How Roundup® Works

This week's molecule is N-(phosphonomethyl) glycine better known as glyphosate, the active ingredient in the herbicide Roundup® [Monday's Molecule #17]. Glycophosate is a potent inhibitor of one of the key enzymes in the pathway for synthesis of the aromatic amino acids, tryptophan, phenylalanine, and tyrosine [How Cells Make Tryptophan, Phenyalanine, and Tyrosine].

Specifically, the herbicide blocks the activity of EPSP synthase, the enzyme that catalyzes one of the steps leading to chorismate. Chorismate is the precursor of all three aromatic amino acids so by blocking this enzyme, the synthesis of three plant amino acids is prevented.


Plants need to synthesize all 20 amino acids so this blockage causes plants to die. The glyphosate mechanism is well known from studies of the homologous bacterial versions of EPSP synthase. An example of glyphosate bound to the active site of the E. coli enzyme is shown on the right. When glyphosate is bound, the enzyme is incapable of catalyzing any reaction.

As pointed out earlier in "How Cells Make Tryptophan, Phenyalanine, and Tyrosine," animals have lost the ability to synthesize chorismate and the aromatic amino acids. They require tryptophan, phenyalanine, and tyrosine in their diet. What this means is that the potent herbicide, glyphosate, has no effect on animals since they have already dispensed with the EPSP synthase enzyme. That's one of the reasons why Roundup® is so safe for humans.

Those of you who have used Roundup® on your driveways and walkways know that it kills all plants indiscriminately. You'd better not get it on your wife's favorite roses (... not that I'm admitting anything, mind you).

You can't spray it on crops, such as soybeans, corn, cotton, granola, and wheat to get rid of weeds because it kills the crops as well as the weeds. Wouldn't it be nice to have Roundup® resistant crops so you could spray them to control weeds?

Monsanto makes Roundup® and and they thought so too. Now, how do you genetically modify plants to make them resistant?

Immigration Critical to Canada

 
All Canadians know how important immigration is to our future. Not only do we benefit from an influx of new ideas and new faces, we also benefit from the increase in population that is so important to maintaining our present high standard of living.

An article on cnews makes the case [Census: Immigration critical to Canada].

Canada saw its native-born populace climb by a modest 400,000 souls between 2001 and 2006. It was the addition of 1.2 million immigrants that helped push the country’s enumerated population total to 31.6 million.

The 2006 census data, released Tuesday by Statistics Canada, shows overall population growth of 5.4 per cent — the highest among the Group of Eight industrialized nations. Canadian growth was up from four per cent in the previous five-year census period, which had been the slowest half-decade in modern Canadian history.

Thank immigration for Canada’s relatively robust growth. An average 240,000 newcomers per year more than compensated for the country’s flat fertility rate.

Canada's immigration rate is the highest in the industrialized world, higher by far than that of the United States, although the US has more immigrants in terms of total numbers (not counting Mexicans, I assume).

Canada’s net migration, per capita, is among the highest in the world. According to the OECD, Canada’s net migration of 6.5 migrants per 1,000 population between 2000-2004 put it at the head of the international pack. Australia, another immigration juggernaut, accepted 6.2 migrants per 1,000 population during the same period.

Canada’s influx offsets a flacid national birthrate of about 1.5 kids per woman, well below the replacement rate of 2.1 and just below the OECD average.

The United States, by way of example, accepts only 4.4 immigrants per thousand but has a fertility rate 25 per cent higher than Canada.

I don't know why the US birth rate is so much higher than Canada's or Europe's. Does anyone have an answer?

Apple Computer Unveils the New iRack

 



[Hat Tip: Sunbeams from Cucumbers]

Roll Up the Rim

 
There's always a long line at my regular Tim Horton's on the first floor of my building. The lines are even longer at this time of year because it's "Roll-up-the-rim" time. Timmy's has a special contest where you can win prizes by simply rolling up the rim of your coffee cup. I'm just about to do it right now ......

Rats! It says, "PLEASE PLAY AGAIN/RÉESSAYEZ S.V.P" (Remember, we're a bilingual country so we get to be disappointed in two languages.) Back in 1993 I won a stereo system by rolling up the rim and I'm hoping for a big screen TV next time.

Believe it or not, some people have trouble rolling up the rim. Apparently, there's an epidemic of broken fingernails and other serious injuries during the Tim Hortons promotion in March and April. That's prompted an Ottawa inventor to come up with a nifty tool to help out [Ottawa invention makes it easy to play again... and again... and...]. I guess they don't have anything better to do up in Ottawa.

The Rimroller tool is marketed by Lee Valley Tools. Now, you may be wondering why a company like Lee Valley would be involved in marketing a tool to roll up the rim of Tim Hortons coffee cups. You weren't? Well I was, so I looked on their website and read what the President had to say.

When we were first shown the Rimroller many months ago, we recognized immediately that this was an elegant, well-designed, and well-manufactured product at a very reasonable price. It was one of those products that just delighted people when they used it. We also recognized that the inventor, Paul Kind, had plowed a ton of time and capital into bringing the product to the point where it was ready to market. So, while Lee Valley is clearly not the most appropriate retailer of this product, we could only stand by for so long watching Mr. Kind work hard to sell this product without success.

That certainly explains it.

Want to know how it works? ....... Okay, I can respect that; but for the rest of you, here are the simple instructions.

This is an easy-to-use product. Essentially a curved clip with two integral (covered) blades, it slices the cup rim twice (1-1/8" apart) when pushed down, and an internal lip unrolls the paper edge when it’s pulled up. Push, pull and you’re done. 2" high, 1-1/2" wide, with an attached split-ring.

Invented and manufactured in Ottawa, Canada.

You can buy them wherever you find a Lee Valley Tools store for $1.95 (+tax). Personally, I'd rather save money on the Rimroller and buy another coffee. I really need that TV 'cause the World Curling Championships are coming up next month.

Kieffer Sutherland In Toronto

 
Here's a picture from the weekend Toronto Star with an interesting caption. Lots of people are upset about torture on "24".

Less Torture in "24"


More on "24" Torture

How Cells Make Tryptophan, Phenyalanine, and Tyrosine

 
Most species have to synthesize all of their amino acids from simple compounds. Several of the metabolic pathways are quite complicated, especially those leading to the complex aromatic amino acids like tryptophan, phenyalanine, and tyrosine. Many animals, including humans, have lost the ability to make these aromatic amino acids. We assume that the loss was not lethal because it was easy to get adequate amounts in the diet. The fact that we can't make them means that tryptophan, phenylalanine, and tyrosine are essential amino acids.

The other essential amino acids also have complicated biosynthesis pathways. We have also lost the ability to synthesize lysine, methionine, threonine, valine, leucine, isoleucine, and histidine.

Let's look at the pathway for the synthesis of tryptophan, phenylalanine, and tyrosine as seen in bacteria, plants, fungi, and protists. These are species that cannot get adequate supplies of pre-formed amino acids so they have to make all of the amino acids needed for protein synthesis de novo.

The first part of the pathway begins with a simple three carbon compound (phosphoenolpyruvate) and a simple carbohydrate derivative (erythrose 4-phosphate). These are combined in a series of four reactions to produce shikimate, a common metabolite in bacteria and most eukaryotes. Shikimate is then phosphorylated by shikimate kinase to make shikimate 5-phosphate.

The next step is very important. A three carbon addition to shikimate yields the complicated product 5-enolpyruvylshikimate 3-phosphate. The addition to the ring will eventually become the core part of the amino acid. This reaction is catalyzed by the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSP synthase) an enzyme that we'll hear more about very soon.

The final step in the first part of the pathway is the removal of the phosphate group to produce chorismate. Chorismate is another common metabolite in all species except animals.


The three aromatic amino acids are all made from chorismate (see below). The pathway to tryptophan is complicated but those leading to phenylalanine and tyrosine are much simpler. In addition to the pathway shown, tyrosine can also be made directly from phenylalanine by hydroxylation, in a reaction catalyzed by phenylalanine hydroxylase. That's why tyrosine is sometimes not listed as an essential amino acid; it's not essential if there are adequate supplies of phenylalanine in the diet. (Defects in phenylalanine hydroxylase are responsible for phenylketonuria.)

The important point for later on is the chorismate pathway. It is absolutely crucial for life in most species but it isn't even present in most animals. Blocking that pathway with a herbicide in plants will be lethal but the herbicide will have no effect on animals.

Douglas Adams Speaks About Religion

 
Coturnix reminds us that yesterday was the birthday of Dougls Adams [Happy Birthday Douglas Adams]. Most of us remember the funny Douglas Adams and, in that vein, Coturnix posted a number of humorous quotations.

But there was a serious side to Douglas Adams and I'm going to post an extended quotation of Adams that I first saw in A Devil's Chaplain by Richard Dawkins. As most of you know, Douglas Adams and Richard Dawkins were friends—Adams introduced Dawkins to his current wife. [Lament for Douglas]

The quotation in A Devil's Chaplain is taken from a speech that Adams gave in Cambridge in 1998. The complete text of the speech is at [Is there an Artificial God?]. You can also listen to a podcast of Douglas Adams giving the speech. Here's what Douglas Adams says about our attitude toward religion.

Now, the invention of the scientific method and science is, I'm sure we'll all agree, the most powerful intellectual idea, the most powerful framework for thinking and investigating and understanding and challenging the world around us that there is, and that it rests on the premise that any idea is there to be attacked and if it withstands the attack then it lives to fight another day and if it doesn't withstand the attack then down it goes. Religion doesn't seem to work like that; it has certain ideas at the heart of it which we call sacred or holy or whatever. That's an idea we're so familiar with, whether we subscribe to it or not, that it's kind of odd to think what it actually means, because really what it means is 'Here is an idea or a notion that you're not allowed to say anything bad about; you're just not. Why not? — because you're not!' If somebody votes for a party that you don't agree with, you're free to argue about it as much as you like; everybody will have an argument but nobody feels aggrieved by it. If somebody thinks taxes should go up or down you are free to have an argument about it, but on the other hand if somebody says 'I mustn't move a light switch on a Saturday', you say, 'Fine, I respect that'.

The odd thing is, even as I am saying that I am thinking 'Is there an Orthodox Jew here who is going to be offended by the fact that I just said that?' but I wouldn't have thought 'Maybe there's somebody from the left wing or somebody from the right wing or somebody who subscribes to this view or the other in economics' when I was making the other points. I just think 'Fine, we have different opinions'. But, the moment I say something that has something to do with somebody's (I'm going to stick my neck out here and say irrational) beliefs, then we all become terribly protective and terribly defensive and say 'No, we don't attack that; that's an irrational belief but no, we respect it'.

It's rather like, if you think back in terms of animal evolution, an animal that's grown an incredible carapace around it, such as a tortoise—that's a great survival strategy because nothing can get through it; or maybe like a poisonous fish that nothing will come close to, which therefore thrives by keeping away any challenges to what it is it is. In the case of an idea, if we think 'Here is an idea that is protected by holiness or sanctity', what does it mean? Why should it be that it's perfectly legitimate to support the Labour party or the Conservative party, Republicans or Democrats, this model of economics versus that, Macintosh instead of Windows, but to have an opinion about how the Universe began, about who created the Universe, no, that's holy? What does that mean? Why do we ring-fence that for any other reason other than that we've just got used to doing so? There's no other reason at all, it's just one of those things that crept into being and once that loop gets going it's very, very powerful. So, we are used to not challenging religious ideas but it's very interesting how much of a furore Richard creates when he does it! Everybody gets absolutely frantic about it because you're not allowed to say these things. Yet when you look at it rationally there is no reason why those ideas shouldn't be as open to debate as any other, except that we have agreed somehow between us that they shouldn't be.

We've discussed this issue many times. What is it about religion that makes us bend over backwards to avoid offense? We wouldn't hesitate to criticize those who fall for "The Secret" or those who are taken in by Sylvia Browne. We challenge those people who claim that the moon landings were faked. We debunk urban legends. We question homeopathy.

But if a man says he can't turn on a light switch because it's Saturday we say nothing. Why is that? Is it because the orthodix Jew is expressing a personal belief that's none of our business? If that's it then what about conspiracy buffs or those who think they've been abducted by aliens? Aren't those harmless personal beliefs as well? Is Adams correct to assume that it's "religion" that's out-of-bounds?

Monday's Molecule #17

 
Name this molecule. You must be specific. We need the correct scientific name and in this case we need the generic and brand names as well.

As usual, there's a connection between Monday's molecule and this Wednesday's Nobel Laureate. This one's a bit of a stretch. Extra bonus points for guessing Wednesday's Nobel Laureate(s).

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

Evolution as Design

 
RichardDawkins.net has posted a collection of interviews with Daniel Dennett where he responds to questions about evolution. You can seem them at [Understanding Genetics - Daniel Dennett Interview].

I have a bit of a problem thinking of Daniel Dennett as a good genetics teacher. I also have difficulty thinking of him as a good teacher of evolution since he seems to think that natural selection is the only game in town. He is a classic Ultra-Darwinian.

One of the problems with the Dennett approach to evolution is the emphasis on "design" in nature. I disagree with the basic concept that nature looks designed and I certainly disagree with the idea that natural selection is responsible for everything we see around us. Listen to how Dennett describes his view of the biological world.

Do you agree with this perspective? I don't. Not only do I think it's wrong, I think it concedes an important point to Paley and the Intelligent Design Creationists. I favor Evolution by Accident. The biological world doesn't look all that well designed to me.

Atheists Get Good Press in the Globe & Mail

 
I almost forgot to mention the article in Saturday's Globe & Mail. It was an excellent introduction to the atheist, skeptic, humanist, freethinker community in Canada. The article introduced the Centre for Inquiry and mentioned that it was having a grand opening yesterday [Standing Room Only].

You can read the entire article on the Richard Dawkins website [ When the ain'ts go marching in]. Here's a short teaser.

The CFI is intended to be a place not just for lectures, but for an eclectic list of activities, from a science book club to less-cerebral pursuits such as yoga for freethinkers and "magic for skeptics."

There's a Sunday-morning meeting to discuss different aspects of humanism, and a monthly spaghetti dinner -- where, instead of a traditional grace, the lauded deity is the Flying Spaghetti Monster, a lampoon concocted a few years ago in response to the Intelligent Design movement's attempts to derail evolutionary teaching in Kansas schools.

The centre is also organizing social services, such as a regular meeting of Secular Organizations for Sobriety, which is an alternative to Alcoholics and Narcotics Anonymous. Another program, Religious Recovery, tries to ease the transition for people who are leaving organized religion.

According to 2001 census figures, nearly five million Canadians identify as having "no religious affiliation," compared with 13 million Catholics and eight million Protestants. That's a 44-per-cent increase since the 1991 census figures. In 1971, less than 1 per cent of the population claimed no religion.

Standing Room Only

 
It was standing room only at the opening of the first Centre for Inquiry in Canada. An attentive audience of more than 150 freethinkers, skeptics, atheists, and humanists listened to a dozen speakers bringing greetings and congratulations from every rationalist organization in Canada.

Unfortunately, Paul Kurtz, the founder of the Centers for Inquiry was unable to make it because he was resting up for open heart surgery next week. We were assured that it wasn't serious and he's expected to recover fully in about six weeks.

Among the speakers we heard from was Coralie D'Souza representing a student group at the University of Toronto. She has been active in many issues of concern to the atheist community, especially prayer before every university graduation ceremony. D'Souza announced that after months of negotiation the university has agreed to drop all prayers at convocation starting this June.

Elka Enola of the Oakville Humanist Community was able to report success in her negotiations with Oakville Hospital. (Oakville is just west of Toronto.) From now on patients who declare "no religion" when they are admitted will have access to non-religious counselors if they need help while they're in the hospital. The hospital will contact the Oakville Humanist Community for a list of suitable social workers and grief counselors.

Mark Robinson of the Clarington Durham Region Humanists presented Justin Trottier with a Centre for Inquiry plaque that he (Mark) made especially for the occasion. (See it in the photo at the bottom of the page.) Mark has been active in the attempt to stop prayers at Durham Region Council Meetings.

Henry Beissel congratulated the Centre for Inquiry on behalf of Secular Ontario. That's the Ontario group trying to stop reciting of the Lord's Prayer at city council meetings. I got a chance to meet James Alcock. He's a Professor of Psychology at York University, here in Toronto. Some you might know him because he's a Fellow and Member of Executive Council, Committee for the Scientific Investigation of Claims of the Paranormal (CSICOP) and a member of the Editorial Board, The Skeptical Inquirer. He brought greetings from Skeptical Inquirer.

We all toasted the successful founding of the Centre for Inquiry. Fortunately, in spite of the huge turnout there was more than enough champagne to go around. There was also plenty of food served by efficient volunteers bustling in and out of the back kitchen. (I loved the little sandwiches.)

This is a wonderful achievement. The Centre for Inquiry brings together many diverse groups such as the Freethought Association and The Humanist Association. Other groups such as Skeptics Canada (that's my organization) will undoubtedly be working closely with the Centre for Inquiry in the future as indicated in an address by its President Eric McMillan.

Most of the Credit goes to Justin Trottier who chaired the celebration and received many accolades from the speakers. I was proud to have my photograph taken with him after the formal part of the celebration was concluded. (Justin is the young handsome one with the name tag.) Congratulations to Justin and all those who made this possible. I'm looking forward to visiting the centre often.

Happy Daylight Saving Time!

 
About twice a month we walk across the road outside of the Medical Sciences building and eat lunch in the cafeteria with the engineers in the Sandford Fleming Building. The building is named after one of Toronto's most famous engineers Sir Sandford Fleming (1827-1915).

Fleming was the Engineer-in-Chief of several railways and played a prominent role in surveying for the transcontinental Canadian Pacific Railway. His work as a surveyor is remarkable. It's commemorated by a large plaque and monument outside of the Sandford Flemming building. A bronze line embedded in the concrete marks the location of the Meridian of Toronto (79°24' WEST OF GREENWICH). The plaque beside it reads ...

This line, in the true north-south direction through the site of the Toronto magnetic observatory, marks the meridian for Toronto that was recognized by scientists around the world until 1908.

Each section of this beam is 3.085 metres long, equivalent to 0.1 seconds of arc of latitude, exmplifying the high precision of the 1883 determination of the latitude and longitude of the observatory, recorded on the transit pillar nearby.

In 1840, magnetic north here was almost coincident with true north, but has drifted slowly westward since that time. By 1898, when magnetic observations had to be abandoned at this site owing to interference from the newly electirfied street railways, the variation had reached 5 degrees.

I always make guests stop to read the plaque and appreciate what 0.1 seconds of arc looks like. They also have to recognize that the line points to the North Pole (and the South Pole). I know it sounds strange, but most of them don't seem to be as excited about this as they should be. And when I tell them that I've stood on the Greenwich meridian their eyes glaze over.

Sandford Fleming is also responsible for "inventing" standard time based on the Greenwich meridian. This "universal time" was adopted at an international conference in 1884. Fleming's initial proposals to divide he world into 24 local time zones were not adopted at that conference but gradually over the course of the next several decades, countries moved to conform to the time zones we now recognize (Sandford Fleming and Standard Time).


Daylight Saving Time came much later. According to the Wikipedia article (Daylight Saving Time ..

Start and end dates and times vary with location and year. Since 1996 the European Union has observed DST from the last Sunday in March to the last Sunday in October, shifting clocks at 01:00 UTC. Starting in 2007, most of the United States and Canada observe DST from the second Sunday in March to the first Sunday in November, shifting clocks typically at 02:00 local time. The 2007 U.S. change was part of the Energy Policy Act of 2005; previously, from 1987 through 2006, the start and end dates were the first Sunday in April and the last Sunday in October, and Congress retains the right to go back to the previous dates once an energy consumption study is done.

Saving daylight was first mentioned in 1784 by Benjamin Franklin in a humorous letter[2] urging Parisians to save money by getting up earlier to use morning sunlight, thereby burning fewer candles in the evening. Franklin did not mention daylight saving time—he did not propose that clock time be changed. His letter was in the spirit of his earlier proverb "Early to bed and early to rise / Makes a man healthy, wealthy, and wise."[3]

DST was first proposed in 1907 by William Willett.[4] An avid golfer, he disliked cutting short his round at dusk. The proposal attracted many eminent supporters, including Balfour, Churchill, Lloyd George, and MacDonald. Edward VII also favored DST, and had already been using it informally at Sandringham. However, Prime Minister Asquith opposed the proposal and after many hearings it was narrowly defeated in a Parliament committee vote in 1909. Willett's allies introduced new DST bills every year from 1911 through 1914, to no avail.

DST was first enacted by a national government by Germany during World War I, starting April 30, 1916. The United Kingdom soon followed suit, first observing it on May 21, 1916. On June 17, 1917, Newfoundland became the first North American jurisdiction to adopt DST with the Daylight Saving Act of 1917. On March 19, 1918, the U.S. Congress established DST from the last Sunday in March to the last Sunday in October. The wartime measure, however, proved unpopular among farmers, and Congress repealed it in 1919. Woodrow Wilson, another avid golfer, vetoed the repeal but the veto was overridden.

The official spelling is Daylight Saving Time, not Daylight SavingS Time.

Saving is used here as a verbal adjective (a participle). It modifies time and tells us more about its nature; namely, that it is characterized by the activity of saving daylight. It is a saving daylight kind of time. Similar examples would be a mind expanding book or a man eating tiger. Saving is used in the same way as saving a ball game, rather than as a savings account.

Nevertheless, many people feel the word savings (with an 's') flows more mellifluously off the tongue. Daylight Savings Time is also in common usage, and can be found in dictionaries.

Adding to the confusion is that the phrase Daylight Saving Time is inaccurate, since no daylight is actually saved. Daylight Shifting Time would be better, but it is not as politically desirable.

Daylight Saving TimeThe USA didn't enact binding federal legislation until 1966 according to a more complete history at The Uniform Time Act section of the Daylight Saving website. Under that law clocks were shifted forward on the last Sunday in March. As mentioned in the Wikipedia article, a new law was passed in 2005 requiring that the shift take place on the second Sunday in March and last night was the first time that change has been implemented. Canada was forced to follow the American lead on this issue because it would have been too confusing for Canada to stick to the old dates.

The reason for extending daylight saving is to save energy. While there is some controversy over the amount of energy that will be saved, there seems to be a consensus that the gains in the evening outweigh the losses in the morning. The original implementation of daylight saving time was justified on several grounds but its acceptance by the general public is mostly related to the extended periods of daylight in the evening. (It's not just golfers who enjoy the extra sunlight.)

If you want to see the effect of daylight saving in different parts of the Northern and Southern Hemispheres, check out this amazing graphic at the Daylight Saving website [Daylight Saving Map]. It's easy to see why countries near the equator don't benefit from shifting their clocks.

But there are other places that don't shift their clocks. In many case it's because the political units fall on one of the standard lines that separate times zones. For example, my home province of Saskatchewan doesn't use daylight saving time for this reason. The map below shows countries and regions that don't use daylight saving time. (Incidentally, this map is an amazing example of the free work done to make Wikipedia an excellent source of information. The figures posted to Wikipedia are released into the public domain.)

[Photo Credit: The photograph of the plaque is by Alan L Brown (March 24, 2004) from the OntarioPlaques.com website.]

Windows, Macs, and BSD

 
David I. Greig (DIG) is the moderator of talk.origins and he swears by BSD. It's the system he uses on "Darwin", the robomoderator of the newsgroup. The box is sitting outside my office right beside "bioinfo," a server that runs on real Linux. DIG can be a bit of a pest when he gets going about BSD but he knows a lot more about this stuff that I do.

Here's a take-off on that obnoxious Mac commercial that you see on TV. I especially like the part about Macs being only 3% of the market—that's why nobody bothers to write viruses for Macs.

I can't tell the difference between Linux and BSD. They look the same to me. What do you think?



[Hat Tip: Jim Lippard]

Canada's Role in Afghanistan

 
Kathy Gannon is a reporter who has been to Afghanistan and writes with clarity and authority. She recently gave a speech in Toronto at a lecture sponsored by the Atkinson Charitable Foundation. Joseph E. Atkinson is the former published of the Toronto Star newspaper.

You can read a summary of Gannon's speech at "Canadian efforts have backfired, writer says".

This is a complicated issue. She makes several points that need to be debated in order to decide whether Canada is doing any good in Afghanistan.

"What they have failed to do is make allies of Afghans. Instead they have made enemies of ordinary Afghans," says Kathy Gannon, an award-winning journalist who has worked in the strife-torn country for more than 20 years.

"That to me is the biggest error that has occurred, (and) it has occurred because they've gone in with a mixed mandate to reconstruct and rebuild as well as go on the offensive. It is very difficult, if not impossible, to do both."

This is a good point but it's one that's often overlooked, both in Afghanistan and Iraq. Is it possible to win the hearts and minds of a people when you're killing them at the same time? Have we blown whatever chance we had to be their friends?

Gannon points out that the troops who are fighting a war against insurgents tend to see everyone as a potential enemy and they tend to be trigger-happy. This is not a criticism, it's quite natural under the circumstances. However, it does make it difficult to be friends and allies of the very people who may be harboring the insurgent who blew up your best buddy yesterday. Troop moral under those circumstances is very much an issue. Our Governor General, Michaëlle Jean, has just returned from Afghanistan in an attempt to show support for the troops. This overt support is increasingly necessary because the soldiers themselves are having doubts about their mission, according to Gannon.

Afghans don't trust foreigners. This seems so obvious when you write it down on paper—after all, they have a 500 year history of fighting foreign invaders. But the truth of the matter is that we often forget that simple fact. We figure we're somehow different than the British and the Russians and everyone else who failed to control Afghanistan in the past. That's very naive. In the eyes of Afghans we're no different that anyone else.

Afghanistan is ruled by warlords. Here's what Gannon says about that,

The Western countries that ousted the Taliban have also made a serious mistake in allowing vicious warlords back into power, said Gannon, who witnessed the collapse of communism, the rise of Osama bin Laden and the war that ousted him along with the Taliban in 2001.

Because of the return of the warlords who killed, raped and pillaged before the Taliban seized power, the Afghan government has lost credibility, Gannon said.

"The Afghans knew exactly who it was that was coming back to power. But ... they really believed the international community understood who they were. That (it) would keep them in line. That (it) wouldn't let them gain control and reduce the country to the anarchy that it was in before."

But, she said, the warlords "behaved exactly as they had the last time. They reduced the country to what it was before, and now you have all those international soldiers in the mix. They are halfway around the world in a completely alien environment to what they know."

There are two problems here. The first is that we are supporting a corrupt, useless, figurehead government that barely controls the capital city. That fact isn't going to win any hearts and minds in Afghanistan. It means that we have a huge uphill battle if we want to convince the average citizen that we're there to help make Afghanistan into a freedom-loving democracy. We look like hypocrites because we are hypocrites.

Second, there is no law and order because the place is controlled by warlords and tribal rulers. If the average citizen doesn't feel secure on a daily basis then a few squads of well-equipped foreign troops zipping through town in their APC's isn't going to make them happy. We aren't fighting the warlords, we're supporting them. And the warlords aren't making the people secure. Is this a good idea? I don't think so.

Finally there's Pakistan. Unless Pakistan controls its borders there's very little we can do to stamp out the one faction of warlords that we've decided to attack. It's a hopeless battle.

Gannon doesn't think the situation is hopeless. She says,

"You have to make allies of the Afghans. You have to stop using a mixed mandate, doing reconstruction as well as an offensive. You have to have better intelligence so you can go after specific individuals."

And, she said, the Canadian forces in Kandahar should find out information on the whereabouts of Afghan prisoners removed by American forces from areas where the Canadians are now posted: that would win them "goodwill from the entire village," she said.

I agree that Canada should find out where the prisoners are and we should stop turning over any more of them to the Americans. It's the last thing we should do before withdrawing our troops. I don't think we can "make allies of the Afghans" at this time. We've had five years and we've blown any opportunity we had after 9/11. Let the Afghans sort out their own problems, if they can. They'll do a better job of it if we get out of their way.

Stealing Plants from the UBC Botanical Garden

 
This is a photograph of Fritillaria imperialis 'Rubra' from the Botany Photo of th Day blog at the University of British Columbia Botanical Gardens. Apparently the photo was taken some time ago because the curators now say that the gardens has only a single plant of this species. Or rather, had a single plant.

Last week it was stolen from the Botanical Gardens. Read the website for an impassioned defense of public gardens and why stealing plants is an ethical violation of a public trust.

There are three things that really disgust me about these thefts: the privatization of a public shared good, the potential impact on research projects in the garden and the loss of public investment. You'll have to excuse my language as I'm not fluent in the words to best express some of these concepts, but I'll explain as best I can.

Only in America

 
It's such a weird country. Americans have a constitutional right to shoot each other but not to universal health care or to marry someone you love if they're the same sex as you.

From ABC News...

Appeals court rejects D-C gun ban
March 09, 2007 14:00 EST

WASHINGTON (AP) -- A long-standing ban on handguns in Washington, D-C, is being overturned by a federal appeals court.

The court is rejecting the city's argument that the Second Amendment right to bear arms only applies to militias.

A lower-court judge had told six D-C residents three years ago that they don't have a constitutional right to own handguns. The plaintiffs include residents of high-crime neighborhoods who wanted the guns for protection.

In today's two-to-one decision, the judge held that the Second Amendment doesn't just apply to militia service, or to people with "intermittent enrollment in the militia."

Human MC1R Gene Controls Hair Color and Skin Color

 
The human MC1R gene encodes melanocortin 1 receptor, a protein found in the membranes of melanocytes. The human gene is orthologous to genes in other mammals that give rise to red coat color. For example, red hair in cattle, mice, guinea pig and horses (chestnut) are all due to variants in this gene.

It is thought that the receptor regulates production of the red melanin known as pheomelanin by stimulating cAMP production in response to the hormone α-MSH (melanocyte-stimulating hormone). Mutations in the gene show reduced levels of cAMP production in response to hormone and this may increase the amount of pheomelanin and reduce the levels of the brown form of melanin (eumelanin). Individuals carrying the variant gene will have fair skin containing pheomelanin as well as red hair and freckles. All three phenotyoes are due to the same variant, as is sensitivity to sunlight [OMIM 155555].

It is often thought that the red hair/fair skin/freckles phenotype is recessive but genotypes of people with these characters are often heterozygous, suggesting that it is inappropriate overproduction of pheomelanin, rather than underproduction of eumelanin, that is mainly responsible for the traits. (Gain-of-function mutations are often dominant.)

The gene (MC1R) is located on chromosome 16 at q24.3 [EntreGene="4157]. The gene is unusual because it does not contain introns and it has large 5ʹ and 3ʹ untranslated regions (UTRs).

There are over 30 known variants of this gene segregating in the human population. The variant responsible for red hair in the British population is a substitution of histidine for aspartate at amino acid 294 (D219H). This single amino acid substitution seems to account for all of the traits associated with red hair.

Human OCA2 Gene Is Responsible for Eye Color and Skin Color

 
Oculocutaneous albinism Type II [OMIN 203200] is a common type of albinism (especially in Africans). It characterized by loss of pigment-containing melanocytes in the skin. The genetic locus of this phenotype was localized to a single region on chromosome 15 and the gene was named OCA2 (oculocutaneous albinism Type II). See Beull's Blog; a blog written by a young man suffering from oculocutaneous albinism Type II.

The gene maps to 15q11-2-q12 and it has 24 small exons spread out over more than 350 kb (350,000 base pairs) [EntrezGene 4948]. The 836 aa coding region produces a protein called P protein, which has been localized to the membranes surrounding melanocytes.

The function of P protein is not well understood. It seems to play a role in the processing and trafficking of proteins that are localized to melanocytes. There is data to suggest an interaction with the melanocortin-1 receptor (MC1R OMIN 155555), a gene involved in the tanning response in fair skinned individuals. Whatever the exact role of P protein, it is clear that severe disruptions of OCA2 result in reduced numbers of melanocytes and low levels of melanin pigment in the skin.

The association between mutations in OCA2 and eye color has been known for some time. The human gene is the ortholog of the mouse pink-eyed (p) dilute gene. A gene scan for eye color variants in a Caucasian population from Brisbane, Australia revealed that 74% of eye color variablity localized to OCA2 (Zhu et al. 2004).

Duffy et al. (2007) examined the known variants of this gene. There are three dozen different alleles segregating in humans. Most of these have no effect on the amino acid sequence of the protein. Substitutions at amino acid 419 effect eye color: the present of glutamine 419Gln is strongly associated with green or hazel eyes. All other variants this position product brown eyes [OMIN 227220].

Blue eye color is associated with neutral mutations that map to the 5ʹ end of the gene suggesting that the actual change that gives rise to blue eyes is in the regulatory sequences that control expression of OCA2. The idea is that down regulation of P protein leads to reduced levels of melanin and this is what gives eyes a blue appearance (Strum and Frudakis, 2004).

The standard explanation for human eye color is based on a two-factor model (see The Genetics of Eye Color). We now know that this model is too simple. The main eye color gene (OCA2) has blue, green, and brown alleles but the expression of the corresponding phenotype is modified by a number of other genes.

Zhu, G., Evans, D.M., Duffy, D.L., Montgomery, G.W., Medland, S.E., Gillespie, N.A., Ewen, K.R., Jewell, M., Liew, Y.W., Hayward, N.K., Sturm, R.A., Trent, J.M., and Martin, N.G. (2004) A genome scan for eye color in 502 twin families: most variation is due to a QTL on chromosome 15q. Twin Res. 7:197-210. [free reprint]

Sturm, R.A. and Frudakis, T.N. (2004) Eye colour: portals into pigmentation genes and ancestry. Trends in Genetics 20: 327-332. [free reprint]

Duffy, D.L., Montgomery, G.W., Chen, W., Zhao, Z,Z,, Le, L., James, M.R., Hayward, N.K., Martin, N.G. and Sturm, R.A. (2007) A Three-Single-Nucleotide Polymorphism Haplotype in Intron 1 of OCA2 Explains Most Human Eye-Color Variation. The American Journal of Human Genetics 80: 241-252. [PubMed]

Cell Phones Can Cause Death in Hospitals

 
Friday's Urban Legend: FALSE

Hospital equipment unaffected by cell phone use, study finds

ROCHESTER, Minn. -- Calls made on cellular phones have no negative impact on hospital medical devices, dispelling the long-held notion that they are unsafe to use in health care facilities, according to Mayo Clinic researchers.

In a study published in the March issue of Mayo Clinic Proceedings, researchers say normal use of cell phones results in no noticeable interference with patient care equipment. Three hundred tests were performed over a five-month period in 2006, without a single problem incurred.

Involved in the study were two cellular phones which used different technologies from different carriers and 192 medical devices. Tests were performed at Mayo Clinic campus in Rochester.

The study’s authors say the findings should prompt hospitals to alter or abandon their bans on cell phone use. Mayo Clinic leaders are reviewing the facility’s cell phone ban because of the study’s findings, says David Hayes, M.D., of the Division of Cardiovascular Diseases and a study author.

Cell phone bans inconvenience patients and their families who must exit hospitals to place calls, the study’s authors say.

The latest study revisits two earlier studies that were done ‘in vitro’ (i.e., the equipment wasn’t connected to the patients), which also found minimal interaction from cell phones used in health care facilities. Dr. Hayes says the latest study bolsters the notion that cells phones are safe to use in hospitals.

PZ's Birthday Blogfest

 

Read all the birthday messages at A Blog Around the Clock, archy, and Living the Scientific Life (grrlscientist).

See PZ's response at Really, it's just the blink of an eye on a geological scale. Leave a message for him on that thread.

Have You Heard of Australia?

 
John Wilkins posted a comment on the thread about favorite countries. He said,

Nobody likes Australia, because nobody has ever heard of it. And that's just the way we like it. So don't spoil it, hey?

I take that as a challenge. I think there are lots of reasons for not liking Australia so I'm going to put it to the test. Anyone reading this post will have heard of Australia and I'm even showing you where it is on a world map (see below). Now let's see if people start liking Australia.

Why Children Love Their Security Blankets

 
A recent study examined Why Children Love Their Security Blankets. This is a subject most parents are familiar with and not just because of Linus. The photo on the left shows my daughter when she was much younger. She was trying to retrieve her pink blanket ("Cubby") after it had been washed and hung out to dry. The photo below is of my son showing off "Baba" after five years of continuous use—I think he still misses Baba. (There're probably going to kill me for posting these photos.)

The study asked whether children felt a special attachment to their favorite things ...

New research, published today in the international journal Cognition, suggests that this might be because children think the toy or blanket has a unique property or ‘essence’.

To support this theory, Professor Bruce Hood from the University of Bristol and his colleague Dr Paul Bloom of Yale University, USA, showed that 3-6 year-old children have a preference for their cherished items over apparently identical duplicates.

Children were introduced to a scientific looking machine that could copy any object but was in fact a conjurer’s cabinet where an accomplice inserted replica items from behind a screen.

Professor Hood said: “When offered the choice of originals and copies, children showed no preference for duplicates of their toys unless the object to be copied was the special one that they took to bed every night. A quarter of children refused to have their favourite object copied at all, and most of those who were persuaded to put their toy in the copying machine wanted the original back.”

Duh!

I have a favorite coffee mug, a favorite chair, a favorite shirt, a favorite pair of sunglasses, and a favorite blogger. I don't want no friggin' copies either and I wouldn't put any of those things in the copy machine. (Well, ... maybe I'd try putting PZ Myers in the copier, just to see what happens .... )

Security blankets and other things don't have any special "essence" that needs to be explained. Their unique property is their history. There's only one thing that was given to you by some special person and uniquely belongs to you. You can't copy that. Children aren't stupid. They know the difference between the original and some cheap copy.

This looks like the kind of study that discovered exactly what everyone expects but they have to hype the results in order to make it look exciting. Did anyone really think that my daughter or my son would have traded their very special blankets for a mere copy? How many of you have tried to con your kids when the security blanket got lost, as they invariably do? Didn't work, did it?

Don't anyone try and swap my coffee mug. If you break it, you die.

Happy Birthday PZ Myers

 
I don't remember exactly when I first encountered Paul Z. Myers, as he was known in those days. (Yes, I do know what the "Zed" stands for but I'm not telling.) I think it was in 1994, or possibly 1993. PZ was a brash youngster jumping into the maelstrom of talk.origins with both feet. It wasn't long before he established himself as one of the regular Howlers. I remember that he had a special fondness for Ed Conrad back in those days. Ed had just made an Earth shattering discovery—man was as old as coal—but Prof. Myers wasn't buying it.

I remember getting into a rather heated discussion about something or other in order to set PZ straight. That happened a lot back then. I suspect it was an attempt by me to correct his adaptationist tendencies. You wouldn't know it now but he was actually a fan of the Richard Dawkins version of evolution in the olden days.

Times have changed. And today he's 50 years young! Happy birthday PZ. (The photo was taken on the Sandwalk. That's not an outhouse we're sitting in. It's a small shelter at the end of the path leading directly from the base of the garden to just before it turns left into the woods.)

I looked for his earliest posting to talk.origins in order to present it to him and the blogger world, but I couldn't find it. The best I could do is this one from Oct. 1, 1997. You'll see that even though he was much younger then, he still had what it takes to explain complex ideas to the average reader—although he does seem to go on and on about this "pharyngula" thingy. It's a harbinger of what's coming when he sets up his blog.

... Raff is contradicting Richardson in a way. Raff says "all chordates ...pass through a pharyngula" while Richardson argues that "there is no highly conserved embryonic stage". My main beef with the Richardson article is not the bashing of Haeckel (he is actually quite reasonable in his comments on that matter), but that he is addressing a straw man. He disproves the *Haeckelian* version of a phylotypic stage, that is a stage when all vertebrates are virtually identical, but I don't consider that a viable possibility to begin with. In the quote above, Raff basically outlines the components of the phylotypic vertebrate: somites, pharyngeal arches, notochord, etc. It does not include specialized trophic structures, precise numbers of somites, or a specific size (when Collins published that nonsense claiming all vertebrates passed through a phylotypic stage when they reached the size of 7-8mm, I know of a few jaws that dropped...especially in the zebrafish community, where we work with an animal that doesn't exceed 3mm until it is well into post-hatching larval stages).

For a good example of the difference, look at Fig. 10 (the last one)in Richardson's paper. This is a set of drawings of the heads of various vertebrate embryos, drawn from photographs and far more accurate than Haeckel's stuff. Richardson's point with the figure is to say, "See how different all these animals are!", and yes, there are lots of superficial differences between the embryos.

When I saw that figure, though, my first thought was how much *ALIKE* they all were. All of them were unmistakeable chordates. All had pharyngeal arches, all had somites, all had that same general shape.

I've never seen Dr. Moran use subtlety in any way -- unless, perhaps, you consider public disembowelment a form of understatement?
Paul Z. Myers
July 10, 1997Richardson was also blurring the boundaries a bit himself. I found the comments about my favorite animal, the zebrafish, a bit troubling. He arbitrarily decided that the criterion for the phylotypic stage in fish was the tailbud stage, the time when the tail first extends off the yolk. This is a criterion that excludes comparison with the chick, for instance, and also causes serious problems for comparisons with teleosts. Zebrafish develop remarkably rapidly, and have a relatively small yolk. The tail buds early, well before the pharyngula stage. That means he looked at zebrafish at this stage and claimed they lacked branchial arches altogether! Just six hours later, though, this animal would have a very nice collection of pharyngeal structures. He has done this for all of these animals: defined some specific criterion for the phylotypic stage, looked at the animals at this one time point, and found variation in certain features. This is fine for demolishing the accuracy of Haeckel's figures. It is *not* good for revealing fundamental homologies between these animals. Chicks do not have just two pharyngeal arches, except at the particular stage Richardson restricted himself to. Zebrafish do not lack arches: they have a very lovely set of six pairs...just not at that one particular time.

He is perfectly correct in showing that the explicit similarities implied in Haeckel's drawings are false. However, note that he does not call Haeckel a fraud in that paper -- what he suggests is that Haeckel was drawing a *stylized* (his word) rendering of the animals. Haeckel was blurring together stages and features to try and put together a stylized composite...admittedly exaggerating and deleting features to fit his thesis. That was wrong. He was caught in it, too, over a hundred years ago.

I think, though, that Richardson has gone too far the other way. He seems to be demanding near-photographic resemblance at a single narrowly defined point in development. That is just too restrictive a demand, and conceals the underlying similarity. I can't think of a single vertebrate embryo that lacks pharyngeal arches; that's too important and universal a feature to deny its significance by saying they don't all have precisely five arches at the same time that they have a tailbud.

There is one final irritation in that paper. Richardson claims that the persistence of the 'myth' of the phylotypic stage is in part due to the fact that so few people actually look at comparative embryology. I would turn that around and accuse him of a rather narrow-minded perspective on comparative embryology. I've done a fair amount of vertebrate embryology, but I've also got several years of work in arthropod development, and have spent a fair amount of time studying marine biology. One reason I can look at Figure 10 and see the huge similarities is that I've also looked at insect and crustacean and annelid and mollusc and echinoderm embryos -- and boy, they don't look nothin' like those chordates at *any* time.

They Like Us, They Really Like Us!

 
BBC News has just published their World Service Poll.

The poll asked 28,000 people in 27 countries to rate a dozen countries plus the EU in terms of whether they have a positive or negative influence.

Canada, Japan and the EU are viewed most positively in the survey.

The competition wasn't too tough 'cause Australia wasn't even in the running. The battle between Canada and Japan was neck and neck until the last round when they counted the absentee ballots from Florida. There are a lot of Canadians in Florida at this time of year.

Canada and Japan had identical "mainly positive" votes but Canada wins first place because it had fewer "mainly negative votes." Tough luck, Japan, maybe next year.

The USA beat out North Korea, Iran, Venezuela, and Russia. Way to go USA! You're number 8! You're number 8!

Jennifer Smith Is Going to Meet Stéphane Dion

 
You remember Jennifer Smith, don't you? She lives in Milton, Ontario. That's the place made famous by PZ Myers 'cause he stopped for a few days to get his car fixed.

Well, it turns out that Jennifer went to a town hall meeting with her MP, the newly Liberalized Garth Turner. During the meeting she so impressed her MP that he invited her to meet with our future Prime Minister next week [All Politics Are Local]. (That's Dion in the picture, with his dog Kyoto.)

Hey, Jennifer, ask him if he'll increase reseach funding when we elect him next Fall.

The Low-Fat Diet Flunks Another Test

 
The title comes from an article by John Tierney on his blog [Tierney Lab: Putting Ideas in Science to the Test].

It's not really news. Low-fat diets have been challenged for years. There is good evidence that the Atkins diet really works for some people and it's healthy. Tierny gives us a quotation from a recent New York Times article that reported on a massive study recently completed.

The largest study ever to ask whether a low-fat diet reduces the risk of getting cancer or heart disease has found that the diet has no effect.

The $415 million federal study involved nearly 49,000 women ages 50 to 79 who were followed for eight years. In the end, those assigned to a low-fat diet had the same rates of breast cancer, colon cancer, heart attacks and strokes as those who ate whatever they pleased, researchers are reporting today.

‘’These studies are revolutionary,'’ said Dr. Jules Hirsch, physician in chief emeritus at Rockefeller University in New York City, who has spent a lifetime studying the effects of diets on weight and health. ‘’They should put a stop to this era of thinking that we have all the information we need to change the whole national diet and make everybody healthy.'’

All studies on human diets and nutrition are suspect, in my opinion. It's just the nature of the game. There are always contradictory results.

I'm not going to say that fat is never bad for you. What I say is that you should be skeptical about all claims concerning diet and health. They all need to be taken with a grain of salt (and a pound of steak ). Whenever you hear someone claiming to have all the answers you can dismiss them without a second thought. Nobody has the answers in this field, and that includes Professors, scientists, and physicians.

Intelligent Design Creationism and the History of Life

 
Denyse O'Leary repeats a common criticism of evolution over on Post-Darwinist [Response to student: Darwinian evolution not random?/ ID is God of the Gaps?].

On the face of it, Darwinian evolution is highly improbable or impossible on mathematical grounds. I mean that the history of complex life on earth (600 mya?) does not likely give us the resources we need for the random mutations. Once the Big Bang theory made it possible to establish an age for the universe (approx 13 bya) and the Earth (approx 4 bya), Darwinism was certain to come under attack.

600 million years is more than enough time for complex single-celled organisms to evolve mechanisms of associating to form complex multicellular organisms. This probability argument is just fancy hand-waving designed to impress the uninformed. (The fact that it's also made by the uninformed is ironic, but not surprising.)

But the real hypocrisy of the intelligent design creationist (IDC) community is in not coming up with a better explanation. Here's your big chance, Denyse. Why not give us a thumbnail sketch of how intelligent design creationism explains the fossil record of animals over the past 600 million years? While you're at it, you might throw in a brief description of how IDC accounts for the genetic data. You know, the genetic data that shows a perfectly reasonable rate of random mutations?

None of the IDiots have ever done this. They rant and rave about how improbable evolution is but they never give us an alternative that explains the facts. Why is that?

I'll make it real easy for you, Denyse. You don't have to explain everything. I'll be quite satisfied if the intelligent design creationists can give me their version of shark evolution. You can start with the separation of bony fish from cartilagenous fish about 450 million years ago. How did God do this? Why did He do it?

You can explain the appearance of Orthacanthus about 250 million years ago and why they look so similar to the species that lived a few million years earlier. Then you can tell us why God waited until 155 million years ago before creating the lamnoids that gave rise to modern looking sharks like the big white shark. Along the way, we eagerly await your explanation for why so many of those species are no longer with us. Did God get angry with them or does he just discard them as useless junk whenever He gets around to updating the latest model?

Here's a cladogram to help you out. When can we expect a response?

Science Blogging and Podcasts

 
Hsien Hsien Lei at Genetics & Health is experimenting with podcasts. She's figured out how to put a podcast on her blog. This is impressive. I haven't been able to do it ... yet.

See the result at Genetics and Health Podcast - Reflecting On My Role. I'm looking forward to more podcasts and to seeing how the experiment plays out.

UPDATE: I'm going to try and embed a podcast. Here's the Nature podcast from March 1, 2007 (I hope).


powered by ODEO

CBC

Canada .... hmmmm

 
You have to watch it right to the end ..... I don't know whether to laugh or cry (it's pretty funny).



[Hat Tip: Canadian Cynic]

Fairy Rings

 
I look at the botany photo of the day every day. This is a service provided by the Botanical Gardens at the University of British Columbia and I really appreciate their attempt to wean us away from animals.

Usually the photographs are spectacular closeup images taken with cameras that are much more expensive than mine. But yesteday's picture was from Google Earth! It shows 100 year old fairy rings near Kensington Palace in central London. The rings are probably caused by Marasmius oreades. Find out how a little fungus can make rings visible from so high.

Innocent Man Released from Jail

 
Mahmoud Jaballah is called a "terrorism suspect." He has been in jail for five years but he's never been found guilty of anything. That means he's an innocent man according to my sense of justice and he'll remain innocent until proven guilty.

Yesterday he learned that he will soon be released. Today's Toronto Star has the story [Terror suspect ordered freed].

Toronto terrorism suspect Mahmoud Jaballah will be released on strict bail conditions after more than five years in jail without charges, despite government protests he remains a danger to Canada.

His release comes on the heels of last month's Supreme Court ruling that struck down an immigration law as unconstitutional and deals another blow to the government's handling of security cases involving non-citizens.