Hunting and Gathering in Washington D.C.

Laurel Kartchner is a Biochem/MCB major at the University of Arizona. She is attending the Experimental Biology 2011 conference in Washington.

Laurel visited all the display booths and collected all the available free loot. Here's her collection. Congratulations, Laurel!



Her poster will be up tomorrow ...

Kartchner, L.B., Malinowski, P., and T-S.Tsao Role of glutathione S-transferase and endoplasmic reticulum chaperone DsbA-L in the assembly of adipocyte hormone adiponectin.

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Cat Bowling

Jerry Coyne posted this [Caturday felids: Lasers!] but I just have to put it on Sandwalk for others to see. You need a cat and a laser pointer ...

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Happy Valentine's Day!

Who was Saint Valentine and why do we (males) have to buy flowers and chocolates today?¹ Nobody really knows very much about the Saints Valentine (there were about a dozen of them). The whole idea of romantic Valentine's day seems to have been invented by Geoffrey Chaucer sometime around 1380.

It seems like people in England just wanted to enjoy a bit of debauchery fun on February 14th so they connected their frolics with a Roman Catholic saint in order to get the permission of the church! Pretty clever, eh?

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1. And why don't women have to reciprocate?

What Is Darwinism?

Allen MacNeill at The evolution list asks What is "Darwinism" and am I a "Darwinist"?.

Read his posting to see what real modern scientists actually think about evolution and Darwinism. For more information you can read my own thoughts on the matter at: What Is Evolution, The Modern Synthesis of Genetics and Evolution, and Why I'm Not a Darwinist.

Now, here comes the fun part. Over on Uncommon Descent Barry Arrington asked the Intelligent Design Creationists to define "Darwinism". The contrast between what they're saying in the comments and what the modern textbooks say about evolution is truly astonishing.

And amusing.

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Sophisticated Theology

 
From Married to the Sea.

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[Hat Tip: Friendly Atheist.]

Math Challenge

 
Jeffrey Shallit posted the questions for the 2010 Bernoulli Trials at the University of Waterloo (Waterloo, Ontario, Canada). This is a math contest for undergraduates. You have to decide whether each of following questions are true or false.

Professor Shallit liked the questions because one or two made him think for a bit. Bully for him! When I looked at the list I can honestly say that none of them (not a single one) made me think of anything except what is a Bernoulli and why is he doing this to undergraduates?

I wonder if I could made up questions like this for biology students? I don't think so—the choices would have to be "mostly true" and "mostly false."

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FOX News Pie Chart

 
One of Ms. Sandwalk's ancestors was William Playfair who invented the pie chart [Bar Graphs, Pie Charts, and Darwin]. That was in 1786.

FOX News has heard of the concept but they don't quite seem to have mastered the technique.

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[Hat Tip: GrrlScientist]

Boring ....

 
Chris Mooney, Matt Nisbet, and Josh Rosenau got their knickers in a knot last week for thinking the Richard Dawkins had become an accommodationist [see Is Richard Dawkins an Accomodationist?].

Dawkins promptly denied it. That leaves these three accommodationists will little choice but to apologize for being so stupid. For an example of how Chris Mooney admits he was wrong (not) see his latest posting: How Richard Dawkins Communicates Evolution (Surprise, It's Not the Same Thing as Atheism).

PZ Myers takes the time to demolish the Mooney posting using images of sad puppies [My regrets on your traumatic brain damage!]. It ain't pretty.

My concern is that Chris Mooney isn't holding up his end of the fight. His postings are becoming quite boring.

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Who's Smarter, Cats or Dogs?

 
Watch the Beagle escape.

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[Hat Tip: Greg Laden]

You Can't Go Home Again

This is a resurrected version of a steroid hormone receptor. It was derived from the modern glucocorticoid receptor (GR) gene by mutating various codons to make them like the predicted ancestral gene. When all of the mutations were introduced, the protein was expressed and its structure was determined.

Glucocorticoid receptor specifically binds cortisol but the ancient protein binds other steroids as well as cortisol. This is pretty much what you might expect. Various gene duplication events lead to a family of proteins and each family member evolved to recognize a single ligand. The fact that you can reconstruct the presumed ancestral protein and show that it bound to multiple ligands is pretty amazing. The work comes out of Joseph Thornton's lab (Ortlund et al. 2007).

Altogether there were about 60 amino acid substitutions along the lineage leading from the ancestral broad-specificity receptor to the cortisol-specific receptor but only two of these turned out to be ones that shifted the specificity. Most of the rest probably had little effect of the function or specificity of the protein. This is the expected result. Most amino acid substitutions during evolution are neutral.

If there are really only two key amino acid substitutions that change specificity then it should be possible to convert a modern glucocorticoid receptor into one that recognizes a broad range of hormones by merely changing two amino acids. In other words, you could revert to the ancient form by reversing evolution and only a few mutations should do it.

Can you go back in time this easily? Apparently not, according to a recent paper from the same lab (Bridgham et al. 2009). Carl Zimmer is on top of this story in a article he published in yesterday's issue of the New York Times "Can Evolution Run in Reverse? A Study Says It’s a One-Way Street."

There's no conceptual advances in this paper, at least for those scientists who have a proper understanding of evolution. Some of the neutral changes along the pathway prepared the way for additional changes that were not possible in the ancestor protein. In other words, strictly neutral changes can add up to significant differences in structural stability making it possible for some adaptive change to occur that could not have otherwise occurred.

This isn't a breakthrough, it's an excellent study that confirms what was predicted on the basis of what we know about evolution. Here's how the authors describe their result in the abstract ...

Using ancestral gene reconstruction, protein engineering and X-ray crystallography, we demonstrate that five subsequent ‘restrictive’ mutations, which optimized the new specificity of the glucocorticoid receptor, also destabilized elements of the protein structure that were required to support the ancestral conformation. Unless these ratchet-like epistatic substitutions are restored to their ancestral states, reversing the key functionswitching mutations yields a non-functional protein. Reversing the restrictive substitutions first, however, does nothing to enhance the ancestral function. Our findings indicate that even if selection for the ancestral function were imposed, direct reversal would be extremely unlikely, suggesting an important role for historical contingency in protein evolution.

Because of "historical contingency" you can't reverse evolution. The path that lineages follow as they evolve is determined, in part, by chance and accident and not by natural selection alone.

You can't go home again.

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Bridgham, J.T., Ortlund, E.A., and Thornton, J.W. (2009) An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461:515-519. [PDF]

Ortlund, E.A., Bridgham, J.T., Redinbo, M.R., and Thornton, J.W. (2007) Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317:1544-1548. [PDF]

Hawks on Campus

 
It's probably just a coincidence but now that students have returned from their summer break there are more and more reports of hawks flying over the main open space on campus just outside my office. I seen them (it?) as well.

The latest issue of the University of Toronto eBulletin has a photo of a red tailed hawk—one of the regular visitors. Darryl Chow took the picture.

Does this explain the noticeable lack of doves on campus? I haven't seen any significant gathering of doves for many years. It used to be a regular occurrence on university campuses.

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The advantages of being close to Canada

 
Razib Khan of Gene Expression has a list [States which do well educationally, blame Canada!].

Living in a state that's close to Canada confers a number of advantages on American citizens. They are smarter, wealthier, healthier, and more likely to have voted Democrat.

Oh yeah, one other thing, being close to Canada helps prevent murder.

Alaska is an exception.

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Get a Ph.D.!!!

 
I already have a degree but for those of you who don't, here's a golden opportunity.

Now you can get real degree just in 4-5 weeks on base of your professional experience

We will get your self a verifiable degree of:
Masters, Bachelors and PhD

Ring right now

1.305.460.5721

Leave your msg, with your full name and number and we will get back to you shortly.

I think it refers to science and engineering degrees. English doesn't seem likely to be one of the eligible categories for Ph.D. studies.

I don't know why it takes so long to get a Bachelor or a Masters degree. Surely you can do it in less time than it takes to get a Ph.D.? Maybe it's cheaper to get a B.Sc. or an M.Sc. The email message didn't mention anything about the cost of the degrees—I'm guessing it would be about 30,000 rubles.

The "personal experience" part is intriguing. Ms. Sandwalk wants to know if you can get a Ph.D. for 35 years of putting up with Ph.D.'s. And I want to know if you can get one for 35 years of putting up with ....... never mind.

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12:34:56 07/08/09

 
Sometime around midday you could write the exact time and date as 12:34:56 07/08/09 and if you were up early you could have witnessed 04:05:06 07/08/09.

But only in Europe—and a few other countries [Date and time notation by country].

In America you celebrated the big day last month and if your country is unlucky enough to have adopted the international standard notation then you've missed the big day by two years.

In Canada we use all three notations and this leads to a great deal of confusion. The good news is that we get to celebrate the sequential date three times. Tonight there will be a huge celebration in downtown Toronto with parades and fireworks and speeches by famous people.

How many more sequential time/dates will we celebrate in Canada this millennium?

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Happy Simcoe Day!!

 

Today is Simcoe Day in Toronto, a holiday named after John Graves Simcoe, the first Lieutenant Governor of Upper Canada (1791-1796).

According to Wikipedia ...

He founded York (now Toronto) and was instrumental in introducing institutions such as the courts, trial by jury, English common law, freehold land tenure, and for abolishing slavery in Upper Canada long before it was abolished in the British Empire as a whole (it had disappeared from Upper Canada by 1810, but was not abolished throughout the Empire until 1834).

The holiday is known by many other names in other parts of Canada including the term "Civic Holiday," a name that brings tears to your eyes.

I think the entire country should name this holiday "Simcoe Day" in honor of John Graves Simcoe, the founder of Toronto, which is, after all, the greatest city in Canada. If Canada were to officially recognize the superiority of Toronto (and Torontonians) it would go a long way toward unifying the country.

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The New Seven Wonders of Nature

 
There are 28 finalists in the running for the New 7 Wonders of Nature. You can see the list here.

Guess who didn't make the cut? Niagara Falls wasn't even on the list of possible wonders because the Americans in New York State didn't want to spend money to promote the Falls as a legitmate contender. (I assume the Canadians didn't want to foot the entire bill themselves.)

If you're Canadian you can vote for the Bay of Fundy and if you're American you can vote for the Grand Canyon. Australians, Germans, Irish, South Africans and Italians can all vote for a 7th wonder form their own country. Even the Swiss have an entry.

If you're from the United Kingdom, you are out of luck. Apparently there's nothing wonderful in the UK.

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[Photo Credit: The Eire Hiker]

Web Site Story

 
I have a confession to make. I've always been a fan of West Side Story. I never saw the Broadway production but I saw the movie and even bought the soundtrack album back in 1961.

Some of the songs are true classics that are still being played on the radio today (Especially if you have satellite radio and listen to the 60s channel or the showtime channel. )

I bet every one of you can since a few bars of "Maria", "Tonight", "America", "I Feel Pretty", or "Somewhere" and probably most of you know a line or two from "Gee, Officer Krupke" and "Something's Coming".

Here's a very clever and funny, updated, version that was posted on A Blog Around the Clock.

See more funny videos and funny pictures at CollegeHumor.

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Timmy's Takes Manhattan

 
Tim Hortons is opening 13 stores in Manhattan and several more in Brooklyn. The first nine stores started serving coffee and donuts yesterday. Click here for a photo of New Yorkers lining up at the Penn Station store. The story even made the New York Times.

This is all part of a secret plot by Canadians to take over the best parts of the USA. (There are no plans to open stores in Texas.) Once we succeed we will impose universal health care¹ and ban Starbucks.

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1. Also known as socialized medicine.

04:05:06 07/08/09

 
Shortly after 4 AM this morning you could write the exact time and date as 04:05:06 07/08/09.

But only in America—and a few other countries [Date and time notation by country].

In Europe you'll have to wait until August 7th and if your country is unlucky enough to have adopted the international standard notation then you've missed the big day by two years.

In Canada we use all three notations and this leads to a great deal of confusion. The good news is that we get to celebrate the sequential date three times. Tonight there will be a huge celebration in downtown Toronto with parades and fireworks and speeches by famous people.

How many more sequential time/dates will we celebrate in Canada this millennium?

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Quacks in the ER

 
Here's what the emergency room would look like if homeopathy and naturopathy became real medicine instead of alternative medicine.

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[Hat Tip: Pharyngula]