Graduate Record Exams: Biochemistry, Cell and Molecular Biology

 
This is the time of year when some undergraduates are getting the results of the GREs (Graduate Record Exams) that they wrote in preparation for graduate school applications. I thought I'd take a look at the practice test for Biochemistry, Cell and Molecular Biology.

This isn't pretty. Many of the questions ask for specific details like what is the initial product of CO₂ fixation in C₃ plants? I know lots of departments that don't teach photosynthesis and CO₂ fixation so students in those departments are screwed.

More importantly, I teach this in my introductory biology class but I tell the students that they don't have to memorize the details. They are allowed to bring their notes to the exam. I try to concentrate on basic principles and concepts and not on the names of enzymes and their specific reactants and products. In the case of CO₂ fixation, the important concepts have to do with the way rubisco works, the usable product of the reaction (not the initial product), and a general understanding of how the original reactant is regenerated. They have to understand the overall stoichiometry of the pathway and how the pathway is related to the pentose phosphate pathway.

Here's the problem. Are teachers like me hurting our students' chances of doing well on the GRE by discouraging rote memorization and regurgitation?

Even worse, I teach that concepts like exergonic and endegonic reactions are almost useless in most cases because most of the reactions in a pathway operate at near-equilibrium conditions where ΔG = 0. Several of the GRE questions ask about exergonic and endergonic reactions. My students will not do well on those questions.

How common is this? Do any other biochemistry teachers find that there's a conflict between what they teach and what is taught at most other schools?

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Monday's Molecule #99

 
Name this molecule. This time we need the common name and the systematic (IUPAC) name. A Nobel Prize was awarded for discovering how this molecule is related to your ability to remember its name and recognize the structure.

The first one to correctly identify the molecule and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are four ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin, Dale Hoyt from Athens, Georgia, Ms. Sandwalk from Mississauga, Ontario, Canada and Alex Ling of the University of Toronto. Dale and Ms. Sandwalk have offered to donate the free lunch to a deserving undergraduate so the first two undergraduates to win and collect a free lunch can also invite a friend. Alex gets the first one.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the "molecule" and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

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

UPDATE: The molecule is cyclic AMP (cAMP) or (1S,6R,8R,9R) -8-(6-aminopurin-9-yl) -3-hydroxy-3-oxo-2,4, 7-trioxa- 3λ5-phosphabicyclo [4.3.0]nonan-9-ol. The Noble Laureate is Eric Kandel. Several people guessed the molecule and Kandel but they added a second Nobel Laureate—one that I had already covered (usually Paul Greengard). Only one person picked up on the clue about memory and named Kandel alone. Congratulations to Timothy Evans of the Dept. of Neuroscience, University of Pennsylvania.

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Religious Freedom and Privacy

 
Phil Plait asks us to watch this video [Freedom of and from religion]. He says,

Watch this video. We need more like it. And I’m amazed some people can’t figure this out. it’s really pretty simple.

I'm one of those people who can't figure it out. I'm all for religious freedom. Everyone has the right to believe whatever they want as long as it doesn't interfere with the rights of others. This applies in all countries, not just in the USA.

But the video seems to imply something more when it talks about "privacy" and "respect." It sounds very much like they are advocating for protection from criticism and challenges to their beliefs.

Is this correct? Is it against the law in America to question religion or make fun of some of the most outrageous examples?

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Serious Question?

 
Nanopublic posted one of the covers of Onion Weekender with the lead story They tried to teach my baby science. Scary stuff.

If you follow the link to the Onion website you'll find all sorts of interesting Christmas gifts. If you're into giving things for Christmas just for the safe of buying presents then this is the place for you. I especially like this T-shift (below) that asks a very profound question.

I don't know the answer. I think you can start teaching them about Jesus when they are still kittens but chances are they'll never give up the idea that cats are the true gods.

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Greg Laden on "Race" (Again)

 
Greg Laden is one of those people who want to abolish use of the word "race" to define genetic subpopulations. He claims that there is no such thing in humans (or in other species). But even if it were biologically correct we shouldn't use the word because is has been misused by non-scientists.

Here's an example of his reasoning from The Scientific, Political, Social, and Pedagogical Context for the claim that "Race does not exist.".

The race concept has been very successful in its many nefarious applications, but this is not what I wish to speak about here. Rather, I want to acknowledge that a concept that divides humans into a particular set of groups in a useful way might be, well, useful and not such a bad thing. The fact that medical researchers use race to divide subjects, and find differences between races, and that these differences are important to know about, is important, even if it does not validate the races. What it means is that an unworkable race concept works sometimes, even if the races themselves don't exist. Nonetheless, it is reasonable to acknowledge that even though races don't really exist and many, if not most, applications of the race concept are obnoxious, it may be that its use is not entirely inappropriate all the time.

I will argue, however, that the down side of the use of race requires its abolition among scientists. Since race is usually not a biologically useful concept for humans (or many other species), and is never a truly valid concept, it is difficult to justify its use given the negative political and social consequences it carries.

Greg and I have been over this ground before. It think it's silly to pretend that races don't exist. That's carrying the anti-racist agenda too far.

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Best Canadian Sci/Tech Blog: Round Two

 
The first round of voting for the best Canadian Sci/Tech Blog is over.

As I said earlier, I voted for Bad Astronomy in the first round [Best Canadian Sci/Tech Blog]. I know Phil Plait isn't a Canadian, but he should be.

Here are the five finalists. I'm voting for Post Darwinist in order to make this contest look as silly as possible.

• Sync, the Tech & Gadgets Blog
• Synchro Blogue
• Post Darwinist
• DeSmogBlog
• Dusan Writer

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The Conservative Party Will Help You Write a Letter to the Editor

 
If you go to the Conservative Party website at Harper Leadership 08 you can get help in writing a letter to the editor. If you enter some sort of name and address you will eventually end up on a page that gives you the latest Conservative version of framing spin.

This is how Harper is going to avoid defeat when he faces the House of Commons. (Click on the image to see a larger version.)

The idea that the opposition parties don't have a mandate to from a coalition is particularly ironic given Stephen Harper's own position just a few years ago. Here's what is reported prominently on the front page of today's Toronto Star

But opposition MPs are accusing the Prime Minister of hypocrisy, charging that Harper is overlooking his own efforts to forge a coalition to replace Paul Martin’s minority Liberal government in 2004.

Harper, then Conservative leader, even joined with NDP Leader Jack Layton and Bloc Québécois Leader Gilles Duceppe to write then-governor general Adrienne Clarkson, urging her to look at "options" if Martin's government fell in the fall of 2004, mere months after it won a minority mandate on June 28.

"We respectfully point out that the opposition parties, who together constitute a majority in the House, have been in close consultation," read the Sept. 9, 2004, letter from the three leaders.

"We believe that, should a request for dissolution arise this should give you cause, as constitutional practice has determined, to consult the opposition leaders and consider all of your options before exercising your constitutional authority."

That message is in stark contrast to the one Harper delivered Friday night, when he charged that Liberals don't "have the right to take power without an election."

"The opposition has been working on a backroom deal to overturn the results of the last election without seeking the consent of voters. They want to take power, not earn it," he said in a statement.

Now Conservative MPs are being instructed to take that message to Canadians.

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[Hat Tip: Canadian Cynic: Because they really do need babysitting, that's why]

Is Superstition the Default Belief?

 
Are you getting tired of the modern mantra about religion—you know, the one that says it's wired into our genes and therefore probably correct or at least beneficial? I am.

So, apparently, is A.C. Graying who writes in Friday's Guardian (UK) [Children of God].

Earlier this week I had occasion to debate – if the soundbite culture of radio news permits that description – with a member of Oxford University's Centre for Anthropology and Mind the "findings" of its cognition, religion and theology project, to the effect that children are hardwired to believe in a "supreme being". The research is funded by the Templeton Foundation, an organisation keen to find, or to insert, religion into science and to promote belief in their compatibility – which, note, comes down to spending money on "showing" in the end that the beliefs of ancient goatherds are as good as modern physics.

Justin Barrett, a Christian and member of the centre's research team (whether it is research or propaganda is the moot question here) says with his colleagues on the centre's website:

"Why is belief in supernatural beings so common? Because of the design of human minds. Human minds, under normal developmental conditions, have a strong receptivity to belief in gods, in the afterlife, in moral absolutes, and in other ideas commonly associated with 'religion' … In a real sense, religiousness is the natural state of affairs. Unbelief is relatively unusual and unnatural."

This claim was the subject of Barrett's lecture at Cambridge, in which he exhibited his reasons for thinking that children are innately disposed to believe in intelligent design/creationism and a supreme being. His real reasons for thinking this, of course, are that he is a man of faith funded by a faith-based organisation; but the reasons he professed were that children have an innate tendency when small to interpret what happens in the world to be the outcome of purposive agency.

Now on this point he and I, an atheist funded by no organisation keen on promoting atheism, agree. Children's earliest experiences are of purposive agency in the adults and other people around them – these being the entities of most interest to them in their first months – and for good evolutionary reasons they are extremely credulous, not only believing that things must be acting as their parents do in being self-moving and intentional, but also believing in tooth fairies, Father Christmas, and a host of other things beside, almost all of which they give up believing before puberty, unless the beliefs are socially reinforced – as with religious and, to a lesser extent, certain other superstitious beliefs. Intellectual maturation is the process in important part of weaning oneself from the assumption that trees and shadows behave as they do for the same reason that one's parents, other humans, and dogs and cats do; it is every bit as natural a fact about children that they cease to apply intentionalistic explanations to everything as that they give them to everything, on the model of their parents' behaviour, in the earliest phases of development.

...

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[Hat Tip: RichardDawkins.net

Kill Him, Kill Him Dead

 
These are interesting times in Canada. We recently re-elected the Conservative Party as the party with the most seats in Parliament—but not a majority. That means Stephen Harper becomes Prime Minister of a minority government.

What this normally means is that the government has to craft legislation that will receive the support of a majority of the house. But that's not what Harper proposes to do. Instead he has come up with a proposal that promotes a hard-core right-wing agenda. He did this because he assumed that the Liberal party would be forced to support the government in spite of the fact that they are ideologically opposed to many of the items in the legislation. Harper thought that the Liberal party was in such desperate shape to avoid an election that they would vote for the devil.

Turns out he was wrong. In an extraordinary development, the three opposition parties—Liberals, New Democratic Party, Bloc Quebecois—have forged a coalition and announced they will vote against the government bill.¹ This will bring down the government. Stephen Harper will not be Prime Minister but there will not be an election. Instead, the coalition will form a new government.

Scott Reid of The Globe and Mail has a column in yesterday's paper that illustrates the seriousness of the crisis. It's unusual to see such language in a Canadian newspaper—especially The Globe and Mail—so I thought I'd reproduce part of his column here to show the world what is going on. I agree with Scott Reid. For the good of Canada Stephen Harper must be stopped before he does serious harm to the country.

First things first: take him out.

After all, Stephen Harper is the most dangerous animal lurking in the jungles of Parliament. He is a threat to the future viability of the Liberals. A blood simple opponent of the NDP and the only serious contemporary challenge to the Bloc Quebecois. Without him, his party is an unlikely combination of Reform Party leftovers, Harris refugees and Red Tory desperates. They don't matter or even exist without Mr. Harper. So before you think a moment longer, opposition leaders, think on that.

And if that's not compelling enough, remember: He doesn't play to win. He plays to conquer. Under his guidance, the public interest is always subjugated to his personal political advancement. And he poisons Parliament with an extreme, bare-fanged breed of partisanship that has no hope of repair until he is banished.

This becomes relevant because suddenly, he is weak. In fact, at this particular moment, he is almost unable to defend himself. Owing to a ridiculously ill-considered act of hubris, he has laid himself vulnerable to his opponents. Their imperative could not be more clear: kill him. Kill him dead. Do not, whatever you do, provide him with an opportunity to extend his hold on power. Because you can be damn certain he will never again be so reckless as to give you a chance to finish him off.

Fate tends to be grudging with gifts of this significance. To ignore it would be an error every bit as historic as the one Mr. Harper himself has made.

So don't get fancy. Don't get confused. And don't get weak in the knees. If you don't put Mr. Harper in his grave, he'll put you in yours.

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1. They will also vote in favor of a non-confidence motion put forward by the Liberal party.

Biochemistry on the Web: The Citric Acid Cycle

Here are some websites that discuss the Citric Acid Cycle [Krebs animation][Wikipedia].

This is one of the fundamental biochemical pathways yet both of these sites contain errors. This is the time of the year when I challenge the students in my introductory biochemistry class to find one single website that correctly shows the reactions of the citric acid cycle with all the correct substrates and products (including water and protons). There are two sites that don't count: ones with images from my book (Horton et al.) and ones that are direct copies of the International Biochemistry and Molecular Biology (IUBMB) website. In five years my students have not succeeded. Can any Sandwalk reader find one?

Here are the links to the IUBMB reactions. They all have the correct reaction at some location. You may have to follow one or more of the links to the reaction to see the complete, correct version.

Enzymes of the Citric Acid Cycle

citrate synthase [EC 2.3.3.1]
aconitase [EC 4.2.1.3]
isocitrate dehydrogenase [EC 1.1.1.41][EC 1.1.1.42]
α-ketoglutarate dehydrogenase [EC 1.2.4.2]
succinyl-CoA synthetase [EC 6.2.1.4][EC 6.2.1.5]
succinate dehydrogenase [EC 1.3.5.1]
fumarase [EC 4.2.1.2]
malate dehydrogenase [1.1.1.37]

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The Yale Experience with Alternative Medicine

 
Do you think that modern medical schools at major universities will never be advocates of quackery? Wrong!

The experience of Yale University's School of Medicine should be a warning that those who believe in evidence-based medicine have to be vigilant. Yale recently held an "Integrative Medicine Scientific Symposium." One of the speaker was David L. Katz, MD, MPH, FACPM, FACP. Katz is associate professor, adjunct, of Public Health and director of the Prevention Research Center (PRC) at the Yale University School of Medicine. He is a proponent of almost every form of non-evidence based medicine that you can imagine.

A short video of his presentation is included below. It's from the blog DC's Improbable Science: Integrative baloney @ Yale. I'm including it because it illustrates the length to which these quacks will go in order to make their point. Note that the quack is introduced by the Dean of Education at Yale—listen to how easily he may have been bamboozled into thinking that this is about legitimate science.

The most important points in the video are the ones where Dr. Katz explains away evidence-based medicine. You see, the problem isn't so much with the lack of "evidence" as with the concept of "evidence" itself. The practitioners of alternative medicine advocate changing the very concept of "evidence" to a "more fluid concept of evidence." What this means is that if a large-scale, double-blind experiment shows no effect it's not the end of the story. There are other kinds of evidence that may show the effectiveness of alternative medicine. (One of them seems to be anecdote.)



I hope that the University of Toronto is not going in this direction.

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Snopes Warns Against Embedded Tracker Programs - Pass It on

 
Friday's Urban Legend: False

Have you ever received an email messgage like this?

Snopes Warning

Pass this one on to all your e-mail buddies and take the time to read the Snopes.com article listed below. It is full of good advice especially about the "cookies."

To whom it may concern:

Just a word to the wise. E-mail petitions are NOT acceptable to Congress or any other municipality. To be acceptable petitions must have a signed signature and full address.

Almost all e-mails that ask you to add your name and forward on to others are similar to that mass letter years ago that asked people to send business cards to the little kid in Florida who wanted to break the Guinness Book of Records for the most cards. All it was, and all this type of e-mail is, to get names and "cookie" tracking info for tele-marketers and spammers to validate active e-mail accounts for their own purposes.

Any time you see an e-mail that says forward this on to "10" of your friends, sign this petition, or you'll get good luck, or whatever, it has either an e- mail tracker program attached that tracks the cookies and e mails of those folks you forward to, or the host sender is getting a copy each time it gets forwarded and then is able to get lists of "active" e mails to use in spam e-mails, or sell to others that do.

Please forward this notice to others and you will be providing a good service to your friends, and will be rewarded by not getting 30,000 spam e-mails in the future.

(If you have been sending out the above kinds of email, now you know why you get so much spam!)

According to snopes.com they have never warned against "tracking programs" embedded in email messages [False Advice]. It may be good advice to not spam your friends but nothing in this email message is directly from the snopes.com website and nobody at snopes.com have authorized it.

If there was such a thing as an embedded email tracking program then passing on this message would be an excellent way to spread it!

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So Many Turkeys

 
This is almost as much fun as curling! Ms. Sandwalk will love this game [Turkey Shoot].

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[Hat Tip: Chaotic Utopia]

Online Curling

 
Even if you don't like computer games, you won't be able to resist this one. It's an online curling game on the Little Mosque on the Prairie website.

Ms. Sandwalk, Jane and Gordon are going to be so excited about this. I can hardly wait to get a tournament going with my children and their American partners, Michael, and Rachel. Such an easy way to teach them the best things about Canadian culture!!

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[Hat Tip: The Unexamined Life]

Thanksgiving Day in the USA

 
Some people give thanks for turkey or pumpkin pie. Some people give thanks for football. Others are truly thankful that they have been blessed with good fortune.

Sean Carroll gives thanks for the spin-statistics theorem.

Most people wouldn't understand but I do. I've hung out with physicists and astronomers. This really is how they think.

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