No Intelligence Allowed

 
Ben Stein is the star of a new film that's about to be released. It's called Expelled: No Intelligence Allowed and it's supposed to document the behavior of the evil atheist Darwinists who are suppressing the truth about how life began. (It was God that did it, dummy.)

Stein is interviewed by Bill O'Reilly, providing us with an excellent example of the intelligence that's being expelled from scientific debate. Why in the world should we have any respect for the opinion of Ben Stein?



One of the things that constantly amazes me about this issue is how people like Bill O'Reilly can survive on a major TV network. I guess intelligence isn't a requirement.

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[Hat Tip: PZ Myers at Pharyngula (Two people vying to out-stupid each other)]

Why Five Fingers?

Josh Rosenau is settling into his new job at the National Center for Science Education (NCSE). Part of his mission is to educate us in the ways of evolution and so far he's doing a great job. NCSE has always had a correct perspective on evolution, as far as I'm concerned, even though some of the people who used to work there tended to favor adaptationism.

Here's Josh's latest from his blog Traveling from Kansas [The Panglossian Paradigm, or as science moves forward, creationists move back]. Note that the opinions on his blog do not necessarily reflect those of NCSE.

For really confused students, I draw on a point Stephen Jay Gould made in Eight Little Piggies (in the essay by the same name), that the number of fingers we have is entirely contingent on history. While one can try to construct an explanation for the superiority of 5 fingers, paleontological history shows that there were potential ancestors of the tetrapod clade (which we are part of) which had as many as eight rays per fin. If they had succeeded, 8 fingers would be the norm, and the Simpsons would look very odd with only 4. As Gould says of historical contingency: "Other configurations would have worked and might have evolved, but they didn't--and five works well enough."

In the essay, Gould is building on a point he made most forcefully in an essay he wrote with Richard Lewontin, "The Spandrels of San Marcos and the Panglossian Paradigm: A Critique of the Adaptationist Program." The point was that biologists were too quick to insist that every feature was adaptive and a result of natural selection. Spandrels are triangular structures produced when two round arches meet. They are necessary byproducts of joining rounded and flat surfaces. Nonetheless, in many churches they are richly decorated and the entire artistic vision for a space can be shaped by the spandrels. One might, Gould points out, be lead to think that the spandrels are there in order to be used for paintings, and not that they are necessary by-products nicely dressed up. The worldview he criticizes treats anything, whether spandrels or five fingers, as the product of intense selection, a perfect solution to the problems it faces.

There's lot more where that came from so get on over to Travelling from Kansas for more information on the "correct" worldview.

By coincidence, today's Scientific American question is Why do most species have five digits on their hands and feet?. While there's a bit of catering to an adaptationist perspective the answer to the question is ...

Is there really any good evidence that five, rather than, say, four or six, digits was biomechanically preferable for the common ancestor of modern tetrapods? The answer has to be "No," in part because a whole range of tetrapods have reduced their numbers of digits further still. In addition, we lack any six-digit examples to investigate. This leads to the second part of the answer, which is to note that although digit numbers can be reduced, they very rarely increase. In a general sense this trait reflects the developmental-evolutionary rule that it is easier to lose something than it is to regain it. Even so, given the immensity of evolutionary time and the extraordinary variety of vertebrate bodies, the striking absence of truly six-digit limbs in today's fauna highlights some sort of constraint.

Remember the take-home lesson (mostly from Josh's article). Living organisms are not well designed in spite of what the creationists and the adaptationists would have you believe.

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Monday's Molecule #48

 
Today's molecule is several molecules and a reaction. You have to identify all the molecules in the reaction and name the common enzyme that catalyzes the reaction.

There's connection between this reaction and Wednesday's Nobel Laureate(s).

The reward goes to the person who correctly identifies the molecules, the enzyme, and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There are only two 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 molecules, the enzyme, 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. This one is easy. Get your response in quickly.

Comments will be blocked for 24 hours. Comments are not open.

UPDATE: We have a winner!

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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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