Gene Genie #18

 

The 18th edition of Gene Genie has just been published on Eye on DNA [Gene Genie #18 with the PG Tips Chimp].

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Is There a Genetic Component to "Intelligence"?

 
This is not my field and, quite frankly, I don't really care about any differences or similarities in intelligence between different human demes. However, the recent kerfuffle over the intemperate remarks of a Jim Watson have raised a number of interesting issues. One of these is whether there is a genetic component to intelligence.

I have always thought there was. I remember reading Richard Dawkins' take on this subject some years ago. He pointed out that if the average "intelligence" of humans has increased over the past million years by evolution then it follows logically that there were genes (alleles) for differences in intelligence that were selected. It seems unreasonable to imagine that all the alleles have reached fixation so that in today's 7 billion members of the Homo sapiens species there is no genetic variation for "intelligence." (I'm putting "intelligence" in quotation marks because I don't want to get into protracted battles about how to measure it or even how to define it. Let's just agree that there's something called intelligence that exists.)

Up until now I have been under the impression that certain genetic defects resulted in lowered intelligence. For example, Down's Syndrome is strongly correlated with low scores on an IQ test suggesting that the presence of extra chromosome 21 genes affects intelligence. That's a genetic component of intelligence by most reasonable definitions.

In spite of evidence to the contrary, there seem to be a number of people who deny that there's a genetic component to intelligence. One of these is Greg Laden, whose opinion I greatly respect. In a recent posting [Watson’s Lecture Canceled] he even disputes the twin studies that show a strong correlation between intelligence and heritability.

Heritability does not distinguish in and of itself between traits passed on with genes from traits passed on via culture, learning, environment, and so on. For instance, which language a person speaks has a very high heritability value, but this “trait” is entirely, 100% learned with absolutely no genetic component whatsoever. Twin studies have been used to suggest that IQ has a component of heritability that is genetic since it is more correlated in twins than in, say, full sibs. However, non-genetic traits can follow the same pattern. Non-genetic traits can show this pattern because, with respect to environments, full sibs who are not twins do not share the same environment as twins. (And for other reasons.)

It seems to me that Greg is arguing against a genetic component to intelligence. He seems to be going out of his way to discredit any studies that suggest otherwise. I'm not sure where he's coming from on this and that's the reason for posing the question in this posting.

Later on in the comments section of Greg's article he says the following.

We have, on this site anyway, not discussed the fact that neural development in humans does not really allow for much influence from genetics in the way that is asserted by the Rushtonian race argument; we have seen some discussion that the allegations that intelligence = g = IQ = something measurable in a simple way = something that varies across individuals because of allelic differences in some set of genes. But there are a LOT of reasons to not accept this idea, aside from the major disconnect between the genome and the functioning of the brain owing to the actual way real brains actually develop in real life. There has been very little discussion regarding the disconnect between the concept of heritability and the concept of subspecies in animals (race is simply another term for subspecies).

There are so many levels at which this is so wrong that I can’t help but feel … and I’ve said this already … that the Race Concept and the intelligence piece of this are simply not valid scientific arguments, and are almost always either political arguments or arguments being made from ignorance. They are political in their motivation, because the science here is simply operating in a totally different place (a little place I call reality).

Clear as mud. I fully sympathize with the mixture of politics and science that confuses this issue. There are people who want there to be differences in intelligence between races because it fits with their political agenda.

I wonder if there aren't people who believe the opposite because it fits with their political agenda? I wonder if there aren't people who go out of their way to construct pseudo-scientific arguments denying that there can be a genetic component to intelligence. Why would they do this? Because if there's no genetic component to intelligence then there can be no differences between demes and this avoids a messy political debate.

Frankly, I'm not sure if Greg Laden is doing this so I'd like to see some clarification. Is there a genetic component to intelligence? Are there "intelligence" alleles segregating within the human population such that some people are smarter than others because of their parents and not just because of socioeconomic environment? Or, are all differences in intelligence due to environment?

Please, let's not let this thread degenerate into a discussion about racism. Let's talk about the science and stick to the question.

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The It's Its There Their They're Quiz

 

You Scored an A

You got 10/10 questions correct. It's pretty obvious that you don't make basic grammatical errors. If anything, you're annoyed when people make simple mistakes on their blogs. As far as people with bad grammar go, you know they're only human. And it's humanity and its current condition that truly disturb you sometimes.

The It's Its There Their They're Quiz

This is a quiz designed to find out whether you know the difference between its, it's, they're, their, and there. I doubt very much whether any blogger, or any reader, would get less than 10 on this quiz.

We all make mistakes from time to time. The problem isn't that we don't know the right word it's that we sometimes slip up when we're typing quickly and not concentrating on grammar. I am not one of those people who jump all over a fellow blogger when they make a mistake. I assume they're just like me. We're perfect in lots of things but attention to silly details like spelling isn't one of them.

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[Hat Tip: GrrlScientist at Living the Scientific Life (How is Your Punctuation and Grammar?]

I knew There Had to Be a Good Reason!

 
(for avoiding tofu)

Eating soya could slash men's sperm count.

Men who eat just half a serving of soya a day have drastically fewer sperm than those who do not consume such foods, according to a small, preliminary study.

The study's researchers say larger trials are needed to determine whether men hoping to conceive a child should try to avoid soya foods, such as tofu, tempeh and soya milk. However, soya industry representatives caution that the new findings contradict earlier studies that have shown no impact on sperm count from soya-based products.

Soya foods contain high amounts of isoflavones, compounds that mimic the effects of oestrogen in the body. For this reason, women sometimes increase their intake of soya foods to treat hot flushes caused by declining oestrogen levels in menopause.

Oestrogen-like compounds can also have a dramatic impact on the male body. And previous rodent studies have suggested that high intake of soya products can reduce male fertility. This has led scientists to wonder how isoflavones might influence men's reproductive function, which is highly sensitive to hormones.

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I'm skeptical of everything about nutrition and health but one of the important things about this study is that it alerts people to the presence of strange chemicals in natural plant foods. This is something that most people need to know in order to put nutritional studies into perspective. There are a lot of potentially dangerous chemicals in plants but the vast majority have no effect whatsoever.

Maher Arar Appears (Remotely) Before US Congressional Committee

 
In September 2002 Maher Arar was detained at New York's JFK Airport on the grounds that he was a suspected terrorist. At the time Maher, a Canadian citizen, was on his way back to Canada.

American officials sent him to Syria were he was tortured and held in prison for a year. When he eventually returned to Canada (avoiding US air space) he was acquitted of all charges in a special hearing and awarded 10 million dollars in compensation.

However, the US government refuses to clear his name and he remains on the no-fly list. Thus, when asked to appear before a joint committee of the House of Representatives he was denied permission to enter the USA and had to appear via a video link from Ottawa. The episode is reported on the front page of today's Toronto Star [U.S. leaders apologize to Arar].

Republicans joined with Democrats yesterday to offer Maher Arar something he has never received from the Bush administration – an apology for the U.S. role in wrongly detaining him, then sending him to Syria where he was tortured.

More than five years after his nightmare began, Arar received the apologies from congressmen as far apart on the ideological spectrum as possible in Washington, even if they differed widely on the value and legality of the Bush administration's practice of "extraordinary rendition" of terror suspects.

Canadians are outraged at the behavior of the Bush administration. There's no reason to keep persecuting a man who has been found innocent in Canadian courts. Doesn't the Bush administration have any respect for the legal procedures of their closest allies?

The surprise was the reaction of California Republican Dana Rohrabacher, a conservative who defended the rendition program, but also offered heartfelt apologies to Arar and said that he should be compensated.

"I join in offering an apology and I wish our government could join me in doing this officially," he said.

"When we make a mistake, we should own up to it."

He said the fact that the administration blocked Arar's personal appearance was evidence of "an arrogance that I don't like to see in our government.

"It only adds insult to injury," he said. "You should be let off the list, compensated and allowed to come here and tell your story."

But the Bush administration has not backed down from its story that Arar was deported, and it has not explained why he was sent to Syria when he asked to be allowed to return to Canada where his family and livelihood awaited.

Besides continuing to bar Arar from the country, the administration is working to block his lawsuit in a New York court.

The appeal will be heard next month.

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The Watson Affair

 
This Watson dust-up is going to get very interesting. First we have all those people who were quick to condemn Jim Watson as a low-life racist bigot on the basis of a few sentences in a newspaper article. That's before even hearing what he had to say about it.

Then we have the Science Museum canceling his talk on the grounds that they don't tolerate bigots. This is an incredible thing to do. Watson has been a well-known figure in scientific circles for half a century. It's just not credible that all of a sudden he has become such a racist that he's no longer welcome. He may be lots of things that people don't like but being a ugly racist isn't one of them.

On the other hand, we have the Newcastle Centre for Life and the Cambridge Union who are going ahead with plans to hear Watson speak. According to the Telegraph [Nobel Prize scientist 'mortified' at racist slur],

His earlier comments caused outrage among politicians and equality campaigners and led to the Science Museum cancelling a talk he was due to give. However, his planned appearance at Newcastle's Centre for Life on Sunday will go ahead, organisers said yesterday.

Linda Conlon, chief executive of the centre, said: "James Watson has been a regular visitor to Life and has often been outspoken and controversial. His views are not those held by the Centre but many people are keen to hear what he has to say. This discussion is part of a well established and popular lecture series, which gives the public an opportunity to explore and challenge topical life science issues."

The Cambridge Union said it would go ahead with a speech Dr Watson is due to deliver on Tuesday.

Roland Foxcroft, President of the Cambridge Union Society, said: "James Watson was invited to address the Union over two months ago. He was invited to discuss his past scientific achievements and the launch of his new book. We were unaware that he would make the comments that appeared in the Sunday Times Magazine, and we certainly did not invite him to speak to the Union in order to air these views or to support them.

"The Standing Committee of the Union has decided that the event should proceed in the name of the values of free speech and academic freedom with which we were founded. We would like to reiterate that Dr Watson's invite stands on the basis of his discovery of DNA and not on the basis of his social views."

Good for them. I'm glad to see that someone has some gumption. Now let's see how this plays out over the next few days and whether some politically correct people are willing to admit they went too far.

Admittedly, second-guessing Watson is complicated. But what upsets me the most is the totally irrational knee-jerk response of labeling him a racist. That just doesn't make sense. If he were the kind of racist that people are claiming he wouldn't have held the positions he held and he wouldn't have any friends in the scientific community.

Those friends have now commented [Nobelist's Race Comments Spark Outrage].

"Jim has a penchant for making outrageous comments that are basically poking society in the eye," Dr. Francis Collins, director of the National Human Genome Research Institute, said Thursday.

Collins, who has known Watson for a long time, said his latest comments "really ... carried it this time to a much more hurtful level."

In a brief telephone interview, Collins told The AP that Watson's statements are "the wildest form of speculation in a field where such speculation ought not to be engaged in." Genetic factors for intelligence show no difference from one part of the world to another, he said.

Several longtime friends of Watson insisted he's not a racist.

"It's hard for me to buy the label `racist' for him," said Victor McElheny, the author of a 2003 biography of Watson, whom he's known for 45 years. "This is someone who has encouraged so many people from so many backgrounds."

So why does he say things that can sound racist? "I really don't know the answer to that," McElheny said.

Biologist and Nobel laureate Phil Sharp at the Massachusetts Institute of Technology, who's known Watson since 1971, said, "I've never considered Jim a racist. However, Jim likes to use statistics and observations to provoke people, and it is possible that he is provoking people by these comments."

Calling Watson "one of the great historical scientific figures of our time," Sharp said, "I don't understand why he takes it upon himself to make these statements."

Mike Botchan, co-chair of the molecular and cell biology department at the University of California, Berkeley, who's known Watson since 1970, said the Nobelist's personal beliefs are less important than the impact of what he says.

"Is he someone who's going to prejudge a person in front of him on the basis of his skin color? I would have to say, no. Is he someone, though, that has these beliefs? I don't know any more. And the important thing is I don't really care," Botchan said.

"I think Jim Watson is now essentially a disgrace to his own legacy. And it's very sad for me to say this, because he's one of the great figures of 20th century biology."

Watson has a history of "poking society in the eye" that's for sure. For some reason, this time it backfired big time. I guess it depends on whose eye is being poked. The Watson affair is sad because I have a fondness for curmudgeons. I hope it isn't a sign that any dissent from standard dogma will be severely punished.

What is this standard dogma? Francis Collins puts it well when he says, "Genetic factors for intelligence show no difference from one part of the world to another." This is something that nobody can question without being called a racist. See Race and Intelligence for more discussion and a possible exception.

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Email Message Warns about Canadian Health Care

 
Friday's Urban Legend: MOSTLY FALSE

The email message begins with,

This was sent from Canada to a friend in the States.

I saw on the news up here in Canada where Hillary Clinton introduced her new health care plan. Something similar to what we have in Canada. I also heard that Michael Moore was raving about the health care up here in Canada in his latest movie. As your friend and someone who lives with the Canada health care plan I thought I would give you some facts about this great medical plan that we have in Canada.

First of all:

1) The health care plan in Canada is not free. We pay a premium every month of $96 for Shirley and I to be covered. Sounds great eh. What they don't tell you is how much we pay in taxes to keep the health care system afloat. I am personally in the 55% tax bracket. Yes 55% of my earnings go to taxes. A large portion of that and I am not sure of the exact amount goes directly to health care our #1 expense.

Snopes.com has examined all the claims in this email message and found that most of them are without merit [Canadian Health Care]. For example, there is not a single health care plan in Canada. There are thirteen different ones, one for each province and territories. Most of them do not charge premiums but the British Columbia plan does and it would cost $96 per month for a family of two. This part of the message is partially correct.

The part about taxes is not. Here's what Snopes.com says.

The highest federal income tax rate in Canada is 29% (for persons with annual taxable income over $120,887), and the highest provincial income tax rate in British Columbia is 14.7% (for those with annual taxable incomes over over $95,909). The typical upper-income level Canadian taxpayer is not in a 55% tax bracket.

By way of comparison, a typical upper-income level American taxpayer residing in California pays a roughly equivalant share of his income (40%-45%) in combined federal and state taxes, even though the U.S. has no national health insurance program.

There are many issues concerning health care and whether the USA should adopt socialized medicine like most civilized countries. It doesn't help when people are spreading false information.

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More Restricted Access to Journal Articles

 
The press release from the Dept. of Energy Joint Genome Institute (USA) sounds really cool [Massive reanalysis of genome data solves case of the lethal genes].

It is better to be looked over than overlooked, Mae West supposedly said. These are words of wisdom for genome data-miners of today. Data that goes unnoticed, despite its widespread availability, can reveal extraordinary insights to the discerning eye. Such is the case of a systematic analysis by the U.S. Department of Energy Joint Genome Institute (DOE JGI) of the massive backlog of microbial genome sequences from the public databases. The survey identified genes that kill the bacteria employed in the sequencing process and throw a microbial wrench in the works. It also offers a possible strategy for the discovery of new antibiotics. These findings are published in the Oct. 19 edition of the journal Science.

In nature, promiscuous microbes share genetic information so readily that using genes to infer their species position on the evolutionary tree of life was thought to be futile. Now, researchers at DOE JGI have characterized barriers to this gene transfer by identifying genes that kill the recipient bacterium upon transfer, regardless of the type of bacterial donor. These lethal genes also provide better reference points for building phylogenic trees—the means to verify evolutionary relationships between organisms.

But it's not true. This article was not published in the Oct. 19 edition of Science. You can see for yourself [Science Oct. 19, 2007].

Instead it was posted on ScienceXpress, Publication ahead of print. Access to those articles is restricted. I can't see them even though the University of Toronto has an excellent system for getting articles from journals. Can anyone else get this article?

This really pisses annoys me. What's the point of putting out a press release if nobody can see the paper?

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Does the Universe Have a Purpose?

 
There's a two page ad in last week's issue of NewScientist. It's paid for by the Templeton Foundation and the ad consists of quotations from various people on the question "Does the Universe have a Purpose?" The link to the Templeton Website gives you the complete essays of all the writers [Purpose].

The Templeton Foundation is interested in promoting a truce between science and religion. They offer a prize worth more than $1,000,000 to people who advance this cause. In most cases it goes to religious scientists.

Some of the responses to the question of purpose are worth a comment or two. For example, here's what Christian De Duve says. (De Duve won the Nobel Prize in 1974.)

I should mention first that this is a loaded question, with several hidden implications. A "purpose" presupposes a mind that conceived it, as well as the ability to implement it. In the present case, this means that the owner of the mind not only created the universe the way it is, but could have created another universe and decided to create the existing one for a specific reason. So the question really deals with the belief in a Creator who enjoys almost infinite power and freedom but, at the same time, goes through the very human process of pondering decisions and acting accordingly. In a way, this is a very anthropomorphic vision of God....

It will be noted that there is no logical need for a creator in this view. By definition, a creator must himself be uncreated, unless he is part of an endless, Russian-doll succession of creators within creators. But then, why start the succession at all? Why not have the universe itself uncreated, an actual manifestation of Ultimate Reality, rather than the work of an uncreated creator? The question is worth asking.

This is the response of an atheist. De Duve doesn't believe in supernatural beings that could have created the universe so the only logical response to the question is NO. There is no purpose.

Not all atheists respond this way and that's what I find interesting. Here's the way Lawrence Krauss answers.

Perhaps you hoped for a stronger statement, one way or the other. But as a scientist I don't believe I can make one. While nothing in biology, chemistry, physics, geology, astronomy, or cosmology has ever provided direct evidence of purpose in nature, science can never unambiguously prove that there is no such purpose. As Carl Sagan said, in another context: Absence of evidence is not evidence of absence....

Thus, organized religions, which put humanity at the center of some divine plan, seem to assault our dignity and intelligence. A universe without purpose should neither depress us nor suggest that our lives are purposeless. Through an awe-inspiring cosmic history we find ourselves on this remote planet in a remote corner of the universe, endowed with intelligence and self-awareness. We should not despair, but should humbly rejoice in making the most of these gifts, and celebrate our brief moment in the sun.

Clearly Krauss doesn't believe that the universe has a purpose because he's an atheist. Nevertheless, he feels compelled to hedge his bets on the grounds that you can't prove a negative. This is a cop-out.

In the absence of any evidence the proper response is NO, bearing in mind that this response could change if evidence for God was ever discovered. No is the answer you give to all other questions of this type such as "Does the tooth fairy exist?" or "Do you believe in UFO's?" In fact, I strongly suspect that Krauss would give this answer if the question was reworded to be "Do you believe that the universe has a purpose?"

It shouldn't make a difference how the question is worded. Note that there are several religious people who answer "YES" to the question. If they were to follow Krauss' advice the best they could say would be "Likely" but they don't do that. We all know about the absence of evidence excuse but for some reason it only seems to apply in practice to questions about religion. You don't believe me? Then how would you answer this question: "Did Saddam Hussein have a secret hidden stockpile of nuclear weapons?"

Finally, let's look at the response of another atheist. This time it's Neil deGrasse Tyson. Here's what he says,

Anyone who expresses a more definitive response to the question is claiming access to knowledge not based on empirical foundations. This remarkably persistent way of thinking, common to most religions and some branches of philosophy, has failed badly in past efforts to understand, and thereby predict the operations of the universe and our place within it....

So in the absence of human hubris, and after we filter out the delusional assessments it promotes within us, the universe looks more and more random. Whenever events that are purported to occur in our best interest are as numerous as other events that would just as soon kill us, then intent is hard, if not impossible, to assert. So while I cannot claim to know for sure whether or not the universe has a purpose, the case against it is strong, and visible to anyone who sees the universe as it is rather than as they wish it to be.

Neil deGrasse Tyson is an atheist. Does that last paragraph sound like someone who's not sure? Of course it doesn't.

When he says that "Anyone who expresses a more definitive response to the question is claiming access to knowledge not based on empirical foundations" he's just pandering to religion. Does anyone seriously believe that he's NOT SURE about the existence of Santa Claus and NOT SURE about the existence of God?

Yes, it's true that we can't prove the non-existence of God and we can't prove that the universe has no purpose but those aren't really related to the type of question being asked. When someone asks whether the universe has a purpose you have every right to interpret this to mean whether in your best judgment the universe is designed with a purpose in mind. Especially if the question is being asked by the Templeton Foundation. Religious scientists answered YES, YES, and CERTAINLY. The religious humanities Professor answered I HOPE SO.

De Duve got it right. It was a loaded question and the responses from the wimpy atheists play right into the hands of the Templeton Foundation. They now have a full page ad where eight academics responded and only two said NO. (The other one is Peter Atkins.)

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Can Someone Explain this Quotation?

 
The latest issue of SEED magazine has a quotation from Sir Paul Nurse, winner of the Nobel Prize in Physiology & Medicine in 2001 for his work on the cell cycle in yeast. Here's the quotation ...

The complexity of living organisms means that the explanations toward which we endeavor may be non-intuitive. The infrastructure may often not be reducible to simple linear pathways of causal events. More likely, they will form interweaving networks with elements of feedback and feedforward, negative and positive loops, redundant steps, and storage devices that operate on many levels simultaneously. Unlike man-made machines, the architecture of the information will change in time and space to generate the richness of emergent behaviors that distinguish the chemistry of living systems from those of non-living ones.

Biology may therefore have to become "more strange" if it is to succeed in describing life. To accomplish this, we will need the assistance of those whose discipline underwent its own transformation to become more strange in the early 2oth century, the physical scientists.

Sounds a bit like vitalism, don't you think? Is he saying that cells don't obey the known laws of physics and chemistry?

Does this mean that those of us who are biochemists and molecular biologists won't be able to figure out how life works unless we call for help from chemists and physicists? What's the evidence for that?

Does he mean that our fundamental understanding of biochemistry is flawed and we need a whole new way of thinking similar to the quantum mechanics revolution in physics? If so, what exactly are those strange things that demand a new way of thinking? I don't see them.

Yes, biology is complicated. Nobody said it was going to be easy. But as far as I can see it's only complicated because of multiple layers of complexity each of which can be fairly simple and each of which obeys the laws of physics and chemistry. There's nothing "strange" going on that I can see. Am I missing something?

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[Photo Credit: Eighth annual Women & Science Lecture and Luncheon
at The Rockefeller University]

Avoid Boring People

 
I suspect most of you have heard about Jim Watson's provocative and politically incorrect comments as quoted in the Sunday Times last weekend [The elementary DNA of Dr Watson]. The article about Watson was written by Charlotte Hunt-Grubbe, a scientist who lived with, and worked with, Watson about ten years ago. You have to read the entire article to get a sense of how she approaches her subject. In my opinion, she presents an accurate view of a man who seeks controversy and hates political correctness. This often gets him into trouble but he likes trouble.

Here's the paragraph that caused all the fuss ...

Back in 1990, the journal Science commented: “To many in the scientific community, Watson has long been something of a wild man, and his colleagues tend to hold their collective breath whenever he veers from the script.” When, in 2000, he left an audience reeling by suggesting a link between skin colour and sex drive – hypothesising that dark-skinned people have stronger libidos – some journalists suggested he had “opened a transatlantic rift”. American scientists accused him of “trading on past successes to promote opinions that have little scientific basis”. British academics countered that subjects should not be off limits because they are politically incorrect. Susan Greenfield, director of the Royal Institution, said that “nothing should stop you ascertaining the scientific truth; science must be free of concerns about gender and race”.

He says that he is “inherently gloomy about the prospect of Africa” because “all our social policies are based on the fact that their intelligence is the same as ours – whereas all the testing says not really”, and I know that this “hot potato” is going to be difficult to address. His hope is that everyone is equal, but he counters that “people who have to deal with black employees find this not true”. He says that you should not discriminate on the basis of colour, because “there are many people of colour who are very talented, but don’t promote them when they haven’t succeeded at the lower level”. He writes that “there is no firm reason to anticipate that the intellectual capacities of peoples geographically separated in their evolution should prove to have evolved identically. Our wanting to reserve equal powers of reason as some universal heritage of humanity will not be enough to make it so”.

Now, Charlotte Hunt-Grubbe is not an idiot. She knew very well that when she printed that part of the interview it would attract attention. The article was commissioned to promote Watson's new book Avodi Boring People and Hunt-Grubbe makes the obvious connection.

Watson will no doubt enthusiastically counter the inevitable criticisms that will arise. He once commented to a fellow scientist – perhaps optimistically – that “the time was surely not far off when academia would have no choice but to hand political correctness back to the politicians”. Even after a year at the lab, I am still unnerved by his devil-may-care compulsion to say what he believes. Critics may see his acceptance of “softer-science” studies – that attempt to link IQ with specific genes, but remove society and other factors from the equation – as a dangerously flippant approach to a complex issue. His comments, however, although seemingly unguarded, are always calculated. Not maliciously, but with the mischievous air of a great mind hoping to be challenged. I ask him how he placates those he offends. “I try to use humour or whatever I can to indicate that I understand other people having other views,” he explains.

As I motor back to New York, I reflect on a man who – at nearly 80 – is, and will remain, an immensely powerful and revered force in science. I wonder whether it’s possible, as his desire to shock seems so strong, that a fear of boring people really does play on his mind. Perhaps the best description of the man is from the driver. “Dr Watson’s so kind and still very young at heart,” he drawls as we leave the campus behind. “He’s got a lot of curiosity about everything and he’s always working. But to him it isn’t work: it’s a challenge to the mind. And if he runs into a problem, it’s fun time.”

Sometimes I wonder whether the world wouldn't be a better place with a few more Jim Watsons around. His honesty—whether you agree with him or not—is refreshing. As a society we often have this unnerving tendency to avoid issues that are too much of a threat to the way we would like things to be. Watson is like the young child who says, "Look, there's an elephant in the room."

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Celebrating the Three Domain Hypothesis

 

This press release from the University of Illinois at Urbana-Champaign (USA) says it all.

Thirty years ago this month, researchers at the University of Illinois published a discovery that challenged basic assumptions about the broadest classifications of life. Their discovery – which was based on an analysis of ribosomal RNA, an ancient molecule essential to the replication of all cells – opened up a new field of study, and established a first draft of the evolutionary “tree of life.”

To mark the anniversary of this discovery, the university is holding a symposium Nov. 3-4 (Saturday-Sunday), with a public lecture at the Spurlock Museum on the evening of Nov. 2. “Hidden Before Our Eyes: 30 Years of Molecular Phylogeny, Archaea and Evolution” will detail the exacting work that led to the discovery of a “third domain” of life, the microbes now known as the archaea. The event will revisit the program of research that led to the discovery, explore its impact on the study of evolution, and describe the way in which genetic analysis continues to revolutionize biology, in particular microbial ecology.

There's nothing in the press release to suggest that the third domain is still controversial. Looking at the list of speakers, it's not clear whether this point will come out in the symposium although I note that Carl Woese is on the program and he's recently been lukewarm about his own hypothesis.

The best hope for the journalists in attendance is Jan Sapp, a biologist at York University here in Toronto (Canada) who has studied the history of this "discovery" over the past three decades. As I reported last year, Sapp has documented the rise and fall of the Three Domain Hypothesis and he has taken note of the fact that former supporters of the hypothesis have recently become more skeptical [The Three Domain Hypothesis (part 2)]. Hopefully, Sapp will say things like the following from his book Microbial Phylogeny and Evolution. On the other hand it may be difficult to rain on the parade so the symposium may end up ignoring the controversy and pretending that the domain of Archaea is established fact.
Theme

The Three Domain Hypothesis

Defection grew from within the ranks of molecular evolutionists during the late 1990s. Several leading microbial phylogeneticists saw in Mayr's critique much that they considered to be true, as central features of the Archaeal story of the 1980s were challenged. First, analysis of whole genomes (more than 70 had been sequenced by 2003) had shown that Archaebacteria and Eubacteria possessed numerous genes in common; they shared a rich biochemical complexity. These data did seem to contradict the hypothesis that the Archaea were so very different from Bacteria because the two groups diverged when life was quite new. Second, comparisons of genes for other functions seemed to contradict the the phylogenetic lineages deduced from rRNA sequences....

There was a third fundamental issue. Not only did the phylogenies from the new genomic studies disagree with the traditional rRNA-based phylogenies but the new genome data also conflicted among themselves. Comparisions of individual gene phylogenies (other than those concerned with the translation machinery) often indicated different organismic genealogies. Phylogeneticists suspected that the mix-up was caused by evolutionary mechanisms whose scope and significance they may have severely underestimated: gene transfer between groups.

I have argued elsewhere that the current consensus among those who are concerned with early evolution is that the early stages were characterized by rampant gene exchanges so that it is simply not possible to say what the phylogeny of bacteria lineages was before the main lines formed. It is not possible to say with any certainty that archaebacteria are one of the earliest branching lineages and in the absence of this certainty it is certainly not possible to say that archaebacteria form a disctinct domain of life.

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Alister McGrath's Defense of Religion

A few months ago I attended a lecture by Alister McGrath on Deluded about God? Responding to Richard Dawkins' God Delusion [Alister McGrath]. The lecture was a big disappointment. I was expecting to hear of some wonderful new proof of the existence of God—one that Dawkins had overlooked. Instead all I heard was banalities about how poor old religion was being misrepresented. The only interesting point was what McGrath thinks about the future of atheism. He thinks it's dying and religion is gaining in popularity. That's a pretty good example of the reasoning ability of this Oxford Professor. The audio recording of this lecture is now available through TV Ontario, which just broadcast it last week [Alister McGrath]. I was reminded of this experience when the videos of a "debate" between Christpher Hitchins and Alister McGrath were posted on the web. The complete "debate" is available below and shorter versions are on YouTube [Christopher Hitchens Debates Alister McGrath 1 of 11].
This is another non-event as far as McGrath is concerned. He might as well have not bothered to show up for all the good he did in advancing his case. The best he can say for religion is that it makes him feel good. Hitchins, on the other hand, is very entertaining. He has the ability to say some outrageous things and get away with it in a way that others can't. Imagine, for example, the reaction if Jim Watson had said those things about religion!

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[Hat Tip: RichardDawkins.net]

Race and Intelligence

 
PZ Myers has stirred up a hornet'e nest by quoting Jim Watson's politically insensitive comments about race and IQ [Eminent scientist behaving badly]. As usual, the dispute rages around the question of whether Africans have lower IQ's than Caucasians or Asians.

Meanwhile, the connection between race and intelligence often goes unchallenged when it comes to other ethnic groups. For example, in the posting on the Ashkenazi Jewish Population I mentioned some explanations for higher intelligence among this group and not a peep was raised about IQ and race [Evolution in the Ashkenazi Jewish Population]. Isn't this strange? If it's okay to talk about one race having a difference in IQ then why isn't it okay to talk about another? [Let my meaning be clear. I doubt very much whether there's a real difference in intelligence between Askenazi Jews and other "races" but I'm willing to entertain the possibility.]

Here's the abstract of a paper by David and Lynn (2007).

A number of studies have found that Ashkenazi Jews in the United States have a high average IQ. It has been proposed by Cochran, Hardy and Harpending (2006) that this can be explained by the occupational constraints imposed on the Ashkenazi for many centuries in Europe, when they were largely confined to money-lending. They propose that this selected for the high verbal and mathematical intelligence that has several times been found in American Ashkenazim. The current study investigates how far this theory holds for European and Oriental Jews in Israel. A review of studies shows that Oriental Jews in Israel have an average IQ 14 points lower than that of European (largely Ashkenazi) Jews. It is proposed that this difference can be explained in terms of the Cochran, Hardy and Harpending theory because Oriental Jews were permitted to engage in a much wider range of occupations and hence did not come under the selection pressure to develop the high verbal and mathematical intelligence that was present for Ashkenazim.

It seems pretty silly to me but it still got published in the scientific literature. Jared Diamond has also favored explanations like this for the higher IQ of this population.

So, the question of the day is why don't we see the same storm of criticism over a paper like this? Basically what they're saying is that the non-Jewish Europeans had lower IQ's than the Jewish population. How is this more politically correct than saying that blacks have lower IQs than whites in America?

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David, H. and Lynn, R. (2007) Intelligence differences between European and oriental Jews in Israel. J Biosoc Sci. 39:465-73.

Nobel Laureate: The Svedberg

 

The Nobel Prize in Chemistry 1926.

"for his work on disperse systems"



In 1926, The (Theodor) Svedberg (1884-1971) won the Nobel Prize in Chemistry for his work on the behavior of molecules in solution. Svedberg is famous in the biological sciences for his development of the high speed ultracentrifuge and the technology for photographing the behavior of molecules during centrifugation. Many biochemical molecules are named for their sedimentation coefficients (e.g., 40S ribosomal subunits) in Svedberg units [The Compositon of Ribosomes]. The Svedberg equation used to be standard material in biochemistry courses but lately it has disappeared to make room for other techniques.

The presentation speech was delivered on December 10, 1926 by Professor H.G. Söderbaum, Secretary of the Royal Swedish Academy of Sciences. At the time, Svedberg was Professor of Physical Chemistry, University of Uppsala in Sweden. There have been an extraordinary number of Swedish scientists who have won Nobel Prizes. (All of them fully deserved—this is not bias.)

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

The Academy of Sciences has decided to award the Nobel Prize in Chemistry for 1926 to The Svedberg, Professor of Physical Chemistry at the University of Uppsala, for his work on disperse systems.

Almost a hundred years ago, or more accurately in 1827, the English botanist Robert Brown discovered with the aid of an ordinary microscope that small parts of plants, e.g. pollen seeds, which are slurried in a liquid, are in a state of continuous, though fairly slow movement in different directions. A more detailed study of this phenomenon during the last few decades has led to extremely interesting results. By means of the ultramicroscope it has been possible to observe a similar, only much livelier movement with very much smaller particles of a colloidal nature. As we have recently heard, Einstein evolved a theory for this so-called Brownian movement which was then developed to a high degree by the now late Smoluchowski. According to these scientists, the movement arises through the impacts of the molecules of the liquid against the particles slurried in the liquid, provided that the latter are sufficiently small. Taking a crude analogy: if a fly or a gnat flies against an elephant, the elephant will not noticeably alter its position, but this can occur if the fly or gnat collides only with a bee.

The theory in question has been confirmed convincingly by experimental investigations of several colloid scientists among whom especially two of today's prize-winners, Perrin and Svedberg, have occupied and still occupy a leading position. Should it now be true that the movement of particles suspended in a liquid, which we can actually observe with the aid of our extremely highly magnifying instruments, can be explained only as a result of the movement of molecules beyond the limits of direct human vision, then this provides visual evidence for the real existence of molecules and consequently also for that of atoms, evidence which is all the more remarkable as not so long ago an influential school of scientists declared these particles of matter to be unreal fictions representing an obsolete viewpoint of science.

It is known that the opposition conducted by the colloid scientists so successfully against this so-called energetic view has been continued by others who have gone much farther in that according to this view not only what we call matter, but also electricity occurs solely as particles of a definite size - the so-called electrons - and even that energy at all is regarded as bound to larger or smaller multiples of a smallest unit, the so-called elementary quantum.

If one has once become convinced of the existence of atoms and molecules, the question as to their real size is naturally - this hardly needs stressing - a question of the very greatest interest. Whereas it was formerly possible to calculate this size only roughly from the properties of gases and in connection with the theory applying to them, the position was now, as happens so often in the history of science, that almost simultaneously several new and considerably more precise methods for determining the natural constant in question appeared. Among these methods those based on colloid-chemical phenomena occupy a special position through their vividness and persuasive power, even though they may be for the time being slightly superseded by other methods in regard to accuracy. Also in this field Svedberg and the school of eminent scientists trained by him, Swedes as well as nationals from more or less distant countries, have achieved extremely valuable results. This has been done in several ways, among others, by determining the speed at which colloidal particles migrate by themselves, or diffuse in a liquid, or by measuring the distribution of such particles in a column of liquid, the latter according to a method proposed originally by Perrin.

In accordance with the theory for the movement of gas and liquid molecules which, as just indicated, has also been applied to colloidal particles, it is assumed that the mean value of the momentum of molecules or particles has a definite magnitude at each temperature, but that the speeds of the individual particles can vary within wide limits. If we now consider a very small volume fraction, the result is that, as Smoluchowski has calculated in detail, the number of particles present simultaneously within this volume can change from one moment to another. Svedberg and his collaborators have been able to confirm this extremely interesting conclusion that a "few-molecular" system having definite limits within a large volume of a material with a definite mean temperature may contain a varying number of particles, partly by counting the colloidal particles, partly in the case of solutions of radioactive substances by counting the number of so-called scintillations, i.e. light flashes, which radioactive particles produce when they impinge upon a screen coated with zinc sulphide.

With the last investigation, however, we have gone beyond the field of actual colloid chemistry, although the solution of a radioactive substance, e.g. polonium chloride, can naturally be called a disperse system, though more accurately it is molecular-disperse because the substance dissolved in the solvent occurs here as molecules, not as molecular aggregates, as is the case in a colloidal solution.

During the last few years Svedberg has completed an extremely ingenious invention, the so-called ultracentrifuge, which enables highly interesting investigations to be made also on such molecular-disperse systems. We know that when a slurry, an emulsion, is put into a rapidly rotating motion, its heavier constituents are thrown outwards in the direction of the periphery of the motion. This happens in the most used of all centrifuges, the milk separator, where the skimmed milk is pressed outwards whilst the lighter fat particles, the cream, accumulate inwards and can therefore be separated. Similarly in a solution, when centrifuging is sufficiently rapid, the molecules of the dissolved substance must accumulate outwards if they are considerably heavier than the molecules of the solvent. After overcoming exceptional experimental difficulties Svedberg succeeded in demonstrating this with the aid of an apparatus which allows the enormous speed of rotation of 40,000 revolutions per minute, and in which through a highly refined arrangement the progressive distribution of the particles within the extremely rapidly whirling solution can be observed and recorded photographically. The molecular weight of the dissolved material can be calculated from this distribution. This has already been done for certain proteins essential for organic life and for other substances allied to them. For example, the molecular weight of the red colouring agent of the blood, haemoglobin, has been determined as approximately 67,000 which assumes that there are in the region of 10,000 atoms in such a molecule.

In view of the fact that this year not less than three Nobel Prizes have been awarded for work in the field of colloid research, some people may ask whether this field really has a corresponding importance "for mankind".

By way of answer the following few remarks may be made.

Inorganic chemistry has revealed more and more cases where only a colloid-chemical approach was able to clarify the observed phenomena.

For physical chemistry colloids form a rich and rewarding field of research.

In organic chemistry we meet the perhaps most important colloids, the proteins and the polymeric carbohydrates, which cannot be studied without the aid of colloid research.

As all living matter is built up largely from organic colloids, the importance of colloid research for physiology and the medical sciences is obvious.

Finally, colloids play an important part in the various branches of chemical industry, such as in dyeing and tanning, in the cellulose, nitrocellulose, celluloid and textile industry, in rubber manufacture, in the pottery and cement industry, in the photographic industry, etc.

Professor Svedberg. With a feeling of sincere pleasure and justified pride the Academy of Sciences again sees itself able to recruit from the ranks of its own members the corps d'élite of researchers which has been set up by Alfred Nobel's legacy.

You have been able to accept on a previous occasion the assurance of the Academy on this together with its sincere congratulations.

In this festive hour we would now only add to this the hope that it may be made possible for you to carry out in your own country the important investigations which have already borne such fine fruit to the honour of Swedish research and which appear to be not less full of promise for the future.

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[Photo Credit: Physical Chemistry: Uppsala University]

The Compositon of Ribosomes

 
The ribosome is an important part of the translation machinery. (The others are mRNA, aminoacyl-tRNAs, and translation factors). The translation machine makes polypeptide chains according to the information encoded in the mRNA molecule

All ribosome are composed of two subunits that separate when translation terminates and reunite when an new initiation complex is formed. The eukaryotic ribosome has 40S and 60S subunits and the prokaryotic subunits are 30S and 50S. As a general rule bacterial macromolecules are smaller that eukaryotic ones and the ribosome is no exception.


Each of the subunits is made up of a combination of RNA and proteins. The ribosomal RNA molecules are named 28S, 18S etc. The "S" at the end of these names stands for a Svedberg unit. It's a measure of the size and shape of a molecule. You can tell that the 28S ribosomal RNA molecule is larger than the 18S ribosomal RNA. Similarly, the 60S subunit is the large subunit and the 40S subunit is smaller

The behavior of molecules in a liquid in a centrifuge depends on many variables including the partial specific volume of the molecule (V_r), its molecular weight (M) and the density of the solvent (ρ). The behavior is expressed as s, which is the rate of sedimentation where

                                             s = M(1-V_r)D/RT

The values for biological molecules fall into range of "s" values between 1 and 500 × 10^-13 seconds. One Svedberg unit (S) is defined as 10^-13 s units.

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Monday's Molecule #47

 

Today's molecule is the eukaryotic ribosome. That's not what you have to identify. What you have to name is the two subunits and each of the RNA components of these subunits. Trivial, common names are required.

There's an indirect direct connection between the names of these ribosome components and Wednesday's Nobel Laureate(s). In order to win you have to tell us how the components were named and supply the relevant equation. See if you can guess the Nobel Laureate. This one is not easy.

The reward goes to the person who correctly identifies the molecules and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There is only ineligible candidates for this Wednesday's reward. The prize is a free lunch at the Faculty Club.

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 the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. This way I may select multiple winners if several people get it right.

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

UPDATE: We have two winners!

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Evolution in the Ashkenazi Jewish Population

 
Over at Eye on DNA Hsien-Hsien Lei has given over her blog over to Jon Entine to promote his new book Abraham's Children [Books About DNA: Abraham’s Children by Jon Entine].

Entine points out that Ashkenazi Jews (he is one) have higher frequencies of certain diseases like breast cancer, Tay-Sachs disease, Bloom's Syndrome etc. He notes, correctly, that Ashkenazi Jews are a relatively homogeneous population in spite of the fact that they are spread out over all of Europe and have since emigrated to North America and back to Israel.

There's nothing special about this group in terms of susceptibility to disease. Other genetically isolated populations, such as French Canadians, also have elevated incidences of some genetic diseases, and lower incidences of others. We usually assume that this altered frequency of alleles is due to random genetic drift: in this case the founder effect. Since the populations were founded by small numbers of people, there were certain alleles that just by chance happened to be over- or under-represented in the ancestors.

All reports suggest that Ashkenazi Jews descend from a small number of people who left the Middle East less than 2000 years ago. Possibly only four females contributed to most of the mitochondrial DNA in today's descendants (Behar et al. 2006). Most of these early descendants settled eventually in the Rhine Valley and from there they spread eastward. The main population expansion probably occurred after 1000 AD. Today their descendants number about 8,000,000 worldwide.

There is evidence for distinct subpopulations, suggesting a number of bottlenecks in the Middle ages (Feder et al. 2007).

Jon Entine is intrigued by stories that the Ashkenazi Jews have higher IQ's than many other ethnic groups. He offers the following speculation,

The book includes a chapter explaining the possible link between so-called Jewish diseases — certain neurological and LSD disorders, as well as DNA repair problems — and the high measured IQ of Ashkenazi (Eastern European origin) Jewry. Although this theory (most recently advanced by Gregory Cochran and Henry Harpending—two non-Jews—is best classified as informed speculation (as I acknowledge in the book) at the moment, it argues persuasively, I believe, that Ashkenazi Jews are a rather distinct population group in which positive selection pressures, balanced against the killer consequences of neurological disease mutations, have led to higher IQs. The “it’s environment and culture” argument are far less persuasive. This is only one chapter in the book–most of AC is a look at our shared Israelite ancestry and history–but it is the most provocative chapter. Wonder where others come down on this issue? Interestingly, “liberal” Jews (of which I’m one) are the one’s most uncomfortable about discussing or (even if they believe it) acknowledging this point.

Leaving aside the truth of the premise, it seems very unlikely that there was selection for higher IQ. We're dealing with a polygenic trait (intelligence) in a population of about 100,000 (average) over a maximum of 70 generations and possibly less than 25 generations. It's very unlikely that the adaptive benefit of a 10% increase in IQ would have an effect in that time frame.

Assuming there really is a genetic difference in intelligence then it is far more likely that it's due to the same factors that are responsible for differences in the allele frequencies of other alleles. It looks like the people in group that left the Middle East were smarter than the ones who stayed!

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[Figure Credit: The image is Figure 2 in Behar et al. (2006)]

Behar, D.M. et al. (2006) The Matrilineal Ancestry of Ashkenazi Jewry: Portrait of a Recent Founder Event. Am. J. Hum. Genet. 78:487-497. [PubMed]

Feder, J., Ovadia, O., Glaser, B. and Mishmar, D. (2007) Ashkenazi Jewish mtDNA haplogroup distribution varies among distinct subpopulations: lessons of population substructure in a closed group. European Journal of Human Genetics 15:498–500. [PubMed]

Why Pigs Don't Have Wings

 
Jerry Fodor publishes a critique of adaptationism in London Review of Books. The title is Why Pigs Don’t Have Wings and it's an excellent read. I wish I could write like this ...

In fact, an appreciable number of perfectly reasonable biologists are coming to think that the theory of natural selection can no longer be taken for granted. This is, so far, mostly straws in the wind; but it’s not out of the question that a scientific revolution – no less than a major revision of evolutionary theory – is in the offing. Unlike the story about our minds being anachronistic adaptations, this new twist doesn’t seem to have been widely noticed outside professional circles. The ironic upshot is that at a time when the theory of natural selection has become an article of pop culture, it is faced with what may be the most serious challenge it has had so far. Darwinists have been known to say that adaptationism is the best idea that anybody has ever had. It would be a good joke if the best idea that anybody has ever had turned out not to be true. A lot of the history of science consists of the world playing that sort of joke on our most cherished theories.

UPDATE: Read Jason Rosenhouse's take on the Foder essay [Fodor on Natural Selection]. Jason makes some good points but I think he misses the main idea; namely that many scientists (and philosophers) have an inordinate confidence in natural selection as the explanation for almost everything in biology that's important (to them).

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[Hat Tip: Andrew Brown at Helmintholog: Adaptationism contested. Andrew is the author of "The Darwin Wars."]

[Photo Credit: Uncyclopedia.]

Mendel's Garden: Halloween Edition

 
The 19th version of Mendel's Garden has just been posted on Discovering Biology in a Digital World [Mendel’s Garden: Halloween Edition]. I don't think Sandra Porter likes October very much but fortunately that didn't prevent her from posting an enlightened selection of blogs from the past month.

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Goodbye John Howard?

 

According to The International Herald Tribune John Howard has called an election for November 24th [Howard announces Australian elections in November]. Chances are he's going to lose. This might be a good thing for Australia except for the fact that the probable winners might not be a great improvement.

I look forward to enlightenment from all my Australian readers. Is Australia going to move away from its close relationship with George Bush?

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Al Gore Wins the Nobel Peace Prize for Framing

 
I'm a fan of Al Gore and I would have voted for him if I'd have been an American citizen in 2000. I'd vote for him today if I could. I think he's done a fabulous job of bringing the issue of global warming to the attention of the public. (I also like his latest book The Assault on Reason).

Gore's advantage is that he is not a scientist. That means that he can spin the global warming debate in a way that advances his cause. There is much that is true in An Inconvenient Truth and that's why I support him, but in order to frame the presentation in a way that resonates with the general public he has to drop some of the nuances and present the science in a way that makes it sound far more solid than it actually is.

This is why Gore will not be receiving a Nobel Prize in Science. There are very few scientists who would be comfortable making the same presentation that Gore makes in his public talks. Most scientists know that some of the "facts" are only half-truths and some of them are still disputed within the scientific community. They believe that scientific integrity requires them to be less dogmatic and more circumspect when they talk about science.

Chris Mooney and Matt Nisbet would like all scientists to adopt the Al Gore method of presenting science in situations where they advocate changes in public policy. It ain't gonna fly for the reason that I just mentioned. What's so astonishing is that Nisbet and Mooney just don't seem to get it. They don't understand why scientists are leery about framing. It's because we can't do what Gore does without feeling a little guilty over being less than honest about the science.

This does not mean that we don't like Al Gore and other politicians who have learned to appreciate science and base their policy on good scientific foundations. It simply means that pushing science and pushing policy are two different things and the tactics used in the political arena do not belong in science. Some scientists may be able to jump back and forth from one arena to the other but its' going to be very difficult to maintain a scientific reputation under such circumstances. What Nisbet and Mooney are suggesting requires that scientists abandon true science in favor of political science.

I suspect they have a hard time seeing the problem because they're not scientists.

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The Most Beautiful Experiment in Biology

 

John Dennehy at Evilutionary Biologust has done it again. This week's citation classic is, indeed, a classic. It's the Meselson-Stahl paper from 1958 demonstrating that DNA is replicated semi-conservatively [The Most Beautiful Experiment in Biology].

The description of the experiment as the "most beautiful experiment in biology" comes from John Cairns as quoted in Horace Judson's book The Eight Day of Creation [see The Story of DNA (Part 1)]. It's a description that few of us could dispute. I grew up on the stories of famous experiments like this one and everyone around me at the time wanted to be like Matt Meselson or Franklin Stahl. If they couldn't be Meselson or Stahl then maybe Jacob, Monod, Hershey, Pardee or a host of other members of the phage group. Personally, I was envious of those who worked on bacteriophage lambda.

Over the years we kept reminding each new generation of the Meselson-Stahl experiment by describing it in the textbooks. The figure on the left is from my 1994 book. I'm sure that any student who took biochemistry or molecular biology in the 70's, 80's, and even part of the 90's, was taught this experiment.

Alas, it's no longer in the textbooks and the current generation of students probably has no idea who Meselson and Stahl are. They're probably befuddled by the reference to the most beautiful experiment in biology.

I vividly remember the debate when we decided to take it out of the textbook. Now that we can describe the molecular machinery of DNA replication it follows naturally that replication has to be semi-conservative. It no longer seems necessary to describe a separate experiment that demonstrates this obvious fact. In fact, it is often counter-productive to do so since it requires setting up the context—a time when this strong prediction of Watson and Crick had not been tested. That's not easy when even high school students know the facts.

So out it went, but not without some sadness for the passing of an era. I suppose it won't be long before some other experiment takes its place as the most beautiful. It will probably be something to do with microarrays or florescent dyes.

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Many of the classic experiments are no longer taught to undergraduates. It's the nature of the beast, I suppose. Those experiments became classics because they showed us something we didn't know previously. That "something" was so important that it now seems obvious. We don't need to teach it.

Evolution: The Triumph of an Idea

 
Evolution: The Triumph of an Idea is a wonderful book by Carl Zimmer. The cover shows a bunch of different eyes ans it's meant to convey the idea that all these eyes have evolved from a common ancestor with primitive eyes.

Bill Dembski doesn't like this idea. He doesn't like the idea of evolution either. Here's a video where Dembski displays his ignorance about evolution in general and molecular evolution in particular. The title of his talk is "Molecular Machines and the Death of Darwinism."

I sometimes wonder just how intelligent Dembski is. Does he really think that the eye is our best example of the evolution of molecular machines. Does he think that the bacterial flagellum is the only other molecular machine? Apparently he does because he doesn't mention replisomes, photosynthesis complexes, blood clotting cascades, the citric acid cycle, or any of the other molecular machines and complex systems where we have a good handle on how they evolved.

But Dembski goes even further than complex machines. He has the inside track on some research that will bring down the Darwinian idol. It's at the level of individual proteins where we're finally going to see proof of the existence of God. I can hardly wait.

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HSP90 Structure

 
Hsp90 is a molecular chaperone that plays a role in the folding and assembly of other proteins. Current ideas suggest that it binds to substrate proteins at a "client" site and this either encourages folding into the proper conformation or prevents aggregation. The binding and release of polypeptides is accompanied by hydrolysis of ATP to ADP + Pi.

The bacterial version of hsp90 is called HtpG. Eukaryotes have several different members of the Hsp90 family including one that resides in the endoplasmic reticulum. The cytosolic protein is called Hsp90 and the ER version is called GRP94. Hsp90 is a highly conserved protein showing significant sequence identity between prokaryotic and eukaryotic proteins. The HSP90 family shares many of the same characteristics of the more highly conserved HSP70s [Heat Shock and Molecular Chaperones, Gene HSPA5 Encodes BiP-a Molecular Chaperone, The Evolution of the HSP70 Gene Family].

Daniel Gewirth and his colleagues have just published the complete structure of GRP94 from dog (Canis familiaris). The article appears in Molecular Cell and their structure is on the cover of the journal (Dollins et al. 2007). This is the endoplasmic reticulum version of Hsp90 and its the only ER version of this protein whose structure is known. Gewirth has been working on the structure since 2001 and he deposited the first structural coordinates of a fragment of this protein back in February 2004. (See the Protein Data Base (PDB) for the structures. Search for "hsp90".)

The complete protein is a dimer of two identical subunits. Each monomer has three distinct domains; an N-terminal domain (N); a middle domain (M); and a C-terminal domain (C). The ATP hydrolysis site sits at the interface between the N and M domains. The C domains interact to form the dimer. The presumed site of binding for misfolded proteins ("client" site") is in the V-shaped pocket formed when the C domains come together.

The mechanism of action of Hsp90 proteins is not known although it presumably involves a conformational change induced by ATP hydrolysis. This paper provides an important clue to that mechanism because the dimer structure differs from that seen with the yeast protein (Hsp82) and the E. coli protein (HtpG) (below).
Each of the structures seems to identify a protein in one of the conformations adopted in vivo. The most likely explanation is that the wings of the protein open and close to capture and release the substrate protein. This conformational change is induced by binding and hydrolysis of ATP.

Now that we have a structure for GRP94 from dog we can compare the structures of proteins from different species to see how closely they resemble each other. Let's look at the N-terminal domain to get an idea of how protein structure is conserved over billions of years. The four structures below are, from left to right, yeast (1zwh), dog (2fyp), human (1us7) and E. coli (2ior).


Aren't they remarkably similar! This is exactly the sort of thing you expect with a highly conserved protein.

By the way, anyone can create these images by going to the PDB site [2ior] and viewing the structures with the MBT SimpleViewer. If you haven't already installed this viewer it will automatically install in your browser and it only takes a few minutes.

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Dollins, E.D., Warren, J.J., Immormino, R.M. and Gewirth, D.T. (2007) Structures of GRP94-Nucleotide Complexes Reveal Mechanistic Differences between the hsp90 Chaperones. Molec. Cell 28:41-56.