This Week's Citation Classic

 
John Dennehy (The Evilutionary Biologist) has posted "This Week's Citation Classic."¹ The classic paper demonstrated back in 1964 that the gene and the protein it encodes are colinear [This Week's Citation Classic]. Remember, this was before DNA sequencing and just around the time that the genetic code was being worked out.

Before you follow the link, try and come up with an experiment that you might have done in 1964 to show colinearity. Are you as smart as Sidney Brenner?

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1. Is it just me, or have we missed a few weeks?

The Globe and Mail Calls for Harper's Resignation

 
The Globe and Mail claims to be Canada's national newspaper. It has a status in Canada that's comparable to that of the New York Times in the USA. Traditionally, the editorial staff of the Globe and Mail has been more conservative than most of the country and they have supported Stephen Harper in the past.¹

Today's editorial calls on Harper to resign for the good of his party and the good of the country [Competence and trust in question].

Not only has Mr. Harper's government failed to adequately address the economic crisis; it has created a political crisis and potentially a national-unity crisis in the process. Rather than working co-operatively on measures to strengthen the economy – something the opposition initially appeared willing to do – Parliament is now locked down, with the government's legitimacy undermined. Meanwhile, the Conservatives' excessive attacks on the Bloc Québécois, and indirectly on the millions of Quebeckers who voted for that party, have fuelled regional divides and reinvigorated the sovereigntist movement – raising a prospect of Quebec's federalist Liberals losing power in Monday's election, or at least failing to win the majority they seemed on track for.

If there is a saving grace in all this, it is that anger with the Conservatives is directed more toward Mr. Harper than his party. That raises the hope that, were he replaced as leader, the greatest barrier to inter-party co-operation with a Conservative minority government would be removed.

It is on that end, rather than the ascent of a coalition government, that the Liberals ought to focus. By hinting that the replacement of Mr. Harper as Tory leader could lessen the crisis, the Liberals would make clear that they are not engaged in a mere power grab – and allow themselves time to resolve their own leadership issues. If the Conservatives accepted that proposition, they could demonstrate that personal interests were secondary to those of the country. Both parties, in other words, could behave like adults. And the economy, rather than the personality of a single polarizing figure, could retake its rightful place as the primary focus of this Parliament.

I agree with the sentiment here. Replacing Harper as leader of the Conservative Party would go a long way toward restoring democracy to Canada.

Incidentally, let's not lose site of the fact that in addition to a provocative budget that the opposition could not accept, and in addition to stoking the flames of bigotry in Western Canada, Harper also misrepresented the nature of our parliamentary system by falsely claiming that it was illegitimate for Parliament to vote him out of office [Harper wrong on democracy claims: experts]. A man like Harper does not deserve to lead my country.

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1. Canadian Cynic provided a link to the Globe and Mail editorial that endorsed Stephen Harper last October 9th. I urge everyone who has an interest in this issue to read that editorial, it is astonishing in it's accuracy and warning of what might happen: Harper is growing into the job .

Say Again?

 
Stephen Harper. the current dictator Prime Minister of Canada received an award in New York City yesterday from Conference of Presidents of Major American Jewish Organizations. Here's the press release.

Prime Minister Harper Given International Leadership Award

Prime Minister Stephen Harper will be honoured today in New York City by the Conference of Presidents of Major American Jewish Organizations, which is presenting him with its first-ever International Leadership Award. Minister of Foreign Affairs Lawrence Cannon will attend the reception and awards ceremony to accept the award on behalf of the Prime Minister.

“I am deeply honoured to be recognized for helping improve Western relations with Israel,” said the Prime Minister. “Canada stands with Israel, and will stand with any nation willing to put its trust in its people and follow the principles of freedom, democracy, human rights and the rule of law.”

The Conference of Presidents of Major American Jewish Organizations was founded in 1954 to promote the State of Israel in the United States. An umbrella group representing 50 national religious, philanthropic and civic American Jewish organizations, it serves as a central coordinating body and primary forum for deliberations and discussions among its members on national and international issues of concern to Jews.

Yesterday was a busy day for Harper. He also shut down the Canadian parliament in order to avoid losing a non-confidence vote.

Interesting how his action contrasts with the words, "Canada ... will stand with any nation willing to put its trust in its people and follow the principles of freedom, democracy, human rights and the rule of law."

Stephen Harper is a threat to Canada and to democracy. He must be removed from office. If that means putting up with a temporary Prime Minister in his place then so be it. This is one of those circumstances where the greater good trumps everything.

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Conservative Lies

 
The Conservative Party under Stephen Harper has been spreading false information about how our parliamentary system works. They have been claiming that the transfer of power from the Conservative Party to the coalition under Stéphane Dion is a "coup" and that Dion does not have the right to lead a government.

Why are the Conservatives doing this? There are two possible explanations ...

• They believe what they are saying, in which case they are stupid and ignorant about how parliament works. They don't deserve to be the government.


• They know they are lying but they hope to convince Canadians that they're telling the truth. Because they are liars and because they have such a low opinion of the average Canadian, they don't deserve to lead a government.

Here's the problem. Harper and his Conservatives are doing great harm to the country by spreading lies. They are trying to convince Canadians that we have a US Presidential style of democracy and that he (Harper) was voted in as Prime Minister. Our young people are confused enough about politics without having this kind of false information spread by our Prime Minister.

Peter Russell is a Professor Emeritus in the Dept. of Political Science at the University of Toronto. We have tangled on a number of issues but always with mutual respect (I hope). He is a very smart man and you don't want him to catch you spreading lies about politics. Here's part of his column in today's Toronto Star [Constitution and precedent are on coalition's side].

If there is an alternative government available that has a reasonable prospect of being supported for a period of time by a majority in the House of Commons, she would have reason to decline Harper's request. Harper would then have to resign, and the Governor General would commission Dion to form a government.

If this happens, again there would be no "usurpation" of power but a proper application of the rules and principles of parliamentary democracy. It has been very disturbing to hear over the last few days, from people who should know better, wild unparliamentary theories about our system of government. Elections are not simple popularity contests in which the leader whose party garners the most votes gets all the power.

I am greatly concerned that there is so little public knowledge of the constitutional rules that govern our parliamentary system of government. These rules are not formally written down in a legal text or taught in our schools. Maybe the most important lesson to take from the situation we are now living through is to begin to codify as much as we can of this "unwritten" part of our Constitution and to ensure that it is well taught in our schools.

Harper is wrong. The only remaining question is whether he is stupid or a liar (or both).

Who is to blame for this mess? Peter has the correct answer ....

These precedents and many, many others illustrate the basic point that in parliamentary democracies we elect parliaments not prime ministers, and that the Governor General (or the presidential head of state in a republican parliamentary system) must be advised by ministers who are supported by a majority in the elected house of parliament.

Now let's apply these rules of parliamentary democracy to the situation Canada now faces. After the Oct. 14 election, Stephen Harper remained Prime Minister, formed a new government and prepared to face the House. Although his party had improved its seat total it was still in a minority position in the House. This meant that to continue in office Harper would have to win enough support from the opposition benches to secure the confidence of the House.

For a few days it appeared that Harper would reach out in a conciliatory manner and garner the parliamentary support he needs on order to have the right to govern.

But, to put it mildly, on Nov. 27 just a few days into the session, through his finance minister's economic update, he made an abrupt U-turn. Instead of seeking support from the opposition, his government presented an in-your-face, take-it-or-leave-it position.

The opposition parties – all three of them – decided not to take it. Instead, they announced that they would use their collective majority in the House to vote no confidence in the Harper government and support an alternative coalition government.

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Nobel Laureate: Eric Kandel

 

The Nobel Prize in Physiology or Medicine 2000.

"for their discoveries concerning signal transduction in the nervous system"

Eric R. Kandel (1929 - ) won the Noble Prize in 2000 for his work on understanding the biochemistry of memory. He discovered that short term memory in the sea slug Aplysia depended on the phosphorylation and dephosphorylation of proteins and that the regulation of these covalent modifications was under the control cyclic AMP mediated signal transduction pathways.

Kandel shared the prize with Arvid Carlsson and Paul Greengard.

Here's what the press release says about Kandel's work

THEME:
Nobel Laureates

Eric Kandel

Sea slug, a model system for learning
A phosphorylation of proteins has great importance also for the discoveries for which Eric Kandel is rewarded, that is for revealing molecular mechanisms, important for the formation of memories. Eric Kandel started to study learning and memory in mammals, but realized that the conditions were too complex to provide an understanding of basic memory processes. He therefore decided to investigate a simpler experimental model, the nervous system of a sea slug, Aplysia. It has comparatively few nerve cells (around 20.000), many of which are rather large. It has a simple protective reflex that protects the gills, which can be utilized to study basic learning mechanisms.

Eric Kandel found that certain types of stimuli resulted in an amplification of the protective reflex of the sea slug. This strengthening of the reflex could remain for days and weeks and was thus a form of learning. He could then show that learning was due to an amplification of the synapse that connects the sensory nerve cells to the nerve cells that activate the muscle groups that give rise to the protective reflex.

Short and long term memory
Eric Kandel showed initially that weaker stimuli give rise to a form of short term memory, which lasts from minutes to hours. The mechanism for this "short term memory" is that particular ion channels are affected in such a manner that more calcium ions will enter the nerve terminal. This leads to an increased amount of transmitter release at the synapse, and thereby to an amplification of the reflex. This change is due to a phosphorylation of certain ion channel proteins, that is utilizing the molecular mechanism described by Paul Greengard.

A more powerful and long lasting stimulus will result in a form of long term memory that can remain for weeks. The stronger stimulus will give rise to increased levels of the messenger molecule cAMP and thereby protein kinase A. These signals will reach the cell nucleus and cause a change in a number of proteins in the synapse. The formation of certain proteins will increase, while others will decrease. The final result is that the shape of the synapse can increase and thereby create a long lasting increase of synaptic function. In contrast to short term memory, long term memory requires that new proteins are formed. If this synthesis of new proteins is prevented, the long term memory will be blocked but not the short term memory.

Synaptic plasticity, a precondition for memory
Eric Kandel thus demonstrated that short term memory, as well as long term memory in the sea slug is located at the synapse. During the 1990's he has also carried out studies in mice. He has been able to show that the same type of long term changes of synaptic function that can be seen during learning in the sea slug also applies to mammals.

The fundamental mechanisms that Eric Kandel has revealed are also applicable to humans. Our memory can be said to be "located in the synapses" and changes in synaptic function are central, when different types of memories are formed. Even if the road towards an understanding of complex memory functions still is long, the results of Eric Kandel has provided a critical building stone. It is now possible to continue and for instance study how complex memory images are stored in our nervous system, and how it is possible to recreate the memory of earlier events. Since we now understand important aspects of the cellular and molecular mechanisms which make us remember, the possibilities to develop new types of medication to improve memory function in patients with different types of dementia may be increased.

Figure 4.
A sea slug, Aplysia, has a simple nervous system and a gill withdrawal reflex that Eric Kandel has utilized to study learning and memory.

Figure 5.
A schematic description of how molecular changes in a synapse may produce "short term memory" and "long term memory" in the sea slug, Aplysia. The figure shows a synapse that is affecting another synapse. Short term memory can be produced when a weak stimulus (thin arrows in the left lower part of the figure) is causing a protein phosphorylation of ion channels, which leads to a release of an increased amount of transmitter. For a long term memory to be created, a stronger and more long-lasting stimulus is required (bold arrows in the figure). This causes an increased level of the messenger molecule cAMP, which causesa further activation of protein kinases. They will phosphorylate different proteins and affect the cell nucleus, which in turn will issue orders regarding the synthesis of new proteins. This may lead to changes in the form and function of the synapse. The efficacy of the synapse can then be increased and more transmitter released.

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[Photo Credit: Eric Kandel: Wikipedia]

Dancing to the Music

 
I have a confession to make. Every Monday night Ms. Sandwalk and I go dancing. We are taking beginner's social dancing at the local community center. This is the fifth time we've taken the beginners' classes.

After the dancing lessons we go with our friends to the pub and eat honey garlic chicken wings and French fries covered with cheese and mayonnaise. Alcohol is consumed.¹

I'm finally getting the hang of the waltz. From time to time I can do the steps without counting out loud. There is, however, one small problem. According to Ms. Sandwalk I don't keep time to the music. Apparently I have no idea how to coordinate the steps and the beats. I'll have to take her word for it 'cause it seems okay to me.

As if I didn't feel bad enough, psa over on Canadian Cynic publishes a video proving that even birds can do it [Go Parrot, Go!].


This is really embarrassing.

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1. It may sound like a bribe but I assure you that I would undoubtedly be going to the dance lessons even if we didn't visit the pub afterward. (Like I have a choice?)

Priceless

 
Canadian Cynic keeps finding these wonderful examples of Conservative stupidity. This one is from The London Free Press [Harper's appeal to flag falls flat].

OTTAWA — An attempt by Stephen Harper to wrap himself in the flag and take a dig at the opposition coalition fell flat Tuesday.

The prime minister has been portraying the Liberal-NDP-Bloc Quebecois government-in-waiting as an unholy alliance of “socialists and separatists.”

During question period, he suggested the opposition parties staged their pact-signing ceremony Monday without a Canadian flag in the background because of the separatist Bloc.

“Yesterday, as part of the culmination of the machinations of the leader of the NDP, we had these three parties together, forming this agreement, signing a document and they wouldn’t even have the Canadian flag behind them,” he said.

“They had to be photographed without it because a member of their coalition does not even believe in the country.”

Video confirms that Harper was technically right. There wasn’t a Canadian flag in the background — there were two.

Wake up Conservatives. It's time to find a new leader before he makes you look any worse than you actually are right now. You are in danger of becoming a mockery of a political party comparable to what your predecessor, the Progressive Conservatives, looked like in December 1979.

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Quote of the Day

 
From A BCer in Toronto comes this quote of the day,

Governor General Michaelle Jean:

"The prime minister and myself need to have a conversation."

which prompts me to express my disgust and point everyone to a recent posting by Ms. Sandwalk [STOP using "Myself" incorrectly].

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Michaëlle Jean

 
This is Michaëlle Jean, the Governor General of Canada. She acts as Canada's Head of State. The Prime Minister is the head of government.¹ Sometime in the next few days Michaëlle Jean is going to have to make some serious decisions. She will have to decide whether to invite the Liberal-NDP coalition to form a new government if Stephen Harper and his Conservatives lose a vote of non-confidence next Monday. I think that's a no-brainer—she has to turn to the coalition.

More importantly, what will she do if Stephen Harper asks her to delay parliament for six weeks (the technical term is prorogue)? Everyone knows that Harper will only do this in order to avoid the non-confidence motion scheduled for Monday. That has never been done before and it is contrary to the standards of a parliamentary democracy. However, it is also important that the Governor General not put herself in the position of second guessing the advice of the Prime Minister. In my opinion, she will have to accept his request to prorogue parliament because to do otherwise is to set a dangerous precedent. The Governor General, like the Queen she represents, is a figurehead and not an active participant in government.

Hopefully, cooler heads will prevail and Harper won't abuse his position by requesting that parliament be suspended. Harper brought this problem upon himself by acting like a petulant, childish, bully and it's time for him to accept his fate and behave like an adult. That goes for his supporters as well.

Grow up Conservatives. You were stupid enough to force the opposition into a corner where they had only two choices, surrender and die, or unite against an unethical minority government. Much to your surprise, they were able to unite and now you must suffer the consequences of your own stupid mistake. Accept it with grace and dignity and stop acting like crybabies [Canadian Cynic].

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1. America is one of the few democracies that combine these two jobs.

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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