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.


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.

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.


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.


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.




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



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



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?




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?


When Rationalism Trumps Superstition

 
Or maybe not ....



[Hat Tip: Canadian Cynic]

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.


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

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]

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.


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.

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.


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.


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?




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.





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.


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.

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.


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?

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.





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.


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].


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.

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]

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.


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.


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).


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”.

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.

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