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Saturday, September 22, 2007

Life in Modern Iraq.

Maclean's magazine has the story by Patrick Graham [How George Bush became the new Saddam].
It was embarrassing putting my flak jacket on backwards and sideways, but in the darkness of the Baghdad airport car park I couldn’t see anything. “Peterik, put the flak jacket on,” the South African security contractor was saying politely, impatiently. “You know the procedure if we are attacked.”

I didn’t. He explained. One of the chase vehicles would pull up beside us and someone would drag me out of the armoured car, away from the firing. If both drivers were unconscious—nice euphemism—he said I should try to run to the nearest army checkpoint. If the checkpoint was American, things might work out if they didn’t shoot first. If it was Iraqi . . . he didn’t elaborate.

Arriving in Baghdad has always been a little weird. Under Saddam Hussein it was like going into an orderly morgue; when he ran off after the U.S.-led invasion of March 2003 put an end to his Baathist party regime, the city became a chaotic mess. I lived in Iraq for almost two years, but after three years away I wasn’t quite ready for just how deserted and worn down the place seemed in the early evening. It was as if some kind of mildew was slowly rotting away at the edges of things, breaking down the city into urban compost.

[Hat Tip: Jennifer smith Best Cover. Ever]

Street Art


BigHeathenMike says this is the coolest street art he's ever seen[Wow]. Who could argue with that? Go to Mike's Weekly Skeptic Rant to find out where this drawing came from.

Friday, September 21, 2007

Avery, MacLeod and McCarty (1944)


This weeks classic on John Dennehy's blog is the famous Avery, MacLeod and McCarty (1944) paper [This Week's Citation Classic]. If you already know about this paper then wander on over to The Evolutionary Biologist whenever you get a chance and refresh your memory. If you don't know what the heck we're talking about then get your butt over there immediately and correct this major deficiency in your education!

Not only was Oswald Avery one of the greatest scientists of the modern era, he was also a Canadian!

What's She Holding in her Hand?

Check out Eva's blog easternblot for a cartoon she just posted [Scientist Illustration]. What is the scientist holding in her hand? Try and figure it out for yourself before reading Eva's answer.

Vote for MMP

Vote for MMP

I'm voting for the Mixed Member Proportional (MMP) electoral system on October 10th [Vote for MMP] [Mixed Member Proportional Electoral System].

See Bloggers for MMP for a complete list.

Thursday, September 20, 2007

Canadian Dollar = American Dollar

Today, for the first time in 30 years the value of the Canadian dollar (loonie) reached parity with the American dollar. It's big news in Canada. Most people think it's a good thing but it's not necessarily a good thing at all. A falling (collapsing?) US currency may be good for America and bad for Canada. [Click on the chart to enlarge.]

If you want to see one reason why this isn't good for Canadians see Jennifer Smith's posting The Parity Blues.

New Panda's Thumb

Check it out at Panda's Thumb.

A lot of people put a great deal of work into the upgrade but the person who deserves the most praise is Reed Cartwright of De Rurum Natura (and Panda's Thumb). You can thank him by going to Upgrade Starts Today.

In case you didn't know. The unofficial mascot at the Panda's Thumb is Prof. Steve Steve. Isn't he a handsome fellow? I think he's a biochemist—or possibly a paleontologist. I always get them mixed up.

Reed Cartwright is the father of Prof. Steve Steve. He's also the father of Prof. Steve Steve and Prof. Steve Steve. They have left home to gallivant around the world but they can often be found in North Carolina or Oakland CA.

There are quite a few bloggers on Panda's Thumb. I don't have a complete list but they include most of the leading lights in the fight against creationism in the USA. Some of them are adaptationists but don't let that deter you. It's good to hear what the other side has to say from time to time. (The adaptationists usually refer to the blog as Mt. Improbable. The unofficial mascot of the adaptationists is Prof. Dick Dick. )

If you aren't reading Panda's Thumb on a regular basis, now is a good time to start. There should be lots of postings as soon as the site is ready.

Mixed Member Proportional Electoral System

The people of Ontario will vote in a referendum on October 10th. The question on the ballot is whether to adopt a new voting mechanism called "Mixed Member Proportional." The new system is described on the government website [Ontario is facing a big decision].

Here's a brief summary of the new system.
If this system is accepted, Ontarians will have two votes in future elections: one for a ‘Local Member’ and one for a political party.

The provincial legislature would have 129 seats: Local Members’ would fill 90 seats while ‘List Members’ would fill 39 seats.

The political party with the largest number of seats in the legislature, including ‘Local Members’ and ‘List Members’, is asked to form a government.

In each electoral district, one vote would be used to elect a 'Local Member' using a First-Past-the-Post system. The candidate with the most votes in an electoral district wins.

The other vote would be for a political party. Votes for parties will be used to determine the number of 'List Members' each party gets. This is the proportional representation part.

If a political party is entitled to more seats than it won locally, 'List Members' are elected to make up the difference. 'List Members' can only be elected from a political party that received more than 3% of these votes.

In the end, a political party's overall share of seats will roughly equal its share of the total votes for parties in the province.

Anyone who meets the rules for eligibility can become a candidate for election as a ‘Local Member’. Some candidates are called “independents” while others represent a political party.

‘List Members’ are candidates from any registered political party. Before an election each political party prepares an ordered list of candidates they would like considered as ‘List Members’.

These lists, and the way they are created, would be made public well in advance of any election in a Mixed Member Proportional system.
I favor the new system because my vote will no longer be wasted if I don't like the candidate who is going to win in my riding. Furthermore, I like the idea that the new system will be more representative of the voters wishes. In many cases this will lead to minority governments and coalitions but that's what we want.

I also like the idea that members can be elected from the lists. While the fear is that this will favor party hacks, the fear is outweighed by the major benefit in my opinion. People who would be excellent additions to the legislature could be elected even if they are not good campaigners. Leaders and cabinet members/critics, if elected from the list, would not have to divide their time between government business and constituency business.

Perhaps some of you who have experienced this system first hand could comment on the benefits and drawbacks? In order to pass the referendum has to be accepted by 60 per cent of all votes cast across Ontario and 50 per cent or more of the ballots cast in at least 64 of 107 ridings. There's a poll running at Mixed Member Proportional. As of today the new system has 60% of the votes.

Calling All Adaptationists (Again)

Have I got a treat for you! Before getting to the special excitement, let me congratulate all of you adapationists for your outstanding performance in the last contest [Calling All Adaptationists]. You did a marvelous job of making up stories to explain homosexuality in humans. Rudyard Kipling would have been proud [Just-So Stories].

Your mission for today, should you choose to accept it, is to explain odorous urine (smelly pee).

Here's the data. Some people produce odorous urine when they eat asparagus. They can transform the chemical, asparagusic acid (1,2-dithiolane-4-carboxylic acid), into smelly compounds like methanethiol, dimethyl sulfide, dimethyl disulfide, bis(methylthio)methane, dimethyl sulfoxide, and dimethyl sulfone (Mitchell, 2001). Other people can eat asparagus 'till the cows come home and their urine remains as pleasantly smelling as usual. The allele for producing the smell is an autosomal dominant trait.

There's an additional complication. Some people can't smell the odorous urine. There's no linkage between excretors and perceivers (able to smell the urine). Some can excrete but not smell and some can excrete and smell. All permutations exist in the population.

This ability to excrete smelly compounds and the ability to smell them are both examples of visible phenotypes. They're not just some neutral variation hiding away in junk DNA. Therefore, many (most?) adaptationists will certainly insist that it has to have an adaptive role in human evolution.

This is untilled soil, as far as I can gather. For some reason the experts haven't published the explanation. At least there's nothing I could find after hunting on the internet. You could become famous if your story makes sense. Let's see what you can come up with. I'll get you started ....
Once upon a time there were naked hunter men running on the savannah while their gatherer wives collected asparagus in the deep water by the sea shore ....

Mitchell, S.C. (2001)
Food Idiosyncrasies: Beetroot and Asparagus. Drug Metabolism and Disposition 4(2):539-543.

Are These Dappers?

Is the first figure a dapper? How about the second figure? What about the third Figure, isn't he dapper in his nice suit?

Check out the definition of this new word from Ryan Gregory, Dog's Ass Plots (DAPs).

The Sun Revolves Around France

I thought the The View would take first prize when it comes to recent stupidity on TV but here's a contender. The contestant doesn't know whether the sun goes around the Earth or not so he polls the audience. 56% of them say yes.

The French accept evolution. Now we have to work on astronomy. I sure hope Phil Plait of Bad Astronomy doesn't see this.

[Hat Tip: Casey Luskin (really!) [The French Reject Prayer while Accepting Evolution and Geocentrism]]

Toronto Catholic District School Board Allows HPV Vaccine

In the fight against superstition there are good days and there are bad days. Today is one of the good days when the Toronto Catholic School Board rejected the advice of the Catholic bishops and decided to go ahead with the HPV vaccination program [Catholic trustees vote to allow HPV vaccine in schools].
TORONTO -- In a move keeping with their counterparts across the province, trustees at the Toronto Catholic District School Board overwhelmingly voted in favour of allowing public health nurses to administer the controversial HPV vaccine in its schools.

After a discussion that lasted more than 90 minutes, trustees voted 9-3 in favour of the motion, rightly putting the health of their daughters over morality, one trustee said.

"I sure don't want to know that the headlines in two decades will read 'Catholic women lead in deaths for cervical cancer,' " trustee Maria Rizzo said during a passionately delivered statement to the board.

"I have a 16-year-old daughter. I'm sorry she's not in Grade 8."

In a separate motion brought forward by Ms. Rizzo, the board also agreed to lobby other levels of government to expand the free vaccination program to all eligible women.

[Photo Credit: The photograph shows the Most Reverend James Wingle, D.D., Bishop of St. Catharines, President of the Ontario Conference of Catholic Bishops, whose advice was rejected by the Toronto Catholic School Borad.]

Evo-Devo: Innovation and Robustness in Evolution

When I first read the paper by Ciliberti et al. (2007) I was disappointed. On the surface, the paper seems to be addressing an important issue in evolutionary theory; namely, how can you get significant innovation in light of the fact that most biological systems resist change? On closer reading, however, it seemed more complicated than that. The authors were actually dealing with a phenomenum called "robustness." This is a popular description of a simple fact—the fact that many mutations are neutral so that there can be many variants of a protein that all carry out the same function. This has been known for decades.

The people who use the word "robustness" tend to elevate it to a level of significance that makes me nervous. Furthermore, they rarely use the term "random genetic drift" or "accident" in their papers, giving the impression that "robustness" is an adaptation that favors evolution.

There's much to criticize in the field of evolutionary developmental biology or evo-devo. Some of the "theories" are little more than wide-eyed speculation. I'm thinking particularly of The Plausibility of Life by Marc Kirschner and John Gehart.
Animal Chauvinism
That's one of the problems I have with this paper. The other problem is that it's a modeling paper. The authors create a model of evolution and demonstrate that their model produces systems that evolve. I have a problem with these models. While a mathematical model is useful to show that a mechanism can work, it does not prove that it does work.

Let me give a quick example to show you why I'm skeptical of claims by modelers. It is possible to model a Lamarckian process where species inherit acquired characteristics. The result will be evolution but that does not mean that the inheritance of acquired characteristics is a real mechanism of evolution. This point is not always made clearly in papers that describe mathematical models of evolution. To often, the fact that the model produces evolution is taken as evidence that the assumptions in the model are correct and it is an accurate representation of real biological evolution. This is the same problem with just-so stories [Just-So Stories].

Let's see how Ciliberti et al. (2007) set up their experiments in the introduction to the paper.
Biologists increasingly realize that genetic systems need to be robust to both genetic and nongenetic change (7–14). Robustness means that a system keeps performing its function in the face of perturbations. For example, many proteins can continue to catalyze chemical reactions, regulate transcription, communicate signals, and serve other roles despite mutations changing many amino acids; regulatory gene networks continue to function despite noisy expression of their constituent genes; embryos continue to develop normally even when faced with substantial environmental variation. Mutational robustness means that a system produces little phenotypic variation when subjected to genotypic variation caused by mutations. At first sight, such robustness might pose a problem for evolutionary innovation, because a robust system cannot produce much of the variation that can become the basis for evolutionary innovation.
The language sounds a little strange to me but I soon realized that there were many other authors who talked about "robustness" in this way. To me, the fact that there's neutral genetic variation in a population is just a natural consequence of chance mutation and random genetic drift. I don't see why biologists think that systems "need" to be robust and I don't see why the presence of neutral variation poses a "problem" for innovative change. It's perfectly acceptable to have beneficial mutations occurring on a background of neutral variation.

The "problem" seems to be more serious for evolutionary developmental (evo-devo) biologists than for others. It has given rise to much speculation about the evolution of evolvability. If you are interested in that sort of thing you should read the book The Plausibility of Life by Marc Kirschner and John Gelhart. (Warning, the contents may not be suitable for pluralists.)

The authors of the paper (Ciliberti et al.) claim that far from being a "problem" the existence of neutral variation is actually required for innovative evolution to occur.
As we shall see, there is some truth to this appearance, but it is in other respects flawed. Robustness and the ability to innovate cannot only coexist, but the first may be a precondition for the second.
This is pretty much where I stopped reading the first time. However, Michael White over on Adaptive Complexity has highlighted this paper in a posting put up yesterday [Evolution's Balancing Act]. This suggest that the paper resonates with some evolutionary biologists and piques my interest.

The paper describes a model of an evolutionary system. It happens to be gene regulatory networks but it could be just about anything. Ciliberti et al. (2007) show that if you have a single system with no variation then the possibility for innovative change is limited. On the other hand, if you have a robust system where there are many different variants—in different species—then there are more pathways to innovative change. Seems like a pretty trivial conclusion to me. It's the sort of thing Sewell Wright was talking about (Wright, 1932).
The course of evolution through the general field [adaptive landscape-LAM] is not controlled by direction of mutation and not directly by selection, except as conditions change, but by a trial and error mechanism consisting of a largely nonadaptive differentiation of local races (due to inbreeding and by occasional crossbreeding) and a determination of long time trend by intergroup selection.
The paper doesn't mention Wright, random genetic drift, or neutral mutations; although it does talk about neutral networks.

Instead, the paper seems to be fitting in with the evo-devo concepts of evolvability and facilitated variation. In other words the idea here seems to be getting very close to the concept that the variations in different species are selected because they increase the long term potential for innovative evolution. This is very different from what Wright was saying. He said—and I agree with him—that the variation is strictly accidental and just happens to provide potential for future evolution. The distinction is important for our understanding of evolution. Does evolution see into the future? Is there a hidden purpose?

Is "robustness" selected? I doubt that any of the authors would answer yes if the question was put directly but the paper certainly gives the impression that there's something positive going on. So does the description offered by Michael White when he says thing like,
Evolution carries out an incredibly tricky balancing act: the genetic program of a species has to be resistant to small changes, yet also susceptible to the adaptive remodeling of natural selection ....

So how does evolution maintain both stability and the potential for innovation?
This could be just metaphoric. The personification of "evolution" as acting to creat robustness may be excusable on that grounds. Nevertheless, a lot of this sort of language is creeping into the evo-devo literature and I wonder if it doesn't mean something more.

S. Ciliberti, s., Martin, O.C. and Wagner, A. (2007) Innovation and robustness in complex regulatory gene networks. Proc. Natl. Acad. Sci. (USA) 104:13591-13596. Abstract

Wright, S. (1932) The roles of mutation, selection, inbreeding, crossbreeding, and selection in evolution. Proc. VI Intl. Cong. Genet. 1:356-366.

Wednesday, September 19, 2007

Sherri Shepherd of The View Doesn't Believe in Evolution

The earlier clip showed that Sherri Shepherd doesn't know if the Earth is flat. Here's a longer version where she admits to not believing in evolution. Whoopi seems to have a problem with this. So do I. There's something about this video clip that's deeply disturbing.

Catholic Public Schools: Constitutional Right or Archaic Privilege

Come to the lecture [Centre for Inquiry]. Unfortunately, I'll be out of town but I'm counting on many of you to attend and tell me all about it.

Starts: Friday, September 21st at 7:00 pm
Ends: Friday, September 21st at 10:00 pm
Location: University of Toronto, MacLeod Auditorium (Room 2158), Medical Sciences Building, U of Toronto, 1 King's College Circle.



Why did the UN condemn Ontario twice for human rights violations?

Why are we spending $0.5 billion/year on a second educational bureaucracy?

Is it true public catholic schools have the right to fire a teacher who isn't catholic?

But aren't separate catholic schools guaranteed indefinitely in the constitution?

And doesn't multiculturalism mean the best solution is to religiously segregate?

Learn why a secular democracy SHOULD NOT publicly fund catholic or other faith based schools and how we can fix the current situation

University of Toronto, Fri, Sept 21, 7pm, MacLeod Auditorium (Room 2158),Medical Sciences Building, U of Toronto, 1 King's College Crl.

Jan Johnstone, Progressive trustees network and trustee for the Bluewater District School Board,
Co-sponsored by University of Toronto Secular Alliance

(also Tues, Sept 18 at U of Guelph and Tues, Sept 25 at Carleton U - see web calendar)

A member of the Green Party-strong one school system supporters-will speak at each event

Learn the truth behind the ongoing debate on the #1 provincial election issue of 2007!

Get your questions answered and engage in a public forum on this crucial issue.