Sandwalk: February 2009

Saturday, February 28, 2009

United Kingdom Protects Science Budget

From NatureNews: Brown pledges to protect science during downturn.

British Prime Minister Gordon Brown said he would not let science "become a victim of the recession" in a speech today at the University of Oxford.

Speaking to an invited audience, Brown said he would defend investment in science by maintaining the ring fence around the science budget, so that it cannot be raided to prop up other areas competing for public funds such as the health service and industry.

He signalled his aim for Britain to move away from an economy "heavily centred" on financial services and towards one focused on science.

....

Responding to Brown's speech, Nick Dusic, director of the Campaign for Science & Engineering in the UK (CaSE), a London-based lobby group says, "The prime minister is absolutely right that now is the time to show the world the UK is the place to do science. Unfortunately he needed to go further today in his commitments because other countries are raising the bar by making science and engineering central to their economic recovery."

Dusic added that just maintaining current spending commitments will mean that Britain loses ground against countries, like the United States, that are giving science a huge boost within their stimulus packages.

Meanwhile, Stephen Harper and the Conservative Party are cutting the budgets of the major granting agencies in Canada.

How stupid is that?

Have You Been Scammed by Nigerians? Get Compensation!!!

Jim Lippard alerts us to the Best Nigerian 419 scam ever.

I think he might be right, but the competition isn't that tough.

Friday, February 27, 2009

Crime and Punishment

True to their ideology, Stephen Harper and the Conservatives have introduced another "get tough on crime" bill. This one increases the jail sentences for gang-related killings.

There's only one problem. It won't work. Everyone with an IQ over 100 knows that you can't stop gang violence by just increasing prison terms for the ones who get caught.

Today's Toronto Star has two articles on the topic. The first one, Tory gang approach too little too late: critics, explains the consensus opinion of leading criminologists.

The punitive response may play well to citizens who fear gun battles erupting on city streets. But that get-tough approach lards the Criminal Code with redundant laws that haven't worked in other countries, says criminologist Irvin Waller.

"This is yet again a debate about penalties when it's very clear from looking south of the border that these penalties do not make a lot of difference to the number of people killed," he said.

"It's not a debate about what will actually stop them from happening."

Waller, a professor at the University of Ottawa, wrote the book Less Law, More Order to educate politicians on prevention and smart policing practices that have worked in other countries.

The second article, Critics say more jail time won't help curb violence, goes into more detail about what the experts are saying.

Criminologists predict tough sentences won't be effective in preventing gun and gang violence

Proposals to slap first-degree murder charges and tougher sentences on gangsters and police assailants will have little practical effect on curbing gang crime and gun violence, criminologists and other critics say.

More front-line officers, more intrusive investigative police powers and more resources for crime prevention are needed, they say.

Ross Hastings, director of the Institute for the Prevention of Crime at the University of Ottawa, joins other criminologists in arguing there is no evidence tougher sentences deter criminals, but the "certainty of being caught" is more likely to do so.

Nonetheless, amid an alarming rise in Vancouver's gang violence, politicians of all stripes rushed yesterday to endorse federal proposals to label gang killings first-degree murder offences, and to stiffen jail terms for drive-by or reckless gang-motivated shootings and assaults on police.

All three federal opposition parties promised to fast-track the measures proposed by the Tories.

I'm disappointed in all four political parties. Most of our MP's have IQ's above 100 and they know the rational response to gang violence. They know that this bill will be completely ineffective.

The only reason for supporting it is to pander to voters who don't understand the problem. There are far too many voters whose knee-jerk reaction in the face of any crime is to call for "justice" by increasing jail time. A majority of those voters probably support the Conservatives so there's nothing to be gained by the opposition parties' lack of fortitude.

Shame on Stephen Harper for his (probable) hypocrisy. Shame on Michael Ingatieff, Jack Layton, and Gilles Duceppe for being even more hypocritical. They should know better.

Darwin Stamps

A few days ago I got a letter from the Royal Mail. It was a complete set of Darwin stamps issued by the Royal Mail in the UK to honour Charles Darwin. You can see some of them on the right. They are stunning. Thank-you Ms. Sandwalk for arranging to have them sent.

I also got a postcard from Kate. She mailed it from London on Darwin's birthday. It was addressed to someone called "The Nutty Professor" but for some strange reason it ended up in my mailbox anyway. Thank-you Kate & Mick.

Great Britain, especially London, was the intellectual capital of the world back in Queen Victoria's time. Most of the world's top scientists were there and the number of scientific advances that came out of that environment was truly amazing.

Much of it was due to the wealth of the British Empire (science loves money) but also to the intellectual freedom, individualism, and entrepreneurship that was characteristic of that society. It was the same society that created the industrial revolution and sustained it for one hundred years.¹

What's amazing is that not only did Victorian England nurture and support men like Charles Darwin but that today, 150 years later, Great Britain is still proud to celebrate the scientist whose name is most closely associated with evolution.

1. Eat your heart out, Ken Miller (Only a Theory). :-)

Matt Nisbet Chooses Sides

Carl Zimmer has posted another article on the Geroge Will affair [Unchecked Ice: A Saga in Five Chapters]. Recall that George Will made a number of scientifically inaccurate comments in his Washington Post article last week. He defends himself in another column today.

Carl dissects the issue in order to set the record, straight. Any decent science journalist should be concerned about accuracy and I'm pleased that Carl has made an effort to stand up for the truth. The Washington Post takes the brunt of the blame.

What has kept me hooked on this saga is not George Will’s errors. Errors are as common as grass. Some are made out of ignorance, some carefully constructed to give a misleading impression. What has kept me agog is the way the editors at the Washington Post have actually given their stamp of approval on Will’s columns, even claiming to have fact-checked them and seeing no need for a single correction.

Chris Mooney has also attacked the newspaper for it's lack of integrity [George Will Lies; His Editor Does Nothing].

Many of the column's incorrect factual assertions were challenged, and as Will is revisiting the column due to the response it has garnered, it's inconceivable that he doesn't know that. For God's sake, Will claimed that "according to the U.N. World Meteorological Organization, there has been no recorded global warming for more than a decade." That's false. And Will doesn't even address the issue at all in his latest column.

Meanwhile, the Post's editorial page editor Fred Hiatt has made himself look terrible over all this. He should have held Will to the truth and thereby upheld his paper's standards. Instead he tells CJR this:
"It may well be that he is drawing inferences from data that most scientists reject -- so, you know, fine, I welcome anyone to make that point. But don't make it by suggesting that George Will shouldn't be allowed to make the contrary point. Debate him."

All of this is good. It is highly appropriate that science journalists reestablish their credibility by criticizing amateurs who don't know what they're talking about.

Where is Matt Nisbet in all of this? Here's what Nisbet says in In the Clamor Over George Will, Pundits Win But Public Loses.

The same observation currently applies to the clamor over George Will's recent syndicated column on global warming. As I detail in a cover article at the March/April issue of the journal Environment, Will's column is part of a decade-old message playbook on climate change, effectively (and falsely) framing the problem in terms of lingering scientific uncertainty.

The irony of this latest netroots clamor is that dozens of bloggers are just feeding the George Will beast, sustaining and amplifying attention to his false claims about climate science while providing easy cues to the public that the issue can be readily interpreted through the lens of partisanship and ideology. (Sound familiar? As I wrote at Skeptical Inquirer, the same thing happened in the initial response to Ben Stein's anti-evolution doc Expelled.)

The conflict and heat generated not only focuses more attention on Will's preferred uncertainty interpretations, but it also distracts from the narratives and frames that are actually likely to build broad-based support for action. As I note in the Environment article, these frames include an emphasis on the moral and religious imperative to action along with a focus on the public health and energy innovation dimensions of climate change.

Over the past two years, many of us have been pointing out the conflict between "framing" and scientific accuracy. Now Nisbet makes it perfectly clear. If you criticize the scientific accuracy of an article in the main stream media then you might be hurting the cause.

The implication is that you should let scientific errors go unchallenged because challenging them give them credence. The more insidious implication is that scientific inaccuracy may be okay as long as it advances the cause.

It seems to me that Nisbet's view and Chris Mooney's recent claims are not compatible. I look forward to seeing how Mooney replies to Nisbet. Chris has already tried to distance himself from Nisbet last Spring over the Ben Stein affair [see For Once, Chris Mooney Talks Sense].

Internecine framing wars, what could be more fun than that?

The Atheist Ad Campaign on The Agenda

TV Ontario (TVO) has a daily program called The Agenda with Steve Paikin. It's usually very good.

Last week they had a show on the atheist bus campaign featuring Justin Trottier of the Center for Inquiry and Robert Buckman, a well-known Toronto atheist. Here's the entire show. I don't think any one of the participants is particularly proud of their performance. But see below ....

At one point in the show, the Christian woman, Kathy Shaidle, brings up the "Stalin, the atheist, killed 30 million people (therefore God exists)" argument and Robert Buckman tries to answer in a reasonable manner. He doesn't do a bad job (excerpt below) but Canadian Cynic has a suggestion: What Robert Buckman should have said.

I caution Sandwalk readers that CC's language can be a bit crude ... but it sure is funny.

Thursday, February 26, 2009

Nobel Laureate: Kary Mullis

The Nobel Prize in Chemistry 1993.

"for contributions to the developments of methods within DNA-based chemistry: for his invention of the polymerase chain reaction (PCR) method"

Kary B. Mullis (1944 - ) won the Nobel Prize in Chemistry for the polymerase chain reaction technique. This technique is used to amplify a given stretch of DNA by repeatedly copying it several dozen times. The technique has been honed and modified and it's now a standard tool in every biochemistry and molecular biology laboratory.

Mullis shared the prize with last week's Nobel Laureate, Michael Smith, who developed the technique of in vitro mutagenesis. I'm not a big fan of awarding Nobel Prizes to those who develop a new technique. I'm much more comfortable with awards to scientists who directly advance our understanding of how life works. That's why my personal favorites are Nobel Laureates like Jacques Monod, François Jacob, Ed Lewis, Otto Warburg, Linus Pauling, André Lwoff, Barbara McClintock, and Peter Mitchell (plus many others).

Fortunately, it usually turns out that the winners of "technology" prizes are very good scientists who have also made a significant contribution to advancing our knowledge of fundamental concepts. That's certainly true of Michael Smith, Walter Gilbert, and Fred Sanger, to name just a few.

Kary Mullis was an unusual recipient in many ways. You can get a flavor for his personality by reading his Autobiography and, especially, his Nobel Lecture. There has never been a speech like that in the history of the Nobel Prize and, chances are, there will never be another.

Read about Kary Mullis on Wikipedia to see what he's been up to since he stopped being an active scientist in 1988. By the time he was awarded the Nobel Prize he was concentrating on being a writer. (This might explain the speech!)

Here's the Press Release describing Kary Mullis' contribution.

THEME:
Nobel Laureates

The "Polymerase Chain Reaction" (PCR)

The PCR technique was first presented as recently as 1985 but is nevertheless already one of the most widespread methods of analysing DNA. With PCR it is possible to replicate several million times, in a test tube, an individual DNA segment of a complicated genetic material. Mullis has described how he got the idea for the PCR during a night drive in the Californian mountains. Two short oligonucleotides are synthesized so that they are bound correctly to opposite strands of the DNA segment it is wished to replicate. At the points of contact an added enzyme (DNA polymerase) can start to read off the genetic code and link code words through which two new double strands of DNA are formed. The sample is then heated, which makes the strands separate so that they can be read off again. The procedure is then repeated time after time, doubling at each step the number of copies of the desired DNA segment. Through such repetitive cycles it is possible to obtain millions of copies of the desired DNA segment within a few hours. The procedure is very simple, requiring in theory only a test tube and some heat sources, even though there are now commercial PCR apparatuses that manage the whole procedure automatically and with great precision.

The PCR method can be used for reduplicating a segment of a DNA molecule, e.g. from a blood sample. The procedure is repeated 20-60 times, which can give millions of DNA copies in a few hours.

As has site-directed mutagenesis, the PCR method has decisively improved the outlook for basic research. The sequencing and cloning of genes has been appreciably simplified. PCR has also made Smith's method of site-directed mutagenesis more efficient. Since it is possible with PCR to perform analyses on extremely small amounts of material, it is easy to determine genetic and evolutionary connections between different species. It is very probable that PCR combined with DNA sequencing is going to represent a revolutionary new instrument for studies of the systematics of plant and animal species.

The biomedical applications of the PCR method are already legion. Now that it is possible to discover very small amounts of foreign DNA in an organism, viral and bacterial infections can be diagnosed without the time-consuming culture of microorganisms from patient samples. PCR is now being used, for example, to discover HIV infections. The method can also be exploited to localise the genetic alterations underlying hereditary diseases. Thus PCR, like site-directed mutagenesis, has a great potential within gene therapy. Without the PCR method, the HUGO project, with its objective of determining every single DNA code in, among other things, the human genetic material, would hardly be realistic. In police investigations PCR can give decisive information since it is now possible to analyse the DNA in a single drop of blood or in a hair found at the scene of a crime.

Another fantastic application is that it is possible to mass-produce DNA from fossil remains. Researchers have, for example, succeeded in producing genetic material from insects that have been extinct for more than 20 million years by using the PCR method on DNA extracted from amber. This possibility has already inspired authors of science fiction. The very popular film "Jurassic Park" is about the fear that arises when researchers using PCR recreate extinct giant reptiles.

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

[Photo Credit: Geschichte der PCR]

Congratulations Carl Zimmer

It's often said that "real" science journalists are passionate about presenting accurate science [see Chris Mooney].

Strangely, in spite of this passion, they've tended to remain very silent when a major newspaper publishes inaccurate scientific information—at least in the fields I'm interested in.

That changed a little bit with the George Will affair in the past week. George Will is a Pulitzer Roze winning journalist (not a science journalist). He wrote about global climate change in The Washington Post. Apparently there's another piece in the press.

Carl Zimmer takes him on: George Will: Locked In Ice!. Congratulations Carl! This is why you are one of the best science journalists.

Teaching the Controversy: Astrology & Genesis

Here's how Neil deGrasse Tyson teaches us about astrology. The idea is to get people to realize that astrology is bunk.

My daughter's teacher (with an M.Sc. in chemistry) used this technique on her Grade 5 class. I dare say it did some good in promoting critical thinking.

Why can't we do the same with some other pseudoscience topics, like Young Earth Creationism? Why can't we teach critical thinking by getting young students to think about the consequences of a deluge that wiped out all of humanity in 2600 BC?¹ They could discuss why the Egyptian records failed to notice that every single Egyptian lost their life sometime during the third dynasty when the pyramids were being built. They could do a simple calculation to see how you get from Noah and his family to 45 million people in the Roman Empire. (And possibly 300 million people in the world at about the time when Julius Caesar was born.)

Why can't we do that? Because religion has special protection from this kind of critical analysis. You can attack astrology but you can't attack anything religious no matter how silly it might be.

We should try and change that. Let's have more classroom discussion about the conflict between science and some religious beliefs. The well known seminar by Ricky Gervais (below) shows how you could do it. It should be required viewing in all Grade 5 classrooms!

1. They could also think about the kind of God who would do this.

[Hat Tip: Friendly Atheist: The Quick Astrology Test]

It's Good to Blog

Today's editorial in Nature declares, It's good to blog.

Indeed, researchers would do well to blog more than they do. The experience of journals such as Cell and PLoS ONE, which allow people to comment on papers online, suggests that researchers are very reluctant to engage in such forums. But the blogosphere tends to be less inhibited, and technical discussions there seem likely to increase.

Moreover, there are societal debates that have much to gain from the uncensored voices of researchers. A good blogging website consumes much of the spare time of the one or several fully committed scientists that write and moderate it. But it can make a difference to the quality and integrity of public discussion.

[Hat Tip: Chance and Necessity]

Is the bus ad campaign working?

The atheist bus campaign is being run and organized by a small group of individuals who have put a lot or work into it. Most of them are members of Freethought Association of Canada whose President is Justin Trottier.

I support the campaign to put atheist ads on city buses for the following reasons.

It supports other atheists and encourages them to "come out of the closet" and discuss their atheism openly.
It stimulates debate and discussion within our society, often raising questions that many have never seriously considered.
For those who get it, it injects a welcome note of humor into a subject that really needs it.

The campaign will be a success if it attracts attention and gets people talking about rationalism and superstition. That discussion has already been kick-started by several best-selling books in the past few years and this ad campaign will keep the discussion going.

Up until recently, atheism was rarely mentioned in the main stream media and atheists were never interviewed on television. All that has changed in recent years and now you can hardly do a story on religion without getting the "other side." That's remarkable progress in a very short period of time. Today, it looks like more that 20% of Canadians are atheists and that number is growing rapidly in spite of what religious leaders might tell you.

Here's an example of what I'm talking about. The atheist bus campaign is worried because Global TV calls Atheists ‘Fanatics’?, but that's missing the point. The point is that a show like this would have been unheard of ten years ago. Look at how Christian, Muslim, and Jewish leaders are now obliged to defend their belief in God.

There's a remarkable segment in this video beginning at 4:30. The head of Toronto's Transit Commission is asked whether the TTC would approve some religious ads written up by the host of the TV show. The TTC head says, "These, would be more than welcome." That's the correct answer. Game on.

Atheist bus ads are up and running in Toronto

I'm told that buses with the atheist ads are on the streets of Toronto, although I haven't seen one yet. If you spot one, you are asked to take a photo and post it on the official website of the Canadian Atheist Bus Campaign [Photos of the Atheist Bus ads in Toronto].

I'm pleased to report that so far there haven't been any reports of people fainting in the street and crime levels have remained steady in spite of the threat to Toronto's morals.

Meanwhile, the ads have been turned down in Ottawa and Halifax. We're waiting to hear from Calgary. Check atheistbus.ca for the latest updates. While you're there, donate some money to the cause. I gave them $100 and that's just a beginning. The campaign has raised $45,500 so far.

Click on the image below to see the fine print. It says "www.atheistbus.ca This advert was paid for by public donations." I'm really proud of the fact that the Canadian campaign doesn't shy away from using the word "atheist." After all, that's what it's all about.

Wednesday, February 25, 2009

Monday's Molecule #109: Winners!

UPDATE: The molecule is the Klenow fragment of E. coli DNA polymerase I. It's the part of the enzyme that's missing the 5′→3′ exonulcease activity. The Nobel Laureate is Kary Mullis, one of the most eccentric scientists ever to win a Nobel Prize—and that's saying a lot because Nobel Laureates are a very unusual group.

The winner is Guy Plunket III from the University of Wisconsin. There was no undergraduate winner this week so I awarded the second prize to Deb McKay, who is currently teaching in a Toronto high school. Her answer wasn't perfect but she offered me a bribe I couldn't refuse.¹

Today's molecule is actually two molecules but we only care about the protein. You need to identify this protein, being as specific as possible. A general description of the type of protein won't do because the image clearly show a particular version.

There's are several possible Noble Laureates associated with this molecule. One of them was Michael Smith—last week's Nobel Laureate. The person I'm looking for was never a Professor. That's not necessarily a bad thing, it just helps you narrow down the field of possible prize winners.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: John Bothwell from the Marine Biological Association of the UK, in Plymouth (UK), Wesley Butt of the University of Toronto, David Schuller of Cornell University, Nova Syed of the University of Toronto, Dima Klenchin of the University of Wisconsin and undergraduate Alex Ling of the University of Toronto, and James Fraser of the University of California, Berkeley.

John, David, and Dima have offered to donate their free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept a free lunch. Please indicate in your email message whether you are an undergraduate and whether you came make it for your free lunch (with a friend).

THEME:

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

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

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

1. A sneak peek at the new science curriculum for Ontario schools. Were you thinking of something else, perhaps?

Tuesday, February 24, 2009

Short Term Gains at NIH (USA)

Alex Palazzo highlights the shortsightedness of the stimulus package when it comes to NIH funded projects [NIH & the Stimulus in the NY Times].

I agree with him 100%. Science doesn't work that way. We once had that problem in Canada. A temporary increase in funding of the granting agencies lead to compounding the pain of the inevitable budget cut a few years later.

At least Alex won't have to deal with that problem when he arrives in Canada this summer. This time our government avoided the problem by starting with the budget cuts! What a relief not to have to worry about how to spent all those extra dollars....

Thank-you Stephen Harper. And thanks also to our Minister of State (Science and Technology), Gary Goodyear. Dr. (sic) Goodyear (above) is a chiropractor. It's nice to know our science policy is in such good hands.

Why We Immunize

Normally I don't write about the people who oppose immunizing children. I leave that to Orac and others. There are so many crazy people out there that the average skeptic simply doesn't have time to fight them all.

Here's an article by Jim Macdonald that Orac linked to: Why We Immunize. Everyone should read it.

Do You Have Biblical Morals?

Oops. I thought for sure I'd do better than PZ Myers.

Your morality is 0% in line with that of the bible.

Damn you heathen! Your book learnin' has done warped your mind. You shall not be invited next time I sacrifice a goat.

Do You Have Biblical Morals?
Take More Quizzes

Monday, February 23, 2009

The Future of Science Journalism

Chris Mooney warns us that science journalism is in trouble. He notes that many newspapers are firing their science writers and he warns of the dangers [The Death and Strangulation of Science Journalism].

What's disturbing, though, is to see a meta-discussion of the "trouble" with the practitioners of science journalism without any discussion of the real "trouble": the economic realities that are killing them off, one by one.

Memo to scientists: If you don't like science journalists, you're going to like even less what you get once they're gone.

I responded by saying ....

Not to worry. We'll figure out some way to frame it so that it sounds like a good thing!

:-)

Seriously, most of what passes for science journalism is so bad we will be better of without it.

Maybe the general public would have been more interested in science if science journalists hadn't been writing so much hype about "breakthroughs" for the past twenty years. Maybe the public would have been more interested in science if so-called "science" journalists hadn't been confused about the difference between science and technology.

Science isn't about what the latest discoveries can do to make your life better. It's about learning how the natural world actually works. It's all about knowledge and not application or politics.

Science journalists have let us down. I say good riddance.

Now Chris has started a separate thread in order to disucuss this point [Science Journalism: When Things Get Rough, You Find Out Who Your Real Friends Are].

My post last week about the death knell of science journalism prompted some incredible responses. Here's Larry Moran, putting it more bluntly than I expected, and enunciating an opinion we'd better hope does not prevail:

...

Breathtaking, huh? I seriously hope opinions like this are not very widespread in the scientific community.

Well Chris, I hate to tell you this but there are plenty of scientists who share my opinion, even though they may not have put it so bluntly.

And you know what, Chris? You and Matt are partly to blame for this sad state of affairs. I know you don't want to talk about framing because you have "moved on," but your criticism of scientists didn't do a lot to inspire our confidence in science journalism.

But let's move on and look at what you have to say today.

Honestly, based upon the foregoing, I have to question whether Larry Moran knows what a science journalist is--or at least, whether we're talking about the same thing. For it seems to me that virtually everything he's complaining about, a real science journalist would complain about as well.

Take the media slights against science described above--the hyping of "breakthrough" findings, the confusion of science and technology, and the swapping of serious science coverage for "feel good" or "news you can use" infotainment fare. Although you will certainly find exceptions, in general these aren't the fault of dyed-in-the-wool science journalists, of the sort that proudly claim membership in the National Association of Science Writers (as I do). In fact, you can bet that within their respective media organizations--when they still were working within them; most of NASW today is freelance--science journalists have fought against many such calls over the years.

And you can also bet that they frequently lost out in those internal battles.

I don't believe you.

But, for the sake of argument, let's assume that you are correct. Let's assume that most science journalists know full well that science doesn't produce weekly breakthroughs (all evidence to the contrary). Let's assume that most science journalists know the difference between science and technology. Let's assume that what they really want to do is write about how science leads to advances in understanding of the natural world instead of sensationalizing the subject by writing about, .... oh, let's say, "hurricanes, politics, and the battle over global warming."

Even if everything you say is true, the bottom line is that science journalists failed to make their case and were "forced" to do the bidding of senior editors—or whoever it is you blame.

If that's case, why should we support the status quo and stand up for the people who have (according to you) failed to deliver the goods?

The point is that nobody loves science more than science journalists--and nobody more devoutly wishes to see it covered accurately and widely, so that the "general public" thereby benefits, and comes to appreciate science more thoroughly. So how is it that now, a scientist like Larry Moran won't stand up for these science evangelists in the media, and blames them for a host of failings that, in truth, they themselves most assuredly abhor?

I gave you my answer. It's because I don't believe you. Is George Johnson one of your examples? How about Graham Lawton?

Now don't get me wrong. I'm not saying that every science journalist is doing a bad job. I've tried hard to pick out the good ones and give them the credit they deserve. What I'm saying is that, from my perspective, the majority of science journalists do not behave in the way you describe. It's all too easy to find articles that get the science wrong and articles that are more hype than reality.

Face the facts Chris, science journalists have not been very successful at finding allies among scientists. There's a very good reason for that. Try reading about the kerfluffle over the New Scientist cover to get a feeling for the problem.

Here's another exercise for anyone who cares about the quality of science journalism, as I do. Read the press releases on ScienceDaily. You won't find very many scientists who are impressed with that kind of science journalism.

Monday's Molecule #109

Saturday, February 21, 2009

Evolution in The Hamilton Spectator

Rama Singh is a Professor in the Department of Biology at McMaster University in Hamilton, Ontario (Canada). He happens to be the supervisor of Carlo Artieri, who writes Musings of the Mad Biologist.

Carlo noted on his blog (Evolution is a fact, not just theory...) that his boss has just published an article on evolution in the local newspaper. Read it at: Evolution is a fact, not just theory.

I'll quote the subheading and a couple of paragraphs and leave it up to my readers to discuss. Is this a good example of how scientists should explain evolutionary biology to the general public?

The only unproven area is Darwin's natural selection

...

Living organisms, on the other hand, evolve by variational evolution that depends on the survival and reproduction of the "fittest" individuals in the population, which is composed of many genotypes.

Unlike evolution, which is taken as a fact, the theory of natural selection, Darwin's mechanism for evolution, has come under criticism as to whether it is sufficient to explain evolution. In particular, early developmental biologists questioned if natural selection was adequate to explain the diversity and complexity of life.

Yet after 150 years of vigorous research (and many Nobel prizes!), no one has come up with a better theory. In fact, the more scientists have explored biology, the more they have become convinced of the facts of evolution.

Natural selection is a fact of everyday life. Resources are limited, individuals differ in their survival and reproduction, and evolution is a common sense conclusion deduced from facts and reasons. The problem with evolutionary change is that it takes place on such a slow place that we do not see it. However, we can imagine how evolution occurs by looking at the spectacular variety of food plants, flowers and domestic animals that we have produced by using the same principles of genetics and selection that nature uses. We may not witness the origin of species, but we have witnessed species becoming extinct in our own life time.

I'll get the conversation going by pointing out that well before the 150 years Professor Singh mentions in his article, random genetic drift was proposed as a pretty good theory about how evolution can occur. It may not be "better" than natural selection but I think it's good enough to have deserved a mention.

"A" for effort

Anyone involved in teaching has heard the sob story. One student works really, really hard in the course but only gets 65% on the final exam. Another student gets 95% without breaking a sweat.

The "C" student thinks this is very unfair. They should get a much higher mark because they put so much effort into the course.

The issue is addressed in the New York Times a few days ago [Student Expectations Seen as Causing Grade Disputes].

In line with Dean Hogge’s observation are Professor Greenberger’s test results. Nearly two-thirds of the students surveyed said that if they explained to a professor that they were trying hard, that should be taken into account in their grade.

Jason Greenwood, a senior kinesiology major at the University of Maryland echoed that view.

“I think putting in a lot of effort should merit a high grade,” Mr. Greenwood said. “What else is there really than the effort that you put in?”

“If you put in all the effort you have and get a C, what is the point?” he added. “If someone goes to every class and reads every chapter in the book and does everything the teacher asks of them and more, then they should be getting an A like their effort deserves. If your maximum effort can only be average in a teacher’s mind, then something is wrong.”

Michelle Cottle has a comment in The New Republic [An A for Effort? Talk About a Lousy Idea]. Now, this isn't a publication that I routinely look to for views that are similar to my own¹ but her comment below pretty much hits the nail on the head as far as I'm concerned.

No, Jason. What would be wrong is if a university trained its students to believe that they were excellent simply for getting up off their futons and doing what was expected of them. Did the reading? Attended class? Stayed up late working on a paper? Good for you, puppy! Sure, you did a craptastic job on that paper--not to mention the final--suggesting that you have no more than a fourth-grader's grasp of the material. But what the hell!? You worked hard. You showed up--even when you had that reallllly bad hangover. You may not have learned much, but you sure did try. Have a nice fat A. And here's hoping it comes in handy when your first employer fires you for not being able to tell your ass from your elbow when it comes to doing your job.

Sweet Jesus, where did such dizzying nonsense come from? Sure, it's easy to blame today's youth for being whiny, spoiled, and entitled. But the kids had to get these delusional ideas from somewhere. I suspect at least part of the blame lies with all those well-intentioned self-esteem-boosting messages that anxious parents, educators, and coaches feel compelled to spout in this era of making every child feel like a winner all the time. You know, the cheery, you-can-do-it mantras along the lines of, "All that matters is that you tried," "The only way to fail is not to try at all."

Um. No. While I understand the self-defeating doubt that we're trying to short-circuit here, there are, practically speaking, lots of ways to fail--much less fail to get an A. One of those is by not having much of an aptitude for a particular area of study. Not all of us are equipped to be rocket scientists, economists, or playwrights, just as not all of us are equipped to be actors or professional basketball players. If anything, a student who tries really, really, really hard at something and still repeatedly falls short might benefit from realizing that his talents lie elsewhere. (As could the rest of us: Not to state the obvious, but I don't want a brain surgeon who graduated at the top of his class because he had perfect attendance. I want one who is an artist with a scalpel.) Go ahead: Aim for the stars. Don't let anyone tell you you can't do something. But if you actually try that thing and it turns out that you're not so hot at it, don't whine about unfair grading. Acknowledge that you have major room for improvement and decide where to go from there. The sooner kids learn how to deal with failure and move on, the less likely we are to have a bunch of whiny, fragile, self-entitled, poorly qualified adults wandering around wondering why their oh-so-stellar efforts aren't properly appreciated in the real world.

Alternatively, now might be a good time to revisit my dream of becoming a concert pianist. I've never had much of an ear for music, but I bet if I quit my day job and worked at it really, really hard--or at least showed up at all my lessons and did the homework--someone would eventually reward my "excellence."

Hopeful Monster has something to say over on Chance and Necessity [Student effort ≠ high grades].

I want students to recognize that part of what we're testing is innate ability, or intelligence. There's no getting around it. If you are smart and you work hard you are going to get a higher grade than a student who works hard but isn't very smart. It's unfortunate that there are very smart students who don't have to work hard to get an "A," but that's life. What should count in university is how well you understand the material, not how much effort you put in while trying to understand.

By the way, I think that university Professors have to shoulder a great deal of the blame for the current sad state of "higher" education. It's not just the students. We Professors have always had the power to fix the problems but for the most part we have done nothing about it. Many of us have actually contributed to the problems by giving out marks for attendance and allowing "extra" assignments to raise your grade.

1. By this, I don't mean to imply that The New York Times is any better.

Shopping for Darwin

What's a celebration without shopping? Now you can enjoy the Darwin year celebrations by buying hundreds of Darwinian items at the Darwin Year Store. Half of the proceeds go to supporting biodiversity conservation-related charities.

I don't look good in T-shirts but there's plenty of other gifts for me on that site. All those shoppers who might be looking to buy me something for St. Patrick's day should check out the large mugs.

Some of them have even seen the very Darwin notebook where this drawing comes from, do you remember, Ms. Sandwalk? I told you it would be important to see this notebook. Now you know why.

[Hat Tip: Ryan Gregory]

Friday, February 20, 2009

Nobel Laureate: Michael Smith

The Nobel Prize in Chemistry 1993.

"for contributions to the developments of methods within DNA-based chemistry: for his fundamental contributions to the establishment of oligonucleotide-based, site-directed mutagenesis and its development for protein studies"

Michael Smith (1932 - 2000) won the Nobel Prize in Chemistry for developing the technique of site-directed mutagenesis. Today this is a common technique in biochemistry labs. It enables researchers to specifically alter a nucleotide in a gene in order to study its effect. It is frequently used in structural biology labs to explore the roles of varous amino acid residues in the function of a protein.

Smith's work was based on the development of DNA sequencing technology in the 1970s and on extensive work on the formation of DNA:DNA double-standed hybrids with oligonucleotides containing mismatches.

Here's the Press Release describing Michael Smith's contribution (there was a co-recipient but we don't mention him unless we have to).

THEME:
Nobel Laureates

Background

Chemically, the genetic material of living organisms consists of DNA (deoxyribonucleic acid). DNA molecules consist of two very long strands twisted around each other to form a double helix. Each strand is formed of smaller molecules, nucleotides, that represent the letters of the genetic material. There are only four different letters, designated A, T, C and G. The two DNA strands are complementary, being held together by A - T and G - C bonds. It is only when the genetic code is to be read off e.g. for protein building in the cell that the two strands are separated. The genetic information in DNA exists as a long sentence of code words, each of which consists of 3 letters which can be combined in many different ways (e.g. CAG, ACT, GCC). Each three-letter code word can be translated by special components within the cell into one of the twenty amino acids that build up proteins. It is the proteins that are responsible for the functions of living cells, including their ability to function, among other things, as enzymes maintaining all the chemical reactions required for supporting life. The proteins' three-dimensional structure and hence their function is determined by the order in which the various amino acids are linked together during protein synthesis.

Site-directed mutagenesis

The flow of genetic information goes from DNA via the translator molecule RNA to the proteins. By re-programming the code of a DNA molecule, e.g. changing the word CAC to GAC, it would be possible to obtain a protein in which the amino acid histidine is replaced by the amino acid aspartic acid. In nature, such mix-programming of the genetic material (mutation) occurs randomly, and is nearly always fatal to the organism. However, a dream of biochemical researchers has been to alter a given code word in a DNA molecule so as to be able to study how the properties of the mutated protein differ from the natural. It was through Smith's oligonucleotide-based site-directed mutagenesis that this dream became reality. As early as the 1970s Smith learned to synthesize oligonucleotides, short, single-strand DNA fragments, chemically. He also studied how these synthetic fragments could bind a virus to DNA. Smith then discovered that even if one of the letters of the synthetic DNA fragment was incorrect it could still bind at the correct position in the virus DNA and be used when new DNA was being synthesized. At the beginning of the 1970s Smith was a visiting researcher at Cambridge and the story goes that it was during a coffee-break discussion that the idea arose of getting a reprogrammed synthetic oligonucleotide to bind to a DNA molecule and then having it replicate in a suitable host organism. This would give a mutation which in turn would be able to produce a modified protein. In 1978 Smith and his co-workers made this idea work in practice. They succeeded both in inducing a mutation in a bacteriophagic virus and "curing" a natural mutant of this virus so that it regained its natural properties. Four years later Smith and his colleagues were able for the first time to produce and isolate large quantities of a mutated enzyme in which a pre-determined amino acid had been exchanged for another one.

A protein with a changed (mutated) amino acid can be
produced with site directed mutagenesis. A chemically
synthesized DNA fragment with a changed code word is bound
to a virus DNA which is multiplied in a bacterium. The DNA
molecule with the changed code word is reduplicated and can
be used for producing the changed protein.
Smith's method has created entirely new means of studying in detail how proteins function, what determines their three-dimensional structure and how they interact with other molecules inside the cell. Site-directed mutagenesis has without doubt revolutionised basic research and entirely changed researchers' ways of performing their experiments. The method is also important in biotechnology, where the concept protein design has been introduced, meaning the construction of proteins with desirable properties. It is already possible, for example, to improve the stability of an enzyme which is an active component in detergents so that it can better resist the chemicals and high temperatures of washing water. Attempts are being made to produce biotechnically a mutated haemoglobin which may give us a new means of replacing blood. By mutating proteins in the immune system, researchers have come a long way towards constructing antibodies that can neutralise cancer cells. The future also holds possibilities of gene therapy, curing hereditary diseases by specifically correcting mutated code words in the genetic material. Site-directed mutagenesis of plant proteins is opening up the possibility of producing crops that can make more efficient use of atmospheric carbon dioxide during photosynthesis

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Darwin on Gradualism

The image on the right was created by Mike Rosulek. You can view the complete set at More Darwin. He's planning to sell T-shirts and poster with all proceeds going to support the National Center for Science Education.

The idea of slow gradual change is an essential component of most people's thinking about evolution.¹ The debate over gradualism began in earnest with the publication of Punctuated Equilibria: an Alternative to Phyletic Gradualism by Eldredge and Gould (1972).

They defined phyletic gradualism as ...

Paleontology's view of speciation has been dominated by the picture of "phyletic gradualism." It holds that new species arise from the slow and steady transformation of the entire population.

They illustrate this point with two "classic" views of gradualism.

In the first view (left) we see speciation by gradual transformation of a single population. This form of speciation is called anagenesis.

This kind of thinking still dominates today. It's the way most people picture the result of natural selection working on a species over time. The species gradually adapts to a changing environment until its descendants come to look very different from its ancestors. This is the way most people think when they're talking about human evolution over the past several million years. It's the model you probably have in mind when you envisage arms races.

The other form of speciation is called cladogenesis. It's when an ancestral species splits into two parts—often due to geographical separation—and each separate population evolves gradually into distinct species. This is the way most people think about adaptive radiations. The key point, according to Eldredge and Gould, is the slow and steady change in each lineage as they diverge from one another.

Eldredge and Gould (1972) proposed a different way of thinking about evolution and speciation based on their observations of numerous fossil lineages. They suggested that speciation normally takes place via geographic separation of a subset of individuals in a species (allopatric speciation). This isolated group can evolve fairly rapidly so that within a relatively short time (tens of thousand of years) it comes to look very different from its ancestors.

If this geographically isolated population becomes reproductively isolated as well, then it forms a new species, distinct from its parents. The new species may then flow back into the same geographical location as the parent and there won't be any mixing of the gene pools. Meanwhile, the parent species has not changed much, so the effect on the fossil record is the rapid appearance of a new species while the old one continues to exist.²

At that point, both species will persist unchanged for millions of years (stasis) until the process of rapid speciation by cladogenesis repeats in one of both lineages. The pattern observed in the fossil record is called punctuated equilibria. It's a pattern that's very different from classic gradualism.

Here's how they illustrate it in their paper.

The important initial claims of the punctuated equilibria model are: (1) most change takes place rapidly during speciation by cladogenesis, and (2) for most of their existence species do not change very much. Later on, the implications of these two observations became more obvious. If the number of species is constantly increasing by splitting then why aren't we overwhelmed by species? The answer is that not only are species "born", they also "die" (become extinct). The overall pattern of evolution is characterized by the differential birth and death of species and this leads to species sorting as an important mode of evolution.

Lot's of people don't like punctuated equilibria and there are legitimate debates over interpretations of the fossil record. Some people say that the pattern is rarely seen, even when you have a complete record over millions of years. Others say that PE occurs in some lineages but it's not common.

Those who oppose punctuated equilibria are often upset about the claims concerning gradualism. The dispute often boils down to denying that anyone was ever a gradualist. The implication is that there's nothing new about punctuated equilibria so why all the fuss?

Much of the dispute hinges on whether Charles Darwin was a gradualist. It's often based on a misunderstanding of the word "gradualism" as it is used by Eldredge and Gould. Some people interpret it to mean "constant speedism" and they comb Darwin's works to find examples where he wrote about different rates of evolution in a lineage. "Aha!", they say, "see, Darwin wasn't a gradualist at all."

Gould addresses these critics in The Structure of Evolutionary Theory. He points out that there are some trivial examples of gradualism in Darwin's writings but the important definition is ...

Slowness and Smoothness (but not Constancy) of Rate
Darwin also championed the most stringent version of gradualism—not mere continuity of information, and not just insensibility of innumerate transitional steps; but also the additional claim that change must be insensibly gradual even at the broadest temporal scale of geological durations, and that continuous flux (at variable rates to be sure) represents the usual state of nature.

Gould goes on to support his claim based, in part, on Darwin's commitment to Lyell's uniformitarianism. Gould also points out that Huxley was vexed with Darwin for adopting such a gradualist approach to evolution.

You can tell from reading The Structure of Evolutionary Theory that Gould was annoyed at some of his critics. Bear in mind that Gould was a student of the history of biology and a collector of old books on the subject. He wrote numerous essays on the misinterpretation of historical figures (e.g. Goldschmidt). When he makes a claim about what Darwin thought, it shouldn't be dismissed as the deranged delusions of an uniformed scientist.

The same might not be true of other scientists, or philosophers, who write about history ....

Since Darwin prevails as the patron saint of our profession, and since everyone wants such a preeminent authority on his side, a lamentable tradition has arisen for appropriating single Darwinian statements as defenses for particular views that either bear no relation to Darwin's own concern, or that even confute the general tenor of his work....

I raise this point here because abuse of selective quotation has been particularly notable in discussions of Darwin's views on gradualism. Of course Darwin acknowledged great variation in rates of change, and even episodes of rapidity that might be labelled catastrophic (at least on a local scale); for how could such an excellent naturalist deny nature's multifariousness on such a key issue as the character of change itself? But these occasional statements do not make Darwin the godfather of punctuated equilibrium, or a cryptic supporter of saltation....

For more on this debate, see John Wilkins on Myth 4: Darwin was a gradualist.

1. The words on the poster are a take-off on one of the campaign slogans of Barack Obama.

2. There are other models that can account for the observations. In other works, Eldredge and Gould have explained how punctuated equilibria is also compatible with sympatric speciation.

Eldredge, N. and Gould, S.J. (1972) Punctuated Equilibria: an Alternative to Phyletic Gradualism. in "Models in Paleobiology" T.J.M. Schopf ed., Freemna, Cooper & Co., San Francisco pp. 82-115. [PDF]

Thursday, February 19, 2009

Subway ads and dead stars

Today I saw this "advertisement" in the subway on my way to work. I think it's an excellent example of science education and I congratulate the people at the Dunlap Institute for Astronomy and Astrophysics, University of Toronto and CoolCosmos for making the effort. (Click on the ad below to enbiggen and read the fine print. Refresh the page on CoolCosmos to see all five ads.)

Phil Plait will be jealous.

We Need this Course at the University of Toronto

Carl Zimmer ran a Science Writing Workshop at Yale University a few weeks ago.

I want him to give the same workshop here but I don't know if we can afford him.

Carl told us on his blog (The Island of Science Writing) about a short course in science writing that he is teaching this summer at the Shoals Marine Laboratory in Maine (USA). That sounded pretty neat so I thought I'd check it out by following the link [SCIENCE WRITING: BIOSM 3110]. I entertained the hope that I could take this course from Carl ... until I saw the price. The total cost for the week ($2,286) includes room and board but it's still a little steep for me, even considering the quality of the lecturer.

Hey Carl, do you have a discount for senior citizens?

Blunt Talk from Four Evolutionists

Do you remember this cover? It caused a minor uproar a few weeks ago [see Explaining the New Scientist Cover].

Today's issue of New Scientist has a letter signed by four people who criticize the journal for its choice of cover design. It may be just about the only important thing those four have in common. There are; Daniel Dennett, Jerry Coyne, Richard Dawkins, and PZ Myers. What a motley crew! [Darwin Was Right].

What on earth were you thinking when you produced a garish cover proclaiming that "Darwin was wrong" (24 January)?

First, it's false, and second, it's inflammatory. And, as you surely know, many readers will interpret the cover not as being about Darwin, the historical figure, but about evolution.

Nothing in the article showed that the concept of the tree of life is unsound; only that it is more complicated than was realised before the advent of molecular genetics. It is still true that all of life arose from "a few forms or... one", as Darwin concluded in The Origin of Species. It is still true that it diversified by descent with modification via natural selection and other factors.

Of course there's a tree; it's just more of a banyan than an oak at its single-celled-organism base. The problem of horizontal gene-transfer in most non-bacterial species is not serious enough to obscure the branches we find by sequencing their DNA.

Darwin was wrong about a lot of things but the tree of life wasn't one of them. It's still an accurate metaphor for most of the history of life—certainly the parts Darwin wrote about.

That's not to deny the fundamentally accurate part of the inside story. At its base the tree of life looks an awful lot like a web. That's correct. It's just that it has nothing to do with Darwin. The magazine's attempt to connect modern molecular evolution with Charles Darwin was just cheap opportunism.

I can't resist noting an irony in the letter. The authors say that, "It is still true that [life] diversified by descent with modification via natural selection and other factors." The irony is that the article inside the magazine discusses molecular evolution ("molecular genetics" in their terminology). The trees derived from those studies are based almost exclusively on neutral mutations that have become fixed in species by random genetic drift. What these studies show is that life diversified by descent with modification via random genetic drift.

Even when they are writing about changes at the molecular level, some adaptationists just can't bring themselves to utter the words "random genetic drift" in public.

Welcome to Canada, President Obama

President Obama (USA) just arrived in Canada. Here he is being greeted by Governor General Michaelle Jean. You can see the complete video on YAHOO! News.

Gosh, there hasn't been this much excitement over a visit to Canada since the Pope came here in 2002! Obama's visit may even be more exciting that the Queen's last trip in 2005.

Wednesday, February 18, 2009

Stephen Jay Gould Challenged the Modern Synthesis

As most of you know, Gould (1941 - 2002) was a critic of the hardened version of the Modern Synthesis. He thought that evolutionary theory needed to be updated to include some things that the originators of the Modern Synthesis were unaware of—or rejected prematurely.

His paper in Science in 1982 reached a wide audience and most biologists first became aware of his challenge by reading this paper (Gould, 1982) [read it here—if you have a subscription to Science].

But two years earlier, Gould published a more scholarly critique in the journal Paleobiology (Gould 1980). The opening sentence of the abstract throws down the gauntlet.

The modern synthesis, as an exclusive proposition, has broken down on both of its fundamental claims: extrapolationism (gradual allelic substitution as a model for all evolutionary change) and nearly exclusive reliance on selection leading to adaptation.

Ryan Gregory discusses this paper in detail on Genomicron [Gould (1980)]. If you want to be informed in this debate you absolutely must read what he has to say about this key paper in evolutionary theory.

Ryan discusses three important myths about Gould. The false myths are: (1) he rejected natural selection, (2) he wanted to overthrow the Modern Synthesis, (3) saltation and punctuated equilibria are somehow connected.

The last myth is so widespread that people as diverse as Jarry Coyne, Greg Laden, and Daniel Dennett have gotten themselves hopelessly confused about punctuated equilibria by not reading carefully [see Macromutations and Punctuated Equilibria]. They should know better.

They will know better (I hope) once they have read Ryan Gregory's posting.

Today, there are many people who want to change the Modern Synthesis. Advocating some new addition to evolutionary theory has become a minor industry—aided and abetted by science journalist who are more interested in controversy than accuracy. But those failings should not blind us to the very legitimate challenges to the Modern Synthesis raised by Gould over twenty-five years ago.

It's disappointing that most of those challenges are still not understood by biologists. Read Ryan's summary of Gould (1980), and learn.

[Image Credit: Photograph of Stephen Jay Gould by Kathy Chapman from Lara Shirvinski at the Art Science Research Laboratory, New York (Wikipedia)]

Gould, S.J. (1980) Is a new and general theory of evolution emerging? Paleobiology 6:119-130.

Gould, S.J. (1982) Darwinism and the expansion of evolutionary theory. Science 216:380-387.