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.

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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.

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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

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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

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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 6Some 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?

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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?

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When Rationalism Trumps Superstition

 
Or maybe not ....

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[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.

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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?

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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.

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[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.

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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.

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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.

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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.

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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?

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