Results of Junk DNA Poll

 
The poll is now closed and here are the final results (see sidebar on the left-hand side of this page). The question was "How much of our genome could be deleted without having any significant effect on our species?"

The results are surprising to me. I would have thought that a far higher percentage would have voted for 50% or more. As it turns out, half of you think that 50% of our genome is essential. That's not right.


Here's the plan. Over the next few days I'm going to try and post a bunch of articles on the composition of our genome. I'll try and explain why most of it is junk. Then I'll re-do the poll to see how many I've convinced to change their minds. Deal?

If anyone else wants to join in, send me the link to your posting and I'll put it on Sandwalk.

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We Hardly Knew Ye

 
Arthur Carty has been dismissed and he won't be replaced when he leaves on March 31.

I'll let that shocking news sink in for a minute or two ....

♪♪ ...musical interlude ..... ♪♪♪

So, are you properly outraged? No?

If you're like 99.99% 0f Canadians you probably didn't know that Arthur Carty is Canada's National Science Advisor. Probably 99% of Canadians didn't even know we had a National Science Advisor.

It really doesn't matter 'cause soon we won't have one. Stephan Harper is eliminating the office of National Science Advisor. Good riddance, I say. I've seen no evidence that our science advisor ever did anything so I'm not going to get too upset about this. Check out the website for the Office of the National Science Advisor. Boooooring ....

Does Canada need a National Science Advisor? No. We already have people who are well-placed to advise the government about science. The heads of the granting councils, for example (Canadian Institutes of Health Research, Natural Sciences and Engineering Research Council).

Of course, they haven't done a very good job either. The head of CIHR recently resigned after a couple of devastating grant competitions where the level of funding was far below what was necessary. Nevertheless, in an ideal world those are the people who should be advising the government on science policy.¹ It's not helpful to have a third party who has no chips on the table.

Lots of people disagree with me (). Over on Canadian Cynic LuLu thinks this is just a reflection of the science illiteracy of the Conservatives [Science? We don't need science.]. That's true but it's not going to be fixed by having a science advisor who hides out in the Department of Industry.

PZ Myers runs a little blog on the edge of Minnesota, near North Dakota, and a few miles south of Canada. He's secretly delighted that our Canadian Prime Minister is behaving as badly as George Bush [Congratulations Canada!]. I don't care. Our science advisor has only been around for three years but that's long enough to demonstrate that it's a useless job. I understand that Americans are upset about the demotion of their Presidential Science Adviser. I guess he was much more successful that Arthur Carty was in Canada. I dunno.

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1. Along with Presidents of scientific societies, Presidents of leading universities, prominent scientists and teachers, and taxi drivers.

[The title of this posting is from an old Irish anti-war song called Johnny I Hardly Knew ye. Check out this version on YouTube.]

Nobel Prizes by Country

 
The number of Nobel Laureates in each country is often a matter of some pride. More importantly, it is often used to bolster arguments about the quality of science in different countries. Recently, I saw a creationist use these numbers to support the claim that acceptance of evolution was irrelevant. According to this IDiot, the USA has the most Nobel Laureates in spite of the fact that 50% of the population don't believe in evolution. He was thinking that scientists who are Christians can be better than scientists who are not.

Here's the data in case anyone is interested. The total number of Nobel Laureates in the sciences is given in column two for each country. Only the top ten countires are listed. The third column gives the population in millions [List of countries by population]¹. The last column is the number of Nobel Laureates per million people.

As you can see, a couple of countries are punching way above their weight (Sweden and Switzerland). Several countries are way further down the list than they should be (Canada, Russia, Japan, China, India). The USA is not getting any more Nobel Prizes than its population warrants.

Country	Nobel Prizes	Popn	Ratio
United States	154	303	0.51
Germany	51	82	0.63
United Kingdom	48	61	0.79
France	20	64	0.31
Netherlands	11	16	0.69
Russia/USSR	11	141	0.08
Switzerland	10	8	1.25
Japan	8	128	0.06
Sweden	8	9	0.89
Canada	8	33	0.24

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1. The population numbers are from the last few years. Since the Nobel Laureates are from the past 100 years, you could argue that the ratios for Canada and the USA should be higher since their populations have grown a lot more than the populations of the European countries and Japan. This would be obvious if we normalized on the 1950 populations.

Intelligent Design Challenge

 
Calling all IDiots! This is your big chance to put your money where your mouth is. Take the Intelligent Design Challenge! on The Panda's Thumb and show us you can distinguish natural DNA from intelligently designed DNA.

If a real genuine IDiot wins the challenge, then in addition to the book prize I'll promise to stop using the word "IDiot" for one week!!

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1,2,3, What're We Fightin' For?

 
From The Independent (United Kingdom) [Sentenced to death: Afghan who dared to read about women's rights].

Everyone who supports Canada's role in Afghanistan should be very certain they know what kind of "freedom and democracy" we're supporting. The conclusion is obvious. It's time to cut and run and let the Afghans sort out things for themselves. We're not helping by choosing to support a government that; (a) can't control more than a tiny percentage of the country; and (b) shouldn't even be allowed to control that small bit. As for the rest of the country, we seem to be fightin' for warlords and the drug trade. Oh yeah, we also support Pakistan who allows a bunch of thugs to control 20% of the country where the meaning of "freedom" is very different from what we mean. [See the following links for other examples of rational thinking: This is what 77 Canadian lives buys]
Those who cannot remember the past are condemned to repeat it.

George Santayana (1905)

A young man, a student of journalism, is sentenced to death by an Islamic court for downloading a report from the internet. The sentence is then upheld by the country's rulers. This is Afghanistan – not in Taliban times but six years after "liberation" and under the democratic rule of the West's ally Hamid Karzai.

The fate of Sayed Pervez Kambaksh has led to domestic and international protests, and deepening concern about erosion of civil liberties in Afghanistan. He was accused of blasphemy after he downloaded a report from a Farsi website which stated that Muslim fundamentalists who claimed the Koran justified the oppression of women had misrepresented the views of the prophet Mohamed.

Mr Kambaksh, 23, distributed the tract to fellow students and teachers at Balkh University with the aim, he said, of provoking a debate on the matter. But a complaint was made against him and he was arrested, tried by religious judges without – say his friends and family – being allowed legal representation and sentenced to death.

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[Photo Credit: Reuters]
[Hat Tip: RichardDawkins.net]

Meet My Cousin!

 


Blue-eyed humans have a single, common ancestor

There's quite a resemblance, don't you think?

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Pictures Worth A Thousand Words

 
A few days ago Jennifer Smith over on Runesmith's Canadian Content reported that Stephan Harper has redecorated the lobbies behind the benches in Parliament. (It's the place where lobbyists used to hang out back in the olden days.) The full description can be found on the Green Party website [Model Parliament].

What may have been the most fascinating part of the afternoon was my time in the Government Lobby. Behind the curtains that run along the last row of benches on both sides of the House, are doors to long skinny living room areas. One is called the Opposition Lobby; the other the Government Lobby. In my pre-Green Party leader life, I have spent a lot of time in both. The Government Lobby was a frequent work space when I was Senior Policy Advisor to the federal Minister of Environment back in the mid-1980s. And I frequented both lobbies when I was with Sierra Club of Canada from 1987-2006. It did not strike me until I walked into the Government Lobby to await my turn as Speaker that I had not been in there since Stephen Harper became Prime Minister.

It used to have some paintings on the wall. Past prime ministers, certainly a formal portrait of the Queen. Landscapes. I know there was the occasional photo of current Prime Ministers, but when I walked in this time, I felt chilled to the bone. Every available wall space had a large colour photo of Stephen Harper. Stephen Harper at Alert. Stephen Harper in fire fighter gear. Stephen Harper at his desk. Stephen Harper meeting the Dalai Lama. Even the photo of the Queen showed her in the company of Stephen Harper. None were great photos. None were more than enlarged snapshots in colour. They didn’t feel like art.

Jennifer wrote to her MP, Garth Turner, to see if this was true and if someone could supply pictures. The title of her latest posting, Ask And You Shall Receive, tells it all.

Not only did Garth Turner MP take pictures, he posted them on his blog [Let me count the ways…]. Cool. I stole some of them so you can see what's become of our government.

We need to withdraw our troops from Afghanistan and send over Stephan Harper, permanently.

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Nobel Laureate: Bruce Merrifield

 

The Nobel Prize in Chemistry 1984.

"for his development of methodology for chemical synthesis on a solid matrix"



In 1984, Bruce Merrifield (1921 - 2006) was awarded the Nobel Prize in Chemistry for discovering a method of synthesizing polymers on a solid matrix. The technique laid the groundwork for the development of peptide and nucleotide synthesizers that are now common in biochemistry laboratories.

The presentation speech was delivered by Professor Bengt Lindberg of the Royal Academy of Sciences.
THEME:

Nobel Laureates

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen,

The chemical reactions which take place in living organisms are not spontaneous, but require the involvement of catalysts. These catalysts are called proteins and are composed of chains of amino acids called peptides. A number of hormones and other substances which regulate different life processes are also peptides. There are about 20 naturally occurring amino acids which are found in such peptides and since the chains can be very long, the number of possible variations is virtually unlimited.

Today we know the structures of a very large number of proteins and peptides. Important contributions to this area of knowledge were made by Fredrick Sanger, who received the Nobel prize in 1958, and Stanford Moore and William H. Stein, Nobel prizewinners in 1972. A very important contribution was also made by the Swedish researcher Per Edman, who unfortunately died relatively young and whose method for the controlled degradation of peptides is now generally used.

The chemical synthesis of peptides is an important task. The principle used in such synthesis is simple and was developed a relatively long time ago by Emil Fischer, who received a Nobel prize in 1902, although for completely different discoveries. Expressed simply, this principle involves the binding together of two amino acids which have been appropriately modified to give a dipeptide. This dipeptide is then combined with a third modified amino acid to give a tripeptide and so on.

Even if the principle is simple, in practice it is difficult to synthesize peptides, since a large number of individual steps is involved. After each step the desired product must be separated from by-products and unreacted starting material and this takes time and involves loss of the product. When Vincent du Vigneaud synthesized a peptide hormone, oxytocin, which is a nonapeptide, for the first time, this represented a great step forward which was rewarded with the Nobel prize for 1955. To use a similar approach for synthesizing a peptide containing 100 or more amino acid residues is truly a heroic task, requiring a very large amount of work and chemicals. This task can be compared to climbing a high mountain peak in the Himalayas, which begins with a large expedition carrying much equipment and ends, if all goes well, with a few lightly equipped alpinists reaching the top.

Therefore, Merrifield's development during the 1960's of a method for carrying out peptide synthesis on a solid matrix revolutionized the field. He attached the first amino acid to an insoluble polymer, a plastic material in the form of small spheres. Subsequently, the other amino acids were added one after one and only after the entire peptide chain had been synthesized was it released from the polymer. The advantages of this method are considerable. The complicated purification of the product after each synthetic step is replaced by simply washing the polymer to which the peptide is attached, so that loss of product is avoided completely. At the same time, the yield for each individual step is increased to 99.5% or better, a goal which cannot be achieved with conventional methods, but which is extremely important in syntheses involving a large number of steps. Finally, this method can be automated and automatic peptide synthesizers are now commercially available.

Thousands of different peptides of different sizes, as well as proteins, peptide hormones and analogues of these compounds have now been synthesized using this method. One milestone in this respect was the synthesis of an active enzyme, ribonuclease, containing 124 amino acid residues, by Merrifield and his coworkers.

The approach of performing a multistep synthesis with a compound attached to a solid matrix as the starting material has also been used in other areas. The most important of these is undoubtedly the synthesis of oligonucleotides, which are needed in hybrid DNA research. In this case as well an automated apparatus which can be programmed to synthesize desired products has been constructed. Although Merrifield has not worked in this area himself, it is clearly his ideas which have found a new application here.

Professor Merrifield,

Your methodology for chemical synthesis on a solid matrix is a completely new approach to organic synthesis. It has created new possibilities in the fields of peptide-protein and nucleic acid chemistry. It has greatly stimulated progress in biochemistry, molecular biology, medicine and pharmacology. It is also of great practical importance, both for the development of new drugs and for gene technology.

On behalf of the Royal Swedish Academy of Sciences I wish to convey our warmest congratulations and ask you to receive your prize from the hands of His Majesty the King.

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Sophophora, the New Model Organism

 
Meet Sophophora melanogaster. It has some major advantages as a model organism. The genome is small and there are only four chromosomes; there are thousands of well-characterized genetic markers; the genome sequence is known; developmental pathways have been worked out; it has a short life cycle.

In summary, it has all the advantages of Drosophila melanogaster. In fact, it is Drosophila melanogaster.

The latest studies show conclusively that the genus Drosophila is paraphyletic. Many of the 1500 species cluster with flies from other genera rather than with those in Drosophila. This will prompt a renaming since taxonomists these days are mostly cladists—as they should be.

The type species for the genus Drosohila is Drosophila funebris. Unfortunately, Drosophila melanogaster is not very closely related so its genus name has to be changed. The new name is Sophophora melanogaster. Read all about it on Catalogue of Organisms [Drosophila forever?M].

Now if they could only get around to changing Caenorhabditis and Saccharomyces, we'd all be much happier .....

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Mike Huckabee Says "It's Just a Theory"

 
This is a video from several years ago when Mike Huckabee was Governor of Arkansas. Here's the description on YouTube.

A young Arkansan asks Mike Huckabee what should be done about schools not teaching evolution properly. The former governor then advocates what the student has already said was against state standards...that schools should teach creationism because evolution's only a theory.

Huckabee is entitled to his opinion about creationism, of course, but what troubles me is his statement that evolution is only a theory. Most of us don't (usually) make statements about things that we know nothing about. I can't believe that Huckabee is completely ignorant about the basic facts of biology. Somebody must have told him at some time during his life that evolution is overwhelmingly supported by solid scientific evidence.

What is it about IDiots that makes them so immune to rationalism? Why aren't people like Huckabee challenged when they lie? Is it because it's not polite?

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Learning About Evolutionary Theory

 
There seems to be a bit of a trend over on ScienceBlogs^TM. First Razib decides that it's finally time to read The Structure of Evolutionary Theory, then John Lynch figures he should too. And now Laelaps gets into the act.

I have long maintained that you can't have a serious discussion about evolutionary theory until you've read Gould's tome. You don't have to agree with him but at the very least you have to understand the arguments and there's no better way to do it than by reading all 1432 pages. Take lots of notes. Write in the margins. Use a highlighter.

There are several things you need to get out of this book. First, Charles Darwin Was a Gradualist. Second, try to understand punctuated equilibria. Don't just assume that you know what it is. Listen to Gould explain it in his own words. An open mind helps. Third, understand what Gould means when he talks about hierarchical theory. Fourth, pay attention to the description of species sorting. Don't read your own biases into the concept.

Enjoy. It's worth the effort.

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Warning: The Structure of Evolutionary Theory is written at a very high level. It's not for high school students. If the language and style turns you off then maybe it's not for you. Try Dawkins or Dennett. Their version of evolutionary theory can be understood by 5th graders.

Who Accepts Evoluton?

 
Half Sigma has posted an interesting article on the results of a 2006 poll about evolution. The survey asked the following question:

Now, I would like to ask you a few short questions like those you might see on a television game show. For each statement that I read, please tell me if it is true or false. If you don't know or aren't sure, just tell me so, and we will skip to the next question. Remember true, false, or don't know. i. Human beings, as we know them today, developed from earlier species of animals. (Is that true or false?)

The overall results are not surprising. They have been discussed before. About 50% of Americans accept the fact of evolution and about 50% reject scientific facts.

The fun part comes when Half Sigma looks at a breakdown of the responses. Men are smarter more likely to accept evolution than women. In New England, 78% accept evoluton while in the states of Kentucky, Tennessee, Alabama, and Mississippi this falls to 32%. This is pretty much as we expect.

The interesting piece of information comes from analysis of the responses of difference races imaginary subgroups.

71% of blacks (Afro-Americans?) reject science. That's much higher than I imagined. What accounts for such a high percentage of IDiots in that subgroup? Is it true that Afro-Americans are much more religious than other groups? Is that why they reject evolution? Or is it a lack of decent science education in those states?

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[Hat Tip: Gene Expression]

Famous Psychic Nikki Predicted Heath Ledger's Death

 
This is Earth-shattering news. If you go to the website of Nikki (psychic to the stars) you'll see that she predicted Heath Ledger's death [Nikki: Predictions].

Death Watch and Health Watch

Annette Funicello, Hillary Clinton, Doris Day, Willie Nelson, Pamela Lee Anderson, Loretta Lynn, Ted Kennedy, Unice Shriver, Fidel Castro, Hugo Chavez, Benazir Bhutto, President Masharaff, Billy Graham, Jerry Lewis, Chareleton Heston, Tony Curtis, Debbie Reynolds, Heath Ledger, Barack Obama, Zsa Zsa Gabor, Nelson Mandela, Farah Fawcett, Nancy Reagan, Dick Cheney, Dick Clark, Elizabeth Taylor, Larry King, Suzanne Pleshette, Mick Jagger, Arnold Schwarzeneger, Kirk Douglas, Hugh Hefner, Shirley Temple Black, Alex Trebek, and French President Sarkozy.

To find out why this isn't the end of rationality and the triumph of superstition, check out Way of the Woo. The surprise isn't that Nikki is a liar, it's that so many people fall for it.

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Showing Respect

 
I couldn't resist copying this cartoon from Friendly Atheist [Lack of Respect]. It's by Don Addis. Hemant Mehta got it from Freethought Today.

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Getting Into Graduate School

 
Julianne Dalcanton is an astronomy professor at the University of Washington. She works on the evolution of galaxies which is sort of like real evolution, but not quite. She blogs at Cosmic Variance.

Julianne decided to enlighten students about the process of getting into graduate school [The Other Side of Graduate Admissions]. It's a very informative posting and I recommend it to anyone who will be applying to graduate school next year, or who is waiting to hear right now.

I think it's really important to give undergraduates the straight dope about getting into graduate school. It's not about grades, as Julianne says. It's about the complete package. In our department we look at five things and each one is important.

1. Grades in undergraduate courses: If your grades are below a minimum value you will need to have something extraordinary to compensate. If grades are too low then nothing will help you. Just because you have high grades doesn't mean you will be admitted.


2. Reference letters: This is much more important than you think. If you don't have good letters then your chances of being admitted are slim. If the letters say that you are passionately interested in becoming a physician but you'll seriously consider graduate school if you don't get into medical school, then you've got a problem. The letters need to tell us that science is your primary objective in life.


3. Courses: You should have taken the right undergraduate courses to prepare you for graduate school. What this means is that you need to have a number of upper level (4th year) courses in the field you're applying to. In some cases, your undergraduate studies may have been in a related field but you still need to demonstrate that you can handle the most difficult undergraduate courses. That means you're ready for graduate school. This can be a problem in our system here at the University of Toronto because we allow student to graduate with a B.Sc. even if they have only taken a few 400-level courses. Those students may not be acceptable candidates for some graduate schools.


4. Research Experience: We look for students who have already demonstrated that they can work in a laboratory. They will have completed a research project in their final year and they will have worked in research labs during the summer. They will have glowing letters from their research supervisors.


5. Motivation/Enthusiasm: This will come out in your letters of reference and in the choices you have made as an undergraduate. In some cases, we will conduct an interview to determine whether you are a suitable candidate for graduate school. We look for students who really want a career in science or who really want to learn more about science at an advanced level in order to pursue a related career (e.g., teaching). Remember, we're not interested in students who are picking graduate school as their second choice.

It's not as bad as it might seem to get an offer of admission. In our department we get about 135 applications in a typical year and we make offers to about 70 of the applicants for a success rate of 52%. About 30 students end up joining our graduate program because most students have multiple offers.

The best advice I can give undergraduates is to apply to many graduate schools in several different countries. If I recall correctly, I applied to 18 graduate departments and got five acceptances. This is not unusual.

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[Photo Credit: Graduate students in the Department of Biochemistry 2007-2008.]