one postulates changes in the bee population but they could also be due to chance.

For an adaptationist like Allen Orr there's no doubt about what happened.
A good example is the evolutionary history of the two monkeyflower species mentioned earlier. Because their pollinators seldom visit the “wrong” species of monkeyflower, the two species are almost completely isolated reproductively. Even though both species sometimes occur in the same locations in North America, a bumblebee that visits M. lewisii almost never visits M. cardinalis, and a hummingbird that visits M. cardinalis almost never visits M. lewisii. Thus, pollen is rarely transferred between the two species. In fact, Schemske and his colleagues showed that pollinator differences alone account for 98 percent of the total blockage in gene flow between the two species. In this case, then, there can be no doubt that natural selection shaped the plants’ adaptations to distinct pollinators and gave rise to strong reproductive isolation.
This is not a good example of speciation by natural selection. We simply don't know if the flower color mutation spread in one of the populations because it conferred a selective advantage on individuals within that population.

Besides, these two "species" will still form viable hybrids so they're not really species in the first place.

The other example of presumed speciation by natural selection comes from studies on Drosophila There are several example of D-M incompatibility alleles that have been identified. In some of them, there is evidence at the sequence level for rapid fixation. If correct, this is a good indication that the alleles have become fixed by natural selection. The resulting reproductive isolation is an epiphenomenon.3

One example is OdsH in Drosophila mauritiana. It appears to result in an increase in sperm production so it may have been selected in the early population of this species, before it became a species. Presumably, the allele was beneficial in the genetic background that had evolved up to that point and presumably it was detrimental in the genetic background of whatever subspecies it was related to.

The genetic background is obviously part of the speciation event. I suppose that if even one of the D-M alleles is selected then it's fair to say that speciation by natural selection took place.

The question is whether this is common or not. Shucker et al. (2005) looked at post-zygotic reproduction isolation in two populations of grasshopper and provided evidence that all the D-M incompatibilities could be adequately explained by random genetic drift. We'll need to have many more examples in order to decide whether natural selection explains most speciation events.

Personally, I find it easier to understand how reproductive isolation could arise by accidental accumulation of many neutral alleles that eventually lead to reproductive isolation. It's harder to envisage alleles that confer a selective advantage within one population but are extremely detrimental in the other.

Orr doesn't agree.
The studies of the monkeyflower and of hybrid sterility in fruit flies only begin to scratch the surface of a large and growing literature that reveals the hand of natural selection in speciation. Indeed, most biologists now agree that natural selection is the key evolutionary force that drives not only evolutionary change within species but also the origin of new species. Although some laypeople continue to question the cogency or adequacy of natural selection, its status among evolutionary biologists in the past few decades has, perhaps ironically, only grown more secure.
I'm not an expert on speciation and I don't hang out with people who work in the field. However, my general impression from reading the scientific literature is that Orr's statements may be somewhat exaggerated. From what I can see, there are a great many evolutionary biologists who question the hegemony of natural selection. Their numbers seem to be growing, not shrinking.

I don't know where Orr is coming from when he implies that laypeople question the adequacy of natural selection. In my experience laypeople only think about natural selection. They have no idea that there are any other mechanisms of evolution.


1. The website title is "Testing Natural Selection with Genetics."

2. In allopatric speciation the two diverging populations are geographically separated. That's what makes them distinct populations. In sympatric speciation the two populations may exist in the same geographical and restricted gene flow between them is due to other factors. It's easier to visualize what's happening during allopatric speciation but the logic can apply to sympatric speciation as well.

3. I don't think Orr is actually proposing that there would be selection for reproductive isolation. How would that work?

Shuker, D.M., Underwood, K., King, T.M., and Butlin, R.K. (2005) Patterns of male sterility in a grasshopper hybrid zone imply accumulation of hybrid incompatibilities without selection. Proc. Roy. Soc. B 272:2491-2497. [DOI: 10.1098/rspb.2005.3242]

Read More...

Buy a Dinosaur

 
Today's the day you can buy a dinosaur fossil. Maynards, in Vancouver, is auctioning off the complete collection of dinosaur fossils from the Seibu Museum in Tokyo, Japan [Auction Details: Dinosaurs].

The collection includes ...

* Eusthenopteron foordi
* Bothriolepis
* Aspidorhynchus
* Araripichthys castilhoi
* Crinoids
* Tyrannosaurus rex
* Ankylosaur
* Dinosaur eggs
* Stegosaurus
* Edmontosaurus annectens
* Triceratops
* Whiteia
* Platecarpus
* Araucarites mirabilis
* Alethopteris

* ...and More

Haven't you always wanted a Stegosaurus in your living room? I think I'll bid on the T. rex. It would look great in my office. Do you think my students might be intimidated?


Read More...

Wednesday, January 07, 2009

Nobel Laureate: Elias Corey

 

The Nobel Prize in Chemistry 1990.

"for his development of the theory and methodology of organic synthesis"



Elias James Corey (1928 - ) was awarded the Nobel Prize for his contributions to the synthesis of organic molecules. Here's the Press Release describing his achievements.

Prize for masterly development of organic synthesis

The development of the art of organic synthesis during little over a hundred years has afforded efficient methods of manufacturing products such as plastics and other artificial fibres, paints and dyes, biocides and pharmaceutical products, all of which have contributed to the high standards of living and health, and the longevity, enjoyed at least in the Western world.

This year's Nobel Prize in Chemistry has been awarded to Professor Elias J. Corey, USA, for his important contributions to synthetic organic chemistry. He has developed theories and methods that have made it possible to produce a large variety of biologically highly active, complicated natural products, thereby making, among other things, certain pharmaceuticals commercially available. Corey's work has also led to new general methods of producing, synthesising, compounds in simpler ways.

The background to Elias J. Corey's successes lies in the fact that he has in a strictly logical way developed the principles of what is termed retrosynthetic analysis. This involves starting from the planned structure of the molecule one wishes to produce, the target molecule, and analysing what bonds must be broken, thus simplifying the structure step by step. One then finds that certain fragments are already known and their structure and synthesis already described. After working backwards in this way from the complex to the already known, it is possible to start building, synthesising, the molecule. This method has proved very amenable to data processing, which has entailed rapid developments in synthesis planning. Combining this synthesis planning with singular creativity, Corey has developed new methods of synthesis. He has produced some hundred important natural products, for example the active substance in an extract from the ginkgo tree, used in folk medicine in China.

Background information

Organic synthesis, that is, the production of complicated organic compounds using simple and cheap starting material, is one of the prerequisites of our civilisation. It is understandable that contributions in this field have often been rewarded with the Nobel Prize in Chemistry. Thus in 1902, only the second year that Nobel Prizes were awarded, the Chemistry Prize went to Emil Fischer for his work on synthesis within sugar and purine chemistry. In 1905 Adolf von Baeyer received the prize in recognition of contributions to the development of the chemical industry through his work on organic dyestuffs. Otto Wallach received the 1910 Prize for contributions to the development of the chemical industry. The 1912 prize went to Victor Grignard for his development of organic magnesium compounds, also termed Grignard reagents, into important intermediates in organic synthesis. In 1950 Otto Diels and Kurt Alder shared the Nobel Prize for discovering the preparatively very useful diene synthesis. Robert B. Woodward received the 1965 prize for his brilliant contributions to the development of the art of organic synthesis. In 1979 Herbert C. Brown and Georg Wittig were rewarded for developing boron compounds and phosphorus compounds, respectively, into important reagents in organic synthesis.

The synthesis of complicated organic compounds often shows elements of artistic creation, as for example architecture. Many earlier syntheses were performed more or less intuitively, so that their planning was difficult to perceive. Asking a chemist how he came upon precisely the starting materials and reactions that so elegantly led to the desired result would probably be as meaningless as asking Picasso why he painted as he did. The process of synthetic planning has been likened to a game of three-dimensional chess using 40 pieces on each side. But the problem may be even harder than this. Over 35,000 usable methods of synthesis are described in chemical literature, each with its possibilities and its limitations. During the synthesis, moreover, new methods appear which can modify the strategy.

Beginning in the 1960's, Corey coined the term, and developed the concept of, retrosynthetic analysis. Starting from the structure of the molecule he was to produce, the target molecule, he established rules for how it should be dissected into smaller parts, and what strategic bonds should be broken. In this way, less complicated building blocks were obtained, which could later be assembled in the process of synthesis. These building blocks were then analysed in the same way until simple compounds had been reached, whose synthesis was already described in the literature, or which are commercially available. Corey showed that strictly logical retrosynthetic analysis was amenable to computer programming. At present, synthesis planning with the help of computers is developing rapidly.

Through his brilliant analysis of the theory of organic synthesis, Corey has contributed in high degree to his own and other researchers' being able, during the last few decades, to complete total syntheses, hitherto impossible, of complicated, naturally-occurring, biologically active compounds, according to simple logical principles.


Elias J. Corey has himself synthesised about a hundred important natural products, of which only a few will be mentioned here. In 1978 he produced gibberellic acid (1), which belongs to a class of very important plant hormones of complicated structure. Recently, he has also synthesised (+)-ginkgolid (2), which owing to its complicated structure is a formidable challenge to anyone working in synthetic chemistry. (+)-ginkgolid is the active substance in an extract from the ginkgo tree, used as a folk medicine in China. The sales value of this natural product is believed to amount to $500 million annually. It is used in treatment of blood circulation disturbances in the elderly, and in asthma. Corey's most important total syntheses concern the medically very important eicosanoids such as prostaglandins, prostacyclins, thromboxanes and leucotrienes, which occur naturally in extremely small quantities. These frequently very unstable compounds answer for multifarious and vital regulatory functions of significance for reproduction, blood coagulation, normal and pathological processes in the immune system, etc. Their importance is witnessed by the award of the 1982 Nobel Prize in Physiology or Medicine to Sune Bergstrom, Bengt Samuelsson and Sir John Vane for the discovery of prostaglandins and closely related biologically active substances. Corey has with enormous skill carried out structural determination and total syntheses of a large number of compounds of many different types of eicosanoids such as prostaglandins and leucotrienes such as lipoxin A (3). It is thanks to Corey's contributions that many of these important pharmaceuticals are commercially available.

To perform the total syntheses successfully, Corey was also obliged to develop some fifty entirely new or considerably improved synthesis reactions or reagents. It is probable that no other chemist has developed such a comprehensive and varied assortment of methods which, often showing the simplicity of genius, have become commonplace in the synthesising laboratory. His systematic use of different types of organometallic reagent has revolutionised recent techniques of synthesis in many respects. He has also in recent years introduced a number of very effective enzyme-like catalysts. These chiral catalysts give only one mirror isomer of the target product, in certain types of synthetically important reaction. The chiral catalysts are simple and easy to recover, and can in some cases be used in their own production.


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.

[Photo Credit: NIH.]

Read More...

A Primer on Skepticism

 
What more could you ask for than A Primer on Skepticism from Mike's Weekly Skeptic Rant? Here are some quotations from that posting to tempt you into reading the whole thing ....

If anyone can show me, and prove to me, that I am wrong in thought or deed, I will gladly change. I seek the truth, which never yet hurt anybody. It is only persistence in self-delusion and ignorance which does harm.
                                                Marcus Aurelius

The invisible and the non-existent look very much alike.
                                                Delos B. McKown

The statistics on sanity are that one out of every four Americans are suffering from some form of mental illness. Think of your three best friends. If they're ok, then it's you.
                                                Rita Mae Brown


Read More...

Democracy and Lawyers

 
In Canada we vote by marking a "X" on the ballot and putting it in a box. The person with the most "X's" wins.

If the vote is close, we count the ballots again and declare a winner.

It doesn't work that way in America as we learned in 2000. It took several truckloads of lawyers and many judges to count the ballots in Florida. Ultimately it was the US Supreme Court who decided that George Bush would be President.

Now they're doing it again, only this time it's a Senate race in Minnesota [Funny Business in Minnesota]. The lawyers and the judges will decide who actually won. Meanwhile, politicians in Washington will fight over which candidate they will put into the Senate while the court cases are being decided. Apparently the Senate doesn't have to accept the recount as long as the loser is unhappy.

This must be why they call America "the greatest democracy on Earth." It's because America has so many lawyers.


Read More...

Probably?

 
In Britain there are 800 buses with the sign, "There’s probably no God. Now stop worrying and enjoy your life." [Atheists Send a Message, on 800 Buses]

Apparently the British atheists wanted to leave out the word "probably" but that wouldn't conform to British advertising guidelines. I wonder if the guidelines apply across the board?

Are there bus and billboard signs that say, "Jesus probably loves you?"

Has the British anthem been changed to, "God probably saves the Queen?"

And what about the coins? Will they be changed to read, "Queen, probably by the grace of God" (D.P.G.) in order to conform to advertising standards?

The best remark comes from an American tourist who spotted the sign on a bus. America is the bastion of free speech (according to some Americans) but only if it's speech that doesn't offend.

Spotting one of the buses on display at a news conference in Kensington, passers-by were struck by the unusual message.

Not always positively. "I think it’s dreadful," said Sandra Lafaire, 76, a tourist from Los Angeles, who said she believed in God and still enjoyed her life, thank you very much. "Everyone is entitled to their opinion, but I don’t like it in my face."


Read More...

Denyse O'Leary and a Lesson on Irony

 
I was going to blog about this last weekend but I put it off until Monday, then I didn't get around to it yesterday. Now Canadian Cynic has used the exact same quotation that I was planning to highlight. His posting is funnier than anything I could have written. Read it at ... If the irony were any thicker ...


Read More...

Tuesday, January 06, 2009

Mendel's Garden #27

 
The 27th edition of Mendel's Garden has just been posted on Another Blasted Weblog [Mendel’s Garden No. 27].

Happy Befana from a freezing Rome. Got myself in a bit of a tizz with all this Blog Carnivalia stuff. I thought I was hosting Mendel’s Garden over at the Agricultural Biodiversity Weblog, but it seems I agreed to do it here instead. Not sure why, especially after my recent idleness. P’raps I’ll cross-post. Anyway, on with the show.


Read More...

Hot Talks - Fact or Friction: The Continuous Tension Between Science and Religion

 

University of Toronto
Hart House, The Arbor Room
Wednesday, January 21st, 6:30 PM


Join us for an evening of open discussion on the topic of the tension between science and religion. There will be a reception following the event at 8:30pm. Speakers for the evening include:

Professor Jan Sapp

Professor Sapp is a professor of Biology and History at York University. His research is focused on the fields of cell and molecular biology, microbial phylogeny, symbiosis, genetics, evolution and ecology – all from an historical perspective. His historical research on evolutionary biology aims to enlarge the boundaries of that history from focusing solely on Mendelian genetics and the development of neo-Darwinian evolutionary theory.

Professor Yiftach Fehige

Professor Fehige is an assistant professor at St. Michael’s College and the Department of History and Philosophy of Science. His research focuses on Christianity and science, thought experiments, revelation, and research ethics. Professor Fehige is currently working elaborating a pragmatic account of thought experiments in terms of a naturalistic theory of intuition.

Professor Amanda Peet

Professor Peet is a fellow of Trinity College and teaches both within the college and across other disciplines including the Department of physics. She is a member of the Canadian Association of Physicists, the Canadian Institute for Particle Physics and the American Physical Society. She focuses on understanding the fundamental dynamics of all forces and particles seen so far in Nature, especially gravity.

Professor Michael Bourgeois

Professor Bourgoeis is an associate theology professor at Emanuel college. He focuses on constructive, historical, and contextual theologies — including both formative and alternative theological traditions. His particular interests include the relation of theology to the natural sciences, especially on questions of the origin and destiny of the universe and divine action; and expressions of religious ideas in popular culture.


Read More...

Get a Job in Newfoundland

 
Memorial University: Departments of Computer Science and Biology

MEMORIAL UNIVERSITY
Tenure-Track Faculty Position in Bioinformatics


The Departments of Computer Science and Biology at Memorial University have each embarked on multi-year renewal programs. Each department currently has more than 20 tenure-stream faculty members, and supports M.Sc., Ph.D. and collaborative graduate programs. For more details, see http://www.mun.ca/biology/Home/ and http://www.mun.ca/computerscience/. Both departments invite applications for a tenure-track position in Bioinformatics, starting no later than September 1, 2009. This will be a joint appointment between the departments. The appointment will be made at the level of Assistant Professor, with the primary appointment in Computer Science, and equal responsibility in both departments, in accordance with the terms of Memorial’s Collective Agreement.

A Ph.D. in Computer Science, Computational Science, Biology, or related fields is required and postdoctoral or equivalent experience is desirable. Applicants should have experience in Bioinformatics, and be keen to do interdisciplinary work between the departments. Applicants should possess a strong research record with outstanding promise for future research, and be able to demonstrate the potential for excellent undergraduate and graduate teaching in Bioinformatics.

Applicants should submit a Curriculum Vitae, statements of research interests, teaching interests and philosophy, and up to three reprints of publications. The application should be accompanied by names of at least three referees of international standing, who are willing to provide letters of recommendation (include details on affiliations, plus phone numbers and email addresses). All material must be received by January 15, 2009; refer to position VPA-COSC-2007-001 in all correspondence, and submit materials to:

Dr. Wolfgang Banzhaf, Head
Department of Computer Science
Memorial University
St. John’s, NL, Canada, A1B 3X5
Email: chair@cs.mun.ca

Memorial University is the largest university in Atlantic Canada. As the Province’s only university, Memorial plays an integral role in the educational and cultural life of the Province of Newfoundland and Labrador. Offering diverse undergraduate and graduate programs to almost 18,000 students, Memorial provides a distinctive and stimulating environment for learning. St. John’s is a very safe and friendly city with great historic charm, a vibrant cultural life, and easy access to a wide range of outdoor activities.

Memorial University is committed to employment equity and encourages applications from qualified women and men, visible minorities, aboriginal people and persons with disabilities. All qualified candidates are encouraged to apply; however, Canadian citizens and permanent residents will be given priority. Partners of candidates for positions are invited to include their resumes for possible matching with other job opportunities.


Read More...

Get Several Jobs in British Columbia

 
University of British Columbia: Departments of Botany and Zoology

Tenure track biology instructor positions

Closing date: January 15, 2009 at 5pm

The Departments of Botany and Zoology at the University of British Columbia (Vancouver, Canada) are seeking candidates to fill at least four tenure-track Instructor positions to teach in the Biology Undergraduate Program. At least two positions will be in cellular and molecular biology, with the remaining positions open to biologists in any area. Candidates must hold a PhD in Biology, have a broadly integrative perspective on the biological sciences, and be committed to the improvement of biology undergraduate teaching. Postdoctoral teaching and/or research experience is preferred.

Successful candidates will demonstrate 1) evidence of outstanding teaching, and 2) the ability to contribute to ongoing curriculum and course redevelopment.

Duties of the positions vary, but may include lecturing in introductory and advanced courses, teaching and administration of a large third-year undergraduate laboratory course in the area of specialty, participation in course and curriculum development, and the training and supervision of graduate student teaching assistants. There are also opportunities to work in collaboration with the Carl Wieman Science Education Initiative (www.cwsei.ubc.ca).

Interested candidates should submit a letter of application, a curriculum vitae, a statement of teaching philosophy, an outline of teaching interests, evidence of teaching effectiveness, and the names and contact information for at least three individuals who would be willing to provide letters of references to jobs@zoology.ubc.ca. Candidates are particularly encouraged to highlight previous experience in fostering the education of students from diverse backgrounds.

Review of applications will begin January 15, 2009 and continue until the positions are filled, with appointments anticipated to begin by July 1, 2009.

The University of British Columbia hires on the basis of merit and is committed to employment equity. All qualified persons are encouraged to apply; however, priority will be given to Canadian citizens and permanent residents of Canada.


Read More...

Get a Job in Ontario

 
University of Western Ontario: Department of Biology

The University of Western Ontario
Faculty of Science
Department of Biology

Applications are invited for a 3-year Limited Term position in Biology commencing July 1, 2009. As a minimum, the preferred applicant will have a Ph.D. in Biology or a related field, and appropriate training in University level teaching. The successful applicant will be expected to contribute to the department’s commitment to excellence in teaching and provide evidence of his/her ability to teach at the undergraduate level. The successful candidate will be responsible for participating in the teaching of courses in cell and developmental biology as well as general biology.

Applications, including a curriculum vitae and names and addresses of three referees whom we may contact, should be submitted to:

Dr. M. Brock Fenton, Acting Chair
Department of Biology
The University of Western Ontario
London, Ontario
N6A 5B7

Applications for this position will be accepted until January 31, 2009 or until a suitable candidate is found.

Positions are subject to budget approval. Applicants should have fluent written and oral communication skills in English. All qualified candidates are encouraged to apply; however, Canadians and permanent residents will be given priority. The University of Western Ontario is committed to employment equity and welcomes applications from all qualified women and men, including visible minorities, aboriginal people and persons with disabilities.



Read More...

Mendel's Stem Length Gene (Le)

 
The seven traits that Gregor Mendel worked with were: seed shape (R/r), cotyledon color (I/i), seed and flower color (A/a), pod shape (V/v), pod color (Gp/gp), flower position (Fa/fa), and stem length (Le/le). The last trait is also known as Tall (T) and short (t).

The gene responsible for cotyledon color has been identified. It encodes an enzyme that degrades chlorophyll [Identity of the Product of Mendel's Green Cotyledon Gene (Update)]. The gene giving rise to the wrinkled phenotype (r) encodes the starch branching enzyme [Biochemist Gregor Mendel Studied Starch Synthesis].

The gene responsible for stem length has also been identified and cloned (Lester et al., 1997). It encodes an enzyme called 3β-hydroxylase. This enzyme is responsible for one of the last steps in the synthesis of the gibberallin GA1. See Monday's Molecule #102 for the structure of a similar gibberellin.

Gibberellins are plant growth hormones and GA1 is required to stimulate the grown of the stem in pea plants. The wild-type enzyme synthesizes GA1 from its substrate GA20. The pea gene (Le) is related to a similar gene in other flowering plants. Defects in those genes produce dwarf plants.

Lester et al. (1997) cloned the pea gene and identified a restriction length polymorphism that was associated with a mutant version of the gene (le). In the mutant, a single alanine residue was replaced by a threonine residue and this resulted in a 3β-hydoxylase activity that was 20-fold less than the wild type level. The reduced amount of gibberellin GA1 could account for the smaller plants.

The restriction length polymorphism was used as a genetic marker in crosses between Le/Le plants and le/le plants. It segregated with the le genotype as expected. This experiment establishes that the gene for 3β-hydoxylase is the Le gene that Mendel studied and the phenotype is due to differing levels of the plant hormone gibberellin GA1.


Lester, D.R., Ross, J.J., Davies, P.J., and Reid, J. (1997) Mendel’s Stem Length Gene (Le) Encodes a Gibberellin 3β-Hydroxylase. The Plant Cell 9:1435-1443. [PDF]

Read More...

Monday, January 05, 2009

Darwin Celebrations at the University of Toronto

 
The University of Toronto is hosting a celebration of Darwin next Novermber [Origin of Species at 150: a celebratory conference].

150 Years after Origin: Biological, Historical, and Philosophical Perspectives

Victoria College, University of Toronto, November 21-24, 2009
Darwin wrote in his autobiography, “In July [1837] I opened my first notebook for facts in relation to the Origin of Species, about which I had long reflected, and never ceased working for the next twenty years.” In 1842, he wrote a “very brief abstract” of his theory (35 pages), which in the summer of 1844 he expanded to 230 pages. Beginning in September 1858, after receiving an essay from Alfred Russell Wallace, “On the Tendency of Varieties to Depart Indefinitely from the Original Type,” which outlined the central mechanism of evolution on which Darwin had been working, he began work on completing the manuscript of The Origin of Species by Means of Natural Selection. John Murray, the publisher, launched the book on November 24, 1859 by releasing 1,250 copies. The impact of The Origin of Species has equalled the impact of Newton’s PhilosophiƦ Naturalis Principia Mathematica. It is the unifying theoretical framework for all modern biology.

November 24, 2009 marks the 150th anniversary of the publication of The Origin and The Institute for the History and Philosophy of Science and Technology, the Department of Ecology and Evolutionary Biology, and the Department of Philosophy at University of Toronto are mounting a Gala Celebratory Conference. The conference will culminate in a gala dinner on November 24 at which participants will toast the tremendous achievement of Charles Robert Darwin.

Five multi-disciplinary symposia have been organized. For each symposium, the panel consists of a biologist, a historian of biology and a philosopher of biology.

The Institute for the History and Philosophy of Science and Technology is located on the elegant, historic Victoria University campus (one of the University of Toronto’s federated universities) and the conference will be held in that location
The emphasis is on history and philosophy. It would be a perfect opportunity to put Darwin into the context of the modern world. It would be a crying shame if the conference was wasted on promoting natural selection and misrepresenting modern evolutionary theory. Do the conference organizers really mean it when they say that a 150 year old book, Origin of Species, is, "the unifying theoretical framework for all modern biology?

Here's the preliminary program.
Saturday November 21, 2009

6-7 pm: Keynote Address: to be announced

7-9pm: Reception

Sunday November 22, 2009

9-10 am: Keynote Address
Evelyn Fox Keller (Massachusetts Institute of Technology)

10 am-12 pm: Symposium:
Gender, Evolution, and Sexual Selection
Lisa Lloyd (Indiana University)
Marlene Zuk (University of California)
Erika Milam (Clemson University)

12-2 pm: Lunch Break

2-3 pm: Keynote Address
Michael Ruse (Florida State University)

3-4 pm: Contributed Papers Session
to be announced

4-5 pm: Contributed Papers Session
to be announced

5-6 pm: Keynote Address
James Moore (University of Cambridge)

Monday November 23, 2009

9-11 am: Symposium:
Evolution and Development
Manfred Laubichler (Arizona State University)
Jane Maienschein (Arizona State University)
Michael Dietrich (Dartmouth College)

11am-12pm: Contributed Papers Session
to be announced

12-2 pm: Lunch Break

2-4 pm: Symposium:
Species
John Beatty (University of British Columbia)
Kevin de Queiroz (National Museum of Natural History)
Marc Ereshefsky (University of Calgary)

4-5 pm: Contributed Papers Session
to be announced

5-6 pm: Keynote Address
Alison Pearn (Darwin Correspondence Project)

6-7 pm: Special Presentation
A Play: "Re: Design (A Dramatisation of the Correspondence of Charles Darwin and Asa Gray)"

Tuesday November 24, 2009

9-11 am: Symposium:
Taxonomy
Mary Winsor (University of Toronto)
Kevin Padian (Berkeley)
Richard Richards (University of Alabama)

11am-12pm

Contributed Papers Session
to be announced

12-2 pm: Lunch Break

2-4 pm: Symposium:
Ecology
Joan Roughgarden (Stanford University)
Gregg Mitman (University of Wisconsin-Madison)
Gregory Cooper (Washington and Lee University)

4-5 pm: Contributed Papers Session
to be announced

5-6 pm: Keynote Address
Sean Carroll (University of Wisconsin-Madison)

6-7 pm: Break

7-8 pm: Keynote Address
Spencer Barrett (University of Toronto)

8-10:30 pm: Origin at 150 Gala Dinner
Most of the speakers are strangers to me. I have no idea where they might be coming from in terms of their understanding of evolutionary theory.

Of the ones I do know, Sean Carroll is a fan of natural selection and Spencer Barrett is a classic adaptationist. It's worrisome that the organizers invited Michael Ruse to give a keynote address. As I've mentioned before, Ruse does not seem to have a very good handle on modern evolutionary theory. I fear that the conference participants will be subjected to a particular point of view that will not be a fair description of how Darwin contributed to modern biology.

If The Institute for the History and Philosophy of Science thinks Michael Ruse is going to give a good overview of Darwin's contribution then this does not bode well for the conference. They should have learned from his appearance at the Royal Ontario Museum last June [Darwinism at the ROM].

At that symposium Ruse asked, "Is Darwin's Theory Past Its "Sell By" Date." I think Michael Ruse has passed his "best before" date. It's time for him to retire.


Read More...

Darwin Week Activity at CFI

 
I attended a lecture by Carl Zimmer last summer at the Chautauqua Institute [Carl Zimmer at Chautauqua]. He posted the text on his blog at: Darwin, Linnaeus, and One Sleepy Guy.

Here's one of the important bits ...

I’d like to thank the Chautauqua Institution for inviting me to speak during this week’s series. I’m particularly grateful that the Chautauqua Institute saw fit to make this week’s theme Darwin *and* Linnaeus. We are now descending into a frenzy of Darwin celebrations, and you’re not going to escape it until the end of 2009. We’ve got his 200th birthday in February, and the 150th anniversary of the publication of the Origin of Species in November. The spotlight is going to be on Darwin, and Darwin alone.

I think this is a mistake. Darwin deserves celebrating, but that doesn’t mean we should fall prey to a cult of personality. Darwin did not invent biology. Darwin did not even find most of the evidence that he used to back up his theory of evolution. And he certainly did not discover all there was to know about evolution. Biologists have discovered many new things about evolution since his time. In some cases, they’ve challenged some of his most important arguments. And that’s fine. That’s the great strength of science.

So today I’m going to take advantage of our dual celebration of Linnaeus and Darwin. I’m going to talk about the process of science, how great thinkers challenge the thinkers of the past, how their own great ideas are altered by future generations. I’m going to talk about why Linnaeus was so important, and how Darwin shattered some of Linnaeus’s most cherished claims. I’m also going to talk about modern biologists have done the same to Darwin.

The best way to convey how drastically biology has changed since Darwin’s day is to focus on one group of living things. It’s a group about which Darwin–and Linnaeus–had little to say. I’m going to talk about microbes.
Carl was pointing out the obvious. Science has not stood still since 1859, the year that Origin of Species was published. As we approach the celebrations in February and November it's important to keep this in mind. That's why I'm giving a talk about the modern view of evolution and how it builds upon, but differs from, the views of Charles Darwin in 1859.

Come listen ...
Darwin Week Activity: Pre and Post Darwinian Science with Larry Moran

Starts: Friday, February 13th at 7:00 pm

Ends: Friday, February 13th at 9:30 pm

Location: Centre for Inquiry Ontario, 216 Beverley St, Toronto ON (1 minute south of College St at St. George St)

What was science like before Darwin, and how did it change after Darwin?

Larry Moran will be discussing our modern scientific world in light of the impact Darwin and his theory of evolution due to natural selection has had on it.

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto.

$5, $3 for students and FREE for Friends of the Centre


Read More...

How Does Your Blood Clot?

 


Some of you have been following the smackdown of Casey Luskin over his attempt to revive the irreducible complexity of the blood clotting cascade. This is a complicated pathway so I wrote a bunch of postings last year to try and explain the pathway at the molecular level.

Theme

Blood Clotting
Here's the complete list in case anyone wants more information in order to follow the discussion.

March 26, 2007
Monday's Molecule #19. Warfarin—an anticoagulant and a rat poison.

March 27, 2007
Vitamin K. Vitamin K plays an important role in blood clotting.

March 28, 2007
Nobel Laureates: Dam and Doisy. Dam: "for his discovery of vitamin K" Doisy: "for his discovery of the chemical nature of vitamin K".

April 2, 2007
Monday's Molecule #20. Heparin—an anticoagulant.

April 2, 2007
Blood Clotting: The Basics. Fibrinogen and how it forms clots.

April 4, 2007
Nobel Laureate: Arne Tiselius. "for his research on electrophoresis and adsorption analysis, especially for his discoveries concerning the complex nature of the serum proteins".

April 4, 2007
Blood Clotting: Platelets. What are platelets and how do they form blood clots?

April 4, 2007
Blood Clotting: Extrinsic Activity and Platelet Activation. Description of the activity of thrombin and the activation of blood platelets.

April 5, 2007
Blood Clotting: Intrinsic Activity. The role of factors VIII and IX. Deficiencies in Factor VIII cause hemophilia A an X-linked form of hemophilia that was common in European royal families descending from Queen Victoria.

April 8, 2007
Genes for Hemophilia A & B and von Willebrand disease. Locations of the F8, F9 and vWF genes on human chromosomes X and 12.

April 12, 2007
Inhibiting Blood Clots: Anticoagulants. How does heparin inhibit blood clotting?

April 15, 2007
Human Anticoagulant Genes. Mapping the genes for anticoagulant factors.

April 16, 2007
Dicumarol and Warfarin Inhibit Blood Clotting. The role of vitamin K in blood clotting.

September 26, 2007
A Synthetic Anticoagulant Related to Heparin. Synthesis of a new anticoagulant to replace heparin.

April 26, 2008
Fibrin and Blood Clots.
What does a blog clot look like?

May 10, 2008
On the Evolution of the Blood Clotting Pathway.
Ian Musgrave explains Russel Doolittle's latest results.


Read More...

George Johnson Revists His Defense of Scienc Journalism

 
John Horgan and George Johnson are at it again. They clarify some important points in a followup to their earlier discussion about science journalism (see Who the Heck Is George Johnson?).


John Horgan asks the key question when he says, "Where do we get informed criticism of science these days?"

George Johnson points out that there's a lot of junk on the internet and this includes most science blogs. He does go out of his way to mention the best science blogs but he seems to be surprised and upset at the amount of junk masquerading as legitimate science.

He's right, of course, but that's not the point. What Johnson still seems to ignore is the criticism of traditional print science journalism. I'm not saying that science blogs are perfect—far from it—what I'm saying is that the hubris of science journalists is unjustified. They're not nearly as good as they think they are. As a matter of fact, in my opinion the quality of science on science blogs is superior to the quality of science described by science journalists in the print media.

As a general rule, science journalists are better writers but they are not necessarily better at describing the correct science. It's the content of articles by science journalists that I'm criticizing, not their literary style. I don't think George Johnson gets this. He seems to put all of his emphasis on the literary aspect of science journalism and not enough on the scientific accuracy part of science journalism. Johnson admires good writing.

John Horgan gets it. His main complaint is that it's the scientists, and not the science journalists who are hyping their discoveries and misrepresenting the importance of their work. Horgan points out that scientists are often too deeply immersed in their work to see the big picture. George Johnson is happy to agree with him. I agree too—it's scientists who are behind bad science.1

However, both Horgan and Johnson see themselves as writers who are able to rise above this self-interest on the part of scientists and put things in proper context. According to them, the role of a science journalist is to pick out the real breakthroughs and to present an accurate view of the science, unencumbered by the prejudices and biases of those scientists who are down in the trenches.

I agree that this should be the goal of science journalism. What I expect of good science journalism is that it avoid the hype and put the science in context. In that sense, Horgan and Johnson are correct—they have identified an important role for science journalism.

So, how's it working out? Badly, I'm afraid. Most science journalists who write about the things I know are failing miserably at this important task. Their prose may be good but they are completely taken in by the scientists who exploit them. This would be unacceptable if we were talking about political reporting or the writings of an art critic. It's just as unacceptable when we're talking about science reporting. That's the issue.

While scientists are responsible for bad science in the first place, it also seems to be scientists who recognize bad science. I don't see too many examples of science journalists who recognize bad science. As a group they seem to be very gullible.

Here's the excerpt where Horgan and Johnson discuss the future of science journalism. Horgan is pessimistic and Johnson is more of an optimist. The first part of this excerpt is where Johnson defends the effort that science journalists put into their work. Science journalists may work hard but you don't get "A's" just for effort.


It's interesting to hear Johnson defend Scientific American and Discovery as good examples of science journalism. It's more evidence that he doesn't know the difference between good science and bad science.


1. Listen to the exchange when John Horgan describes evolutionary psychology. Horgan knows that a lot of it is garbage. Johnson doesn't. I think this is part of Johnson's problem. He doesn't seem to have a good feel for the difference between good science and bad science in spite of the fact that he (Johnson) brags about the amount of work that goes into good science journalism and how important it is to have good sources. Johnson seems to think that most articles written by science journalists must be accurate because science journalists are supposed to do their homework. That's a bad assumption.

Read More...

Monday's Molecule #102

 
Name this molecule. Your task is to identify the molecule and give it a biochemically accurate name (the IUPAC name would be perfect, but it's not required). A Nobel Laureate is associated with this molecule, and similar molecules, because the prize was awarded, in part, for synthesizing them in the laboratory.

The first one to correctly identify the molecule and name the Nobel Laureate 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 three ineligible candidates for this week's reward: Alex Ling of the University of Toronto, Timothy Evans of the University of Pennsylvania, and John Bothwell of the Marine Biological Association of the UK in Plymouth, UK. John, Dale, and a previous winner (Ms. Sandwalk) have offered to donate their free lunch to a deserving undergraduate so the next two undergraduates to win and collect a free lunch can also invite a friend. Alex got the first one.

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 Laureate(s) 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. I reserve the right to select multiple winners if several people get it right.

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

UPDATE: The molecule is gibberellin A3 (GA3), a plant hormone. The Nobel Laureate is Elias Corey. The winner is, once again, Dima Klenchin of the University of Wisconsin. Congratulations Dima.


Read More...

Sunday, January 04, 2009

The Open Laboratory 2009

 
The best science postings have been selected for the 3rd edition of The Open Laboratory. See the results: The Open Laboratory 2008 - and the Winners are......

There are 50 articles. This year the number of postings from the SEED consortium is only 20% of the total, indicating that there are a lot of other science blogs out there.

Out of the eclectic mix I picked the few that discussed evolutionary biology or the molecular biological sciences. Here they are.

Important new flu paper in Cell: part I

Detecting natural selection: a pika's tale

Space Invader DNA jumped across mammalian genomes

Finches, bah! What about Darwin's tomatoes?

Biochemistry of Halloween: Installment 1



Read More...

What Does Your Genome Sequence Reveal?

 
John Hawks has some interesting comments about your DNA. What does it actually tell you about your risk of dying or inheriting some nasty symptoms? What would a third party do with your genome scan? Will newspapers publish the results of secretly obtained genetic information from politicians and other famous people?

Would that be an invasion of privacy? Of course it would.

Read Privacy, politicians, and genetic testing.



Read More...

Thursday, January 01, 2009

Top Ten Evolution Articles from New Scientist

 
In my opinion, New Scientist is the best of the current crop of science magazines for the general public, although, in all honesty, the competition is not very challenging.

New Scientist has published Darwin's dangerous idea: Top 10 evolution articles. Most of them are fairly respectable. The main exception is an article on epigenetics [Rewriting Darwin: The new non-genetic inheritance]. That article is an embarrassment.

One of the best articles is Evolution: 24 myths and misconceptions. I've already posted my kudos at: Evolution: 24 myths and misconceptions. One of the nicest things about the series of articles is their description of random genetic drift as an important player in evolution; for example, Evolution myths: Natural selection is the only means of evolution.

Which brings me to the last article in the top ten list: Freedom from selection lets genes get creative. Here's what it says about random genetic drift.

Natural selection, first identified by Charles Darwin in On the Origin of Species, occurs when genetic mutations cause changes in the body and behaviour of an animal that affect its ability to survive and pass on its genes. Some mutations will have positive effects, others may kill an animal outright or somehow affect its offspring's ability to survive and reproduce. Harsh climates, sparse food and relentless predators destroy many individuals, leaving only those that survive best under exactly those pressures. As a result, the more intense the pressure of natural selection, the tighter the fit between a species and its niche.

So, what happens when the pressure is off? You might think there would be little impetus to adapt, so that species would pretty much stay the same. Not so, says Deacon. Animals still change because genes mutate all the time. The constant rewriting of DNA supplies the raw material from which natural selection picks its winners and losers, and when selection is relaxed, the process of weeding out is less ferocious. Instead, a process called genetic drift kicks in as mutations proliferate and animals with a much wider variety of traits are able to survive and reproduce. Some of the classic traits of a species may be lost, while others can arise for no reason other than that it simply doesn't matter if they do.
Close, but it doesn't quite merit a cigar. Drift does not "kick in" when selection pressure is lifted. Drift occurs all the time. It even competes with natural selection.

And while it's partially true that, "the more intense the pressure of natural selection, the tighter the fit between a species and its niche" it's also true that intense "pressure" increases the chance of extinction.

It seems strange that popular journals can publish articles about evolution that disagree with each other and nobody (editors?) seems to notice.


Read More...

Happy New Year

 
This is a year to celebrate Charles Darwin and evolution. In order to start off on the right foot here are some simple1 thoughts from our Intelligent Design Creationist friends over at Uncommon Descent [TEN THOUGHTS DARWINISTS NEED TO PONDER BEFORE BREAKFAST].

As we head into the new year and the impending Darwin bi-centennial on February 12th, we’re sure to be regaled with story after story of the wondrous things that Darwinian evolution hath wrought. A friend e-mailed the following to me, and with his permission, I reproduce it here below the fold. Perhaps pondering some of these questions might bring some balance to what is otherwise sure to be a lopsided Darwin love-fest for the next couple of months. The original of this can be found at the University of California Santa Barbara Veritas Forum website.
  1. Evolution by natural selection is more plausible in a theistic world than an atheistic world.
  2. Darwin never accounted for the arrival of the fittest. Naturalism’s god-of-chance is always called upon to do the job.
  3. Science rules out the possibility that natural processes might prevent major evolutionary change simply by definition because biological stability and conservation would imply that creation events had taken place since the creation of the universe.
  4. Creation preceded Evolution anyway.
  5. Edward Blyth described the process of natural selection well before Darwin and Wallace. He concluded that it acted as a force of conservation eliminating deterimental variations from populations.
  6. Darwin admitted that based upon the data published in his Origin of Species, one could come to “directly opposite” conclusions. For example, natural selection can prevent major evolutionary change from occurring on a gradual step-by-step basis by eliminating useless transitional stages thus explaining the lack of transitional sequences leading to all of the major body plans (phyla) in the fossil record.
  7. Natural selection better describes biology’s “ordinary rules of stability” than major evolutionary change.
  8. Darwinian theory predicts a pervasive pattern of natural history that is upside-down from the pattern found in the fossil record.
  9. Natural history is more compatible with progressive creation than Darwinian evolution.
  10. The ultimate origin of Nature itself cannot be natural. Either Nature or a Natural Law Giver has always existed. Nature has not always existed. What do you conclude?
All these questions, and more, will be answered at the Darwin 2009 Festival in Cambridge, July 5-10, 2009. Speakers include Sir David Attenborough, Dr. Matt Ridley, Lord John Krebs, Professor Steve Jones, Dame Gillian Beer, Lord Robert May, Richard Dawkins, Professor Dan Dennett, Ian McEwan and AS Byatt.

Is anyone from North America interested in going?


1. I use the term very literally.

Read More...

Another Way of Knowing?

 
Thanks to one of our favorite IDiots, Michael Egnor, we now have an answer to an important question. The question is whether there are ways of knowing other than science (evidence + rationalism). Egnor's answer is .... wait for it .... subjective experience! [My Challenge to Dr. Novella: The Materialist Color Tutor’s Dilemma].

Imagine a tutor who specializes in teaching children about color. He’s a materialist, named…Steve. He knows all that is known about color. He knows the physics, the optics, the chemistry, the neurobiology, everything. A family retains him to teach their child, a prodigy, all that can be known about color.

Tudor Steve goes to work. He teaches the little genius about quantum mechanics with relevant application of string theory to flesh out the more subtle issues, then goes on to teach the precocious child chemistry, optics, neurobiology, all of the material and physical facts about color. The child excels in color class in school, acing all of the exams on the physics and the chemistry and the neurobiology.

Then, one day, the boy confides in tutor Steve: the child is color-blind. He has learned all of the physical facts about color, but he has no idea what color looks like. He knows that tutor Steve is a materialist, so he assumes that all there is to know about color can be explained from a materialistic standpoint, including what color looks like. That’s why the child’s parents hired Steve the materialistic color tutor.

So the boy asks tutor Steve:

"Please explain to me what color looks like."

Materialist color tutor Steve has a dilemma. Material facts about color can, of course, be taught. But can ‘what it is like to see color,’ the subjective experience of color, be taught? If it can’t, then there is knowledge of color that is not material knowledge. Therefore materialism cannot completely explain the subjective experience (the qualia) of color. Therefore subjective experience is something in addition to matter. And therefore dualism is necessary to explain the mind.

How would materialist tutor Steve explain what color looks like to a person who is color blind?
That's a tough question all right. But it's only one of many difficult questions of this type. Here are some others that Michael Egnor might want to ponder.
  • How do you explain intelligence to someone who is stupid?

  • How do you explain what it's like to be abducted by UFO's if you've never been kidnapped by aliens?

  • How does a bat explain echolocation to a human?

  • How do you explain astrology to someone who doesn't know their birthday?

  • How do you explain love, or anger, to someone who has never been angry or in love?

  • How do you explain homeopathy to someone who has never been cured by drinking water?

  • How do you explain Canada to someone who has never been there?

  • Where are the weapons of mass destruction?

  • Does Michael Egnor exist?
Hands up, all those who think these questions reveal non-scientific ways of knowing about the truth? How many think that human feelings and emotions cannot be explained by science and scientific reasoning? Has Michael Egnor proved that UFOs astrology homeopathy God exists?