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Friday, September 12, 2008

PZ Myers Is Coming to Toronto

 

PZ Myers will be giving a talk in Toronto in an event sponsored by the University of Toronto Secular Alliance (UTSA) and the Toronto Center for Inquiry.1


CFI ONTARIO HOSTS PZ MYERS IN TORONTO

TICKETS AVAILABLE FOR WORLD LEADING ATHEIST & SCIENCE BLOGGER


"SCIENCE EDUCATION: THE WAR BETWEEN SCIENCE AND RELIGION!"2


Friday, October 31, 7:30 pm - 9:30 pm

location - MacLeod Auditorium Medical Science Building, 1 King's College Circle, Room 2158, Toronto, ON, M5S1A8

Centre for Inquiry - Ontario and the University of Toronto Secular Alliance present the popular biologist and author of the stimulating blog Pharyngula. Pharyngula is the world's leading blog dealing with science, atheism, religion and education, especially the creationism-evolution controversy. Dr. Myers was featured prominently in the recent film Expelled: No Intelligence Allowed, dealing with the supposed conspiracy to keep ID out of American universities. Dr. Myers was famously "Expelled" from the premiere screening of the very same film.

Dr. Myers is an associate professor of biology at the University of Minnesota, Morris. He obtained his B.S in zoology from the university of Washington and his Ph.D. in biology from the Institute of Neuroscience, University of Oregon.

TICKETS and PRICES!

*NEW AND RENEWING CFI MEMBERS: FREE!!
By becoming a CFI member you will gain free admission to our events, discounts on conferences at all branches, 15% discount on selected Prometheus books, access to FREE MEMBERS ONLY receptions with selected speakers, and reduced subscription rate to Free Inquiry and Skeptical Inquirer.  Upcoming events include JAMES BISS - Magician and Mentalist, NICA LALLI - Author, 9/11 DEBATE, DAN FALK - Science Journalist, and many more!

*STUDENTS AND MEMBERS: $5

*REGULAR ADVANCED: $8

*REGULAR AT THE DOOR: $10

Get your tickets in advance to ensure a spot! Buy early as prices may rise. You may:
  1. Buy tickets online through paypal at PZ Myers Comes to Toronto.

  2. Buy tickets in person at the Centre for Inquiry - Ontario (216 Beverely St.) during our opening hours (1-9pm Mon-Fri, 1-5pm Sat-Sun).

  3. Buy tickets through a cheque to: Centre For Inquiry 216 Beverley St. Toronto, ON M5T 1Z3
    *Please note if you are sending a cheque please send it before October 24th
Please note that you WILL NOT be given a physical ticket. Your name will be added to a ticket list. Thus you should *arrive early*  at the event location to find the appropriate line-up and gain access to the event. Please arrive at least a half an hour before the event. Box Office opens at 6pm.

Full event info: PZ Myers Comes to Toronto.
Please Note:  The J.J.R. MacLeod Auditorium is located in the Medical Sciences Building, University of Toronto on the north-west corner of College and University Ave. The closest subway station to the Medical Sciences Building is the Queens
Park exit.


1. We will be sponsoring a number of parties and social events in honor of PZ's visit to Toronto. Watch this blog for more information as the date approaches. We may even invite PZ to some of the events so you can meet him in person. He's actually a pretty nice guy when you get to know him.

2. Here's what PZ says about this talk as he leaves for Denver, "I'm going to gargle some tabasco before giving it, because this one needs to contain some bile and pepper, sorry to say. I'm going to say exactly what's wrong with the state of science education today, and it's all those weasely suck-ups who make excuses for religious idiocy. Anyway, if you can't make the talk, now you know what I'm going to say. It should be fun. It's OK if people argue with me, too. I expect people to fight back."

Lucky Dinosaurs

 
More and more biologists are beginning to realize that the history of life is not as determined by natural selection as they once thought. They are beginning to take to heart the idea that if you rewind and rerun the tape of life it will not turn out the same. A lot of the history is due to chance, luck, and accident.

This week's issue of Science contains a paper by Brusatt et al. (2008) discussing the evolution of dinosaurs. The dinosaurs (Dinosaura) rose to prominence around 200 million years ago in what is often called an "adaptive radiation." The idea was that dinosaurs outcompeted all other land animals because they were better able to adapt to new environments.

At the beginning of this period, the main competitors were the crurotarsans, animals that resembled dinosaurs in many ways but which aren't classified as dinosaurs. Crocodiles are crurotarsans but all other families have gone extinct.

Recent work has revealed that the crurotarsans were as diverse and abundant as the dinosaurs 200 million years ago. The authors explain the problem ...
The critical interval to consider is the Late Triassic, especially the Norian and Rhaetian (Fig. 1), a 28-million-year span between the CNEE [Carnian-Norian extinction event] and TJEE [Triassic-Jurassic extinction event]. The key "competitors" of the early dinosaurs were the crurotarsans, the "crocodile-line" archosaurs, which show a range of morphologies and adaptations during this time: long-snouted fish- and flesh-eating phytosaurs, armored herbivorous aetosaurs, and large to giant carnivorous "rauisuchians." The crurotarsans even replicated many dinosaurian body plans (large terrestrial predators; small swift predators; mid- to large-bodied low-browsing herbivores; agile bipedal herbivores). Several new discoveries show striking convergences between crurotarsans and dinosaurs (10), and many Triassic crurotarsans were previously erroneously identified as dinosaur ancestors (11) or even as true dinosaurs (12). Such morphological convergence suggests that dinosaurs and crurotarsans were exploiting similar resources in the Late Triassic. In some Norian faunas, crurotarsans were numerically more abundant than dinosaurs (3) and seem to have exploited a wider range of body plans. However, by the end of the Triassic all crurotarsans were extinct, save a few lineages of crocodylomorphs.

The key question is why the major dinosaur lineages survived the TJEE, ushering in the 135-million-year "age of dinosaurs," while most crurotarsan groups went extinct.
ResearchBlogging.orgBrusatte et al. measured evolution rates, speciations, and morphological disparity for the two groups (crurotarsans and dinosaurs) before the Triassic-Jurassic extinction event. They found no evidence that the dinosaurs were evolving more quickly or were becoming better adapted than the crurotarsans.

So, if crurotarsons were so successful why did they die out and why did the dinosaurs survive? Maybe the dinosaurs weren't better adapted, maybe they were just lucky.

The lead author of the study, Steve Brusatt, an M.Sc. student, puts it very well in the press release [Good Luck, Not Superiority, Gave Dinosaurs Their Edge, Study Of Crocodile Cousins Reveals].
"If we were standing in the Late Triassic, 210 million years ago or so, and had to bet on which group would eventually dominate ecosystems, all reasonable gamblers would go with the crurotarsans. There was no sign that dinosaurs were eventually going to succeed so why did they? The answer is two mass extinction events: the dinosaurs not only got lucky, but they got lucky twice.

"They first weathered the storm during the Carnian-Norian event 228 million years ago, but so did the crurotarsans. In contrast, many other potential competitor groups went extinct. Then dinosaurs weathered a second, much bigger, storm 200 million years ago. This was the end Triassic extinction event, which was a sudden and catastrophic extinction caused by rapid climate change, possibly facilitated by an asteroid impact. Strangely, and suddenly, all crurotarsans except for a few lineages of crocodiles went extinct. On the other hand, the dinosaurs did not. They survived and then radiated in the Early Jurassic, and very quickly established themselves as the dominant vertebrate group on land across the world.

"Why did crurotarsans go extinct and not dinosaurs? We don't know the answer to that, but we suspect that it was nothing more than luck, plain and simple.
This paper is relevant for a number of reasons unrelated to the history of dinosaurs.

  1. It shows a trend away from pure adaptationist thinking toward consideration of other explanations (e.g., accident).
  2. It emphasizes the importance of understanding mass extinctions and incorporating them into macrevolutionary studies. The conclusions echo those of David Raup in his book Extinction: Bad Genes or Bad Luck [see Good Science Writers: David Raup].
  3. It is relevant to the discussion about convergent evolution—a feature of the history of life used by theistic evolution proponents to indicate that there's a plan to evolution [Convergence]. Note that there are many examples of convergence in the crurotarsan and dinosaur lineages. Similar examples with marsupials and placental mammals are used as evidence that evolution may have had a purpose in mind. But if we apply the same reasoning to crurotarsans and dinosaurs, the purpose becomes less obvious, since both groups eventually become extinct.


[Image Credit: The drawing of a crurotarsan archosaur is from the Palaeos website, specifically Archosauromorpha: Rauisuchiformes]

Brusatte, S.L., Benton, M.J., Ruta, M. and Lloyd, G.T. (2008) Superiority, Competition, and Opportunism in the Evolutionary Radiation of Dinosaurs. Science 321:1485-1488. [DOI: 10.1126/science.1161833]

S. L. Brusatte, M. J. Benton, M. Ruta, G. T. Lloyd (2008). Superiority, Competition, and Opportunism in the Evolutionary Radiation of Dinosaurs Science, 321 (5895), 1485-1488 DOI: 10.1126/science.1161833

Daylight Saving Causes Global Warming


 
Friday's Urban Legend: True

Is it true that the following letter was published in the Arkansas Democrat-Gazette on 16 April 2007?
You may have noticed that March of this year was particularly hot. As a matter of fact, I understand that it was the hottest March since the beginning of the last century. All of the trees were fully leafed out and legions of bugs and snakes were crawling around during a time in Arkansas when, on a normal year, we might see a snowflake or two.

This should come as no surprise to any reasonable person. As you know, Daylight Saving Time started almost a month early this year. You would think that members of Congress would have considered the warming effect that an extra hour of daylight would have on our climate. Or did they?

Perhaps this is another plot by a liberal Congress to make us believe that global warming is a real threat. Perhaps next time there should be serious studies performed before Congress passes laws with such far-reaching effects.

CONNIE M. MESKIMEN
Hot Springs
Yes, it's true. But Connie Meskimen is lawyer whose hobby is writing sarcastic letters to the local newspaper according to Snopes.com [Daylight Exacerbates Warming].


[Image Credit: simplehuman]

Leaving Afghanistan

 
Canada is in the middle of an election campaign. Prime Minister Stephen Harper has announced that Canadian troops will be pulled out of Afghanistan when the current mission is up in 2011. This is a change in policy since previously Harper had argued that setting a deadline for withdrawal was a bad idea.

The announcement prompted a comment from Jim Davis, the father of a soldier killed in Kandahar two years ago. Here's what the father said according to CTV News [Tories suspend key aide over remarks on soldier's dad].
Earlier Thursday, Davis said it would be ideal to have Canadian soldiers home by 2011 but setting a deadline "undermines the work our soldiers are doing and it undermines the mission."

He said the deadline makes it difficult for Canadian soldiers to win the hearts and minds of the Afghan people if they know troops will be gone in two years.

"I would never want to see another soldier go in harm's way so I can justify my son's death," Davis told CTV's Canada AM.

"But at the same time if we pull up stakes and come home when we're not ready to -- when the mission is not complete -- if we did that then my son died in vain."
I think we should cut and run right now. We are not going to win the hearts and minds of the Afghan people as long as we continue to occupy their country and bomb them.

Does that mean that all of our Canadian soldiers died in vain in a failed mission? Yes, unfortunately, it does mean that. Should we continue the mission just because some soldiers have already lost their lives? No, that doesn't really make sense, does it? If we realize that we made a mistake and will have to withdraw sooner or later before winning hearts and minds, then what's the point of staying and sacrificing more Canadian lives?

I wish people would stop trying to justify continued involvement in Afghanistan by using the argument that our soldiers will have died in vain. Sometimes we make mistakes and soldiers pay the ultimate price for our errors. It's not their fault. They are doing their job and should be respected for that—perhaps they should be respected even more for doing their job in spite of the flawed policies of our politicians.


Thursday, September 11, 2008

An Interview with Richard Lewontin

 
Most of you know Richard Lewontin as one of the authors on a paper that every student of evolution must read [The Spandrels of San Marco and the Panglossian Paradigm].

He's also famous for other reasons [Good Science Writers: Richard Lewontin] [The Cause of Variation in a Population].

Lewontin was interviewed last February by Susan Mazur as part of her coverage ot the Altenberg 16 [see We Need to Soften the Modern Synthesis]. Lewontin starts off well by explaining that natural selection isn't the only game in town [THE ONE AND ONLY RICHARD LEWONTIN].
Suzan Mazur: Is it your opinion that natural selection is here to stay?

Richard Lewontin: Natural selection occurs. The problem for the biologist is that natural selection is not the only biological force operating on the composition of populations. There are random forces because after all population is only finite in size. And even if there’s no natural selection, everybody does not have exactly two children. Every couple doesn’t exactly have two children to replace it. And there’s randomness in which sperm fertilizes which egg. So things change for that random reason. And things change because species go extinct. Nobody knows why any particular species ever went extinct. But every species goes extinct.


Matt Tries Framing for the Umpteenth Time

 
Matt Nisbet promotes two of his essays that have just been published. He summarizes them in Two Essays on Expelled, Dawkins, and PZ by saying ...
In both essays, I draw attention to the confusing messages that scientist pundits such as Richard Dawkins and PZ Myers continue to send to the wider American public. By combining their attacks on religion with their defense of evolution, they blur the lines between science, religion, and atheism, providing fodder to creationists who claim that evolution is part of a larger atheist agenda. These confusing messages are only likely to be amplified next year during the anniversary celebration of Charles Darwin, as Dawkins goes on a publicity tour for his new book and Myers is reported to also have a book in the works.
Poor old Matt. He just doesn't get it. There's no confusion. Dawkins and PZ (and me) are on the side of rationalism in the war between rationalism and superstition. Evolution is part and parcel of the rationalism perspective while religion and creationism are on the other side.

The only person who is confused is Matt Nisbett because he wants to spin frame the debate differently. It isn't working for him 'cause Dawkins and PZ aren't playing his game.

At the end of the second essay Matt Nisbet comes very close to saying that Dawkins and Myers should shut up because they are interfering with the Nisbett spin frame.


Everything Is There for a Reason?

 
Nils Reinton of The Sciphu Weblog has just posted an article entitled Junk, DNA, RNA, Brain, Biology and Possible Solutions.

Nils makes the point that biology is very complex and we may only have scratched the surface. He then writes,
New ideas, approaches and tools are needed to explain how this seemingly chaotic system works. Dismissing reasons for the obvious complexity using terms like “junk-DNA” is not going to get us anywhere.

Instead, let’s start by acknowledging that we know very little. All we know is that function comes out of an apparent chaotic mixture of DNA protein and RNA. Let’s assume that everything is there for a reason. Without reason you loose hope and visions and those are qualities that science is vitally dependent upon.
This statement combines two of my pet peeves. First, our use of the term "junk" DNA is not based on ignorance in spite of what Nils implies. We know, for example, that 50% of our genome consists of defective transposons. That looks like junk to me [Genomes & Junk DNA]. It makes me really, really annoyed when fellow scientists assume that junk DNA supporters are basing their entire argument on lack of knowledge about biology. Instead, it appears that the other side is the guilty party.

Second, by explicitly stating that one should assume that everything is there for a reason, Nils is making the case for adaptationism. It's a weak case. Why should we assume, without evidence, that everything is an adaptation? Why not consider the possibility that it may have no function and proceed to investigate while keeping an open mind? [Adaptationomics] If becoming a pluralist makes you lose hope and visions then maybe you're in the wrong business.


We Need to Soften the Modern Synthesis

Lately there's been a lot of talk about updating evolutionary theory. Much of the hype has been generated by journalist Susan Mazur who has been drawing attention to a meeting that took place in July. At that meeting there were 16 people interested in evolution. They met at the Konrad Lorenz Institute for Evolution and Cognition Research in Altenberg, Austria. Their goal was to reach a consensus on what needs to be added to evolutionary theory in order to bring it up to date. They've been dubbed the "Altenberg 16."

The current version of evolutionary theory is often referred to as the Modern Synthesis—a term coined by Julian Huxley to describe the consensus reached by evolutionary biologists in the late 1940's. That version of evolutionary theory was appropriately pluralistic, giving prominence to random genetic drift as an important mechanism of evolution.

By the time of the Darwinian centennial celebrations in 1959, the Modern Synthesis had hardened to the point where random genetic drift was barely mentioned. Most prominent evolutionary biologists were confirmed adaptationists—including those who had been more open-minded a decade earlier.

The Altenberg 16 have some interesting ideas but unfortunately, they are also lending their reputations to some ideas that are just plain crazy. Let's see how a prominent science journalist, Elizabeth Pennisi, handles the issue in an article for Science magazine [Modernizing the Modern Synthesis].
That hyperbole has reverberated throughout the evolutionary biology community, putting Pigliucci and the 15 other participants at the forefront of a debate over whether ideas about evolution need updating. The mere mention of the "Altenberg 16," as Mazur dubbed the group, causes some evolutionary biologists to roll their eyes. It's a joke, says Jerry Coyne of the University of Chicago in Illinois. "I don't think there's anything that needs fixing." Mazur's attention, Pigliucci admits, "frankly caused me embarrassment."
That's a pretty accurate commentary on how the Alternberg 16 are viewed by most evolutionary biologists. They don't think the Modern Synthesis needs fixing. But—and this is a big "but"—they are referring to the hardened version of the Modern Synthesis; the version that can be described as ultra-Darwinian. The version that Stephen Jay Gould and others have been trying to change since 1970.

Elizabeth Pennisi seems completely unaware of this controversy in evolution. Here's how she describes modern evolutionary theory ...
Modern tradition

The modern synthesis essentially represents a marriage of the 19th century concept of evolution with Mendelian genetics, which was rediscovered at the beginning of the 20th century; the birth of population genetics in the 1920s added to the intellectual mix. By the 1940s, biologists had worked out a set of ideas that put natural selection and adaptation at evolution's core. Julian Huxley's 1942 book, Evolution: The modern synthesis, brought together this work for a broad audience.

Simply put, the modern synthesis holds that organisms have a repertoire of traits that are passed down through the generations. Mutations in genes alter those traits bit by bit, and if conditions are such that those alterations make an individual more fit, then the altered trait becomes more common over time. This process is called natural selection. In some cases, the new feature can replace an old one; in other instances, natural selection also leads to speciation.
This is definitely not the pluralism promoted by Gould and others and it's not even the original version of the Modern Synthesis published in the 1940's. Two of the key principles of the original Modern Synthesis were ...
5. Evolutionary change is a populational process: it entails, in its most basic form, a change in the relative abundances (proportions or frequencies) or individual organisms with different genotypes (hence, often with different phenotypes) within a population. One genotype may gradually replace other genotypes over the course of generations. Replacement may occur within only certain populations, or in all the populations that make up a species.

6. The rate of mutation is too low for mutation by itself to shift a population from one genotype to another. Instead, the change in genotype proportions within a population can occur by either of two principle processes; random fluctuations in proportions (genetic drift), or nonrandom changes due to the superior survival and/or reproduction of some genotypes with others (i.e., natural selection). Natural selection and random genetic drift can operate simultaneously. (Futuyma, 2005)
The hardened version of the Modern Synthesis only talks about natural selection and random genetic drift barely gets mentioned. It's too bad that Pennisi only interviewed adaptationists and it's too bad that she didn't bother to read an evolution textbook.

The current, most popular view of evolutionary theory needs to be changed. Random genetic drift needs to be restored to its rightful place. At the same time, other points of view should be considered. The problem with the current debate is that the emphasis is on the wrong problem. It's not that we need to incorporate evo-devo; instead. we need to re-incorporate well-established ideas (random genetic drift) that have been known for fifty years!


Futuyma, D. (2005) Evolution, Sinauer Associates, Inc. Sunderland, MA, USA (p. 10)

Wednesday, September 10, 2008

Should Science Speak to Faith?

 

The Scientifi American website has articles on the Evolution vs. Creationism debate. My students might be interested in a debate over how to present science to people of faith [Should Science Speak to Faith?]. The debate is between Lawrence M. Krauss and Richard Dawkins. Here's a teaser ...
Krauss: Both you and I have devoted a substantial fraction of our time to trying to get people excited about science, while also attempting to explain the bases of our current respective scientific understandings of the universe. So it seems appropriate to ask what the primary goals of a scientist should be when talking or writing about religion. I wonder which is more important: using the contrast between science and religion to teach about science or trying to put religion in its place? I suspect that I want to concentrate more on the first issue, and you want to concentrate more on the second.

I say this because if one is looking to teach people, then it seems clear to me that one needs to reach out to them, to understand where they are coming from, if one is going to seduce them into thinking about science. I often tell teachers, for example, that the biggest mistake any of them can make is to assume that their students are interested in what they are about to say. Teaching is seduction. Telling people, on the other hand, that their deepest beliefs are simply silly—even if they are—and that they should therefore listen to us to learn the truth ultimately defeats subsequent pedagogy. Having said that, if instead the primary purpose in discussing this subject is to put religion in its proper context, then perhaps it is useful to shock people into questioning their beliefs.

Dawkins: The fact that I think religion is bad science, whereas you think it is ancillary to science, is bound to bias us in at least slightly different directions. I agree with you that teaching is seduction, and it could well be bad strategy to alienate your audience before you even start. Maybe I could improve my seduction technique. But nobody admires a dishonest seducer, and I wonder how far you are prepared to go in “reaching out.” Presumably you wouldn’t reach out to a Flat Earther. Nor, perhaps, to a Young Earth Creationist who thinks the entire universe began after the Middle Stone Age. But perhaps you would reach out to an Old Earth Creationist who thinks God started the whole thing off and then intervened from time to time to help evolution over the difficult jumps. The difference between us is quantitative, only. You are prepared to reach out a little further than I am, but I suspect not all that much further.

...

Dawkins: I like your clarification of what you mean by reaching out. But let me warn you of how easy it is to be misunderstood. I once wrote in a New York Times book review, “It is absolutely safe to say that if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I’d rather not consider that).” That sentence has been quoted again and again in support of the view that I am a bigoted, intolerant, closed-minded, intemperate ranter. But just look at my sentence. It may not be crafted to seduce, but you, Lawrence, know in your heart that it is a simple and sober statement of fact.


15 Answers to Creationist Nonsense

 
The Scientific American website has several articles on Creationism Vs. Evolution.

One of the articles is 15 Answers to Creationist Nonsense from their June 2002 issue. The answers suffer from the same confusion about evolution that I've been addressing for years. It does not distinguish between evolution and natural selection and it fails to mention random genetic drift as a dominant mechanism of evolution. This is most obvious in the response to a question about speciation.
11. Natural selection might explain microevolution, but it cannot explain the origin of new species and higher orders of life.

Evolutionary biologists have written extensively about how natural selection could produce new species. For instance, in the model called allopatry, developed by Ernst Mayr of Harvard University, if a population of organisms were isolated from the rest of its species by geographical boundaries, it might be subjected to different selective pressures. Changes would accumulate in the isolated population. If those changes became so significant that the splinter group could not or routinely would not breed with the original stock, then the splinter group would be reproductively isolated and on its way toward becoming a new species.

Natural selection is the best studied of the evolutionary mechanisms, but biologists are open to other possibilities as well. Biologists are constantly assessing the potential of unusual genetic mechanisms for causing speciation or for producing complex features in organisms. Lynn Margulis of the University of Massachusetts at Amherst and others have persuasively argued that some cellular organelles, such as the energy-generating mitochondria, evolved through the symbiotic merger of ancient organisms. Thus, science welcomes the possibility of evolution resulting from forces beyond natural selection. Yet those forces must be natural; they cannot be attributed to the actions of mysterious creative intelligences whose existence, in scientific terms, is unproved.
One can easily imagine cases where speciation is driven entirely by natural selection but most of the textbooks are more pluralistic. The standard models have two populations diverging in phenotype due to either natural selection or random genetic drift or a combination of the two mechanisms.

The standard models postulate that divergence is initiated when two populations become geographically isolated as described above. If the two locales are different then the population that occupies the new environment might undergo adaptive selection, causing the divergence in morphology. However, if the two locales are similar the populations might just diverge by chance when they become geographically isolated.

Speciation occurs when the two populations have diverged to the point where they can no longer interbreed. At this point they become not only geographically isolated but also reproductively isolated.

There's no obvious way that the evolution of reproductive isolation could be due to natural selection. This would require that one population keep testing itself against the other with lack of cross-fertility providing some benefit to individuals in one of the populations. Instead, it's extremely likely that reproductive isolation is due to chance mutations that become fixed by random genetic drift. John Wilkins, our blogger expert on speciation, described this in a 2006 article that introduces sympatric speciation. Here are the relevant parts concerning the much more common mode of allopatric speciation.

Nobody denies, not even the most ardent antiadaptationist [that's me!], that aspects of organisms are strongly subject to selection, whether during speciation or after it. The critical issue is whether selection is a cause of speciation itself.

The allopatric consensus view allows for local adaptation, of course, when isolated from the parent metapopulation. What it denies is that selection for RI [reproductive isolation] occurs - how could it when speciation is occurring without contact with the reproductively isolated populations? There is selection of RI, of course, since RI on that account is a byproduct of changes in the population that are selectively favoured for ecological reasons. But not selection for RI itself [the selection of and selection for distinction is due to Elliot Sober]. So, argue allopatrists such as Jerry Coyne and Allan Orr, selection is not a cause of speciation in allopatry. And this seems right.

... If we think of speciation as "what makes a species" then we get ecological and other selective processes. If we think of speciation as "what makes it not the same species", then the explanatory focus shifts, and here the answer is, in cases when divergent selection is not going on, populations simply drift away from the reproductive reach of the ancestral population.
The bottom line here is that much of what we call speciation—especially the crucial reproductive isolation—is probably not due to natural selection. Instead, random genetic drift is the culprit. What this meams is that the answer to the question above is somewhat misleading. As it turns out, natural selection cannot account entirely, or even mostly, for all speciation events.

Some of you might recall a discussion I had in July with my colleague Spencer Barrett on this issue. He acted very annoyed when I suggested that random genetic drift might play an important role in speciation [see Species Diversity, Darwinism at the ROM]. This disagreement was made obvious to me today when I took a poll of my students in our class on Scientific Misconceptions. I asked them what they had learned from Professor Barrett in their first year class on evolution and more than 70% of them defined evolution as adaptation and were unable to identify random genetic drift as a mechanism of evolution. This means I'm going to have to explain evolution before we can discuss the evolution vs creationism controversy.

Go back and look at the second paragraph of the Scientific American answer (above). Isn't it strange that they don't even mention random genetic drift when listing other mechanisms of evolution? What's going on here? Do the science writers1 at scientific American not know about random genetic drift or do they not think that it's a valid mechanism of evolution according to their definition of evolution. I suspect both.


1. The article was written by John Rennie, a science writer who currently serves as editor in chief of Scientific American.

[Image Credits: The top image comes from webpages on evolution at CUNY Brooklynn (New York). The accompanying text reads, ""In small populations, other forces are at work. When a population is small, the presence or absence of a single individual can have a profound effect on the population gene pool. A sudden reduction in population size can also alter the remaining gene pool. This is the bottleneck effect.

A change in the gene pool brought about by chance is a genetic drift.

An extreme form of genetic drift, combined with the bottleneck effect is called the founder effect, which depends on a small group becoming isolated from the larger group, and can rapidly lead to the creation of a new species."

The bottom image comes from another article by John Wilkins, Explanation, that discusses, among other things, the role of stochastic events, such as random genetic drift, in speciation.]

Six Different Kinds of Slime Moulds

 
Which one doesn't belong on the list?
  1. Myxogastrea
  2. Dictyostelia
  3. Protostelia
  4. Buddenbrockia
  5. Myxococcales
  6. Labyrinthulea
  7. Acrasea

Check out Catalogue of Organisms, The Diversity of Slime Moulds for the correct answer.


The Nature of Science: Is Science the only Way of Knowing?

In my course today I described science as a way of knowing based on evidence and rational thinking. The key point is that science is a process, or a way of thinking. Science—the process—is not confined to the "natural" sciences. It can be used in any type of investigation that's designed to seek factual knowledge about the universe we inhabit (see Sokal, 2008).

Are there any other ways of knowing? Well, that depends on what kind of knowledge you seek. If you're interested in "truth", which I loosely define as factually correct information, then my answer is no. The application of evidence and rationality is the only way to go.

Lots of people disagree. For the sake of discussion, I've selected some examples from an article on The Nature of Science and Scientific Theories published by the Arkansas Science Teachers Association 2006. They propose four different ways of knowing.
People have several ways that they know about their world.  The chart below lists some of the ways of knowing.  One way of knowing is no more valid that another to most people.  However, as you read the chart please note that science is a way of knowing that requires the use of certain rules and methods that differs from the other means of knowing.  Scientific knowledge limited to the natural world. Scientific knowledge and religious knowledge do not have to be contradictory.  It is important to know these differences, so that they can be complementary.

Religious Knowledge
  • Seeks answers to any question that can be posed including answers to the ultimate questions (What is my purpose? What is the meaning of life? Is there a supreme being? etc.).
  • Explanations can include supernatural forces.
  • Is a belief system and seeks truths.

Philosophic Knowledge
  • Seeks answers to any question that can be posed including answers to the ultimate (What is my purpose? What is the meaning of life? Is there a supreme being? etc.).
  • Explanations can include supernatural forces and viewpoints
  • Is a point of view and seeks truths.

Cultural Knowledge
  • Seeks answers to any question that can be posed including answers to the ultimate questions (What is my purpose? What is the meaning of life? etc.), but generally relates to how people treat one another.
  • Explanations can include supernatural forces and other historical viewpoints.
  • May be a belief system rooted in historical views and seeks truths.

Science Knowledge
  • Can only seek answers about the natural world but cannot answer ultimate questions (Is there a god? What is the meaning of life?).
  • Explanations cannot include supernatural forces.
  • Is not a belief system nor seeks truths.
Why can't the science way of knowing address questions like "Is there any evidence of purpose in evolution?" "Does life have any meaning?" and "Is there any evidence of Gods?" Why are these questions arbitrarily ruled out of bounds? Does it mean that we can't apply evidence and rationality to questions about the possibility of purpose?

If religious, philosophical and cultural knowledge can be "beliefs" or "points of view" then what kind of knowledge is that? These may be some sort of "ways of knowing" but knowing about what? Surely not factual knowledge of the sort that would be convincing to an impartial observer?

Finally, why are the other three "ways of knowing" referred to as ways of "seeking truths" but science is the only one that does NOT "seek truth"? What does the scientific way of knowing seek ... lies?


Sokal, Alan (2008) What is science and why should we care?, Third Annual Sense About Science lecture February 27, 2008, University College London (UK)

Nobel Laureate: Kurt Wüthrich

 

The Nobel Prize in Chemistry 2002.

"for his development of nuclear magnetic resonance spectroscopy for determining the three-dimensional structure of biological macromolecules in solution"



Kurt Wüthrich (1938 - ) received the 2002 Nobel Prize in Chemistry for his contribution to solving complex three-dimensional structures using nuclear magnetic resonance (NMR) spectroscopy. He made significant advances in the technique of using NMR to solve the structures of proteins. Here's the description in the press release.
At the beginning of the 1980s, Kurt Wüthrich developed an idea about how NMR could be extended to cover biological molecules such as proteins. He invented a systematic method of pairing each NMR signal with the right hydrogen nucleus (proton) in the macromolecule (see fig. 4). The method is called sequential assignment and is today a cornerstone of all NMR structural investigations. He also showed how it was subsequently possible to determine pairwise distances between a large number of hydrogen nuclei and use this information with a mathematical method based on distance-geometry to calculate a three-dimensional structure for the molecule.

The first complete determination of a protein structure with Wüthrich's method came in 1985. At present 15-20% of all the thousands of known protein structures have been determined with NMR. The structures of the others have been determined chiefly with X-ray crystallography; a few with other methods such as electron diffraction or neutron diffraction.

Wüthrich shared the 2002 Nobel Prize with John B. Fenn and Koichi Tanaka.

THEME:
Nobel Laureates
The presentation speech was delivered in Swedish on December 10, 2002 by Professor Astrid Gräslund of the Royal Swedish Academy of Sciences,
Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

What would life be without proteins! Proteins are large molecules that do almost all the work in our cells. Every living organism, including a human being, has a large array of various kinds of proteins. Like diligent worker bees, they take care of what needs to be done. In principle, it works the same in this flower as in me or you.

To learn more about the diligent workers inside of cells, we want to know how they look, in order to understand what they do. This year's Nobel Laureates in Chemistry have developed methods that enable us to weigh and create pictures of giant molecules like proteins in new ways that we could hardly believe were possible. I am convinced that biochemistry is now standing on the threshold of a new era – we are beginning to become acquainted with the complete genetic code of many organisms. Soon we will be able to survey all the thousands of protein varieties that work simultaneously in a given cell. It is in this new era that the discoveries of the 2002 Nobel Laureates are so important.
Mass spectrometry has been part of the chemist's toolkit for identifying small molecules since the beginning of the 20th century. But for many years, being able to make accurate measurements of the molecular masses of large proteins was a dream for chemists. For this reason, it caused a minor revolution in the field when John Fenn and Koichi Tanaka, each in his own way, succeeded to making intact proteins fly through the mass spectrometer.

Fenn discovered that it was possible to spray a water solution of the protein, in the presence of an electrical field, in order to obtain hovering electrically charged drops. The water evaporates and the drops are scattered by their electrical charge, becoming smaller and smaller. Finally only pure protein molecules are left. Then their mass is determined by measuring the time it takes them to accelerate across a given distance – the principle being that the heavier the molecule is, the more slowly it moves.

Tanaka's special method was to fire a laser pulse toward the sample. With the right wavelength in the laser, he could make the proteins be released from their surroundings without falling apart, so that they hovered freely as charged particles. Their mass could then also be determined by measuring their time of flight.

This was one half of the year's Chemistry Prize – now I will move to the second half. This time it is not a matter of flying proteins, but swimming proteins. Using nuclear magnetic resonance, or NMR, a method that Kurt Wüthrich has further refined, it is now possible to determine the three-dimensional structure of protein molecules in a water solution. NMR is one of the chemist's best methods for examining molecules, and it has been used extensively for small molecules since the mid-20th century. But large molecules like proteins involve special problems. One of the fine points of NMR is that it enables us to see individual signals, for example, from each hydrogen nucleus in a molecule. But because a protein can contain thousands of hydrogen nuclei, how do you know which signal belongs to which nucleus?

Wüthrich devised a way of systematically determining how each signal fits together with its special hydrogen nucleus. In the bargain, he was also able to determine a large number of pairwise distances between hydrogen nuclei. This enabled him to calculate a three-dimensional structure for the protein molecule. It is something like drawing a picture of a house if you know a large number of distances in the house. So thanks to Wüthrich's discovery, we can now use NMR to examine and depict proteins in their natural environment, surrounded by water like in a cell.

So, what would life be without proteins? Since I view the world through the eyes of a biochemist, my answer is: nothing at all! Next question: How would life be as a biochemistry researcher without the tools that this year's Nobel Laureates have given us? My answer to this question is: much more difficult, and also more dull! So I would like to conclude by saying to the 2002 Nobel Laureates in Chemistry: Thank you for your fantastic contributions, which help us to better understand the chemical miracles that constantly occur in our cells – what we call life.

Dr. Fenn, Mr. Tanaka and Dr. Wüthrich,

You have made pioneering contributions to the development of methods for identification and structure analyses of biological macromolecules. Your work to make mass spectrometry and NMR applicable for detailed studies of large molecules like proteins has given us new tools for investigations of the processes that constitute life. In recognition of your services to chemistry, the Royal Swedish Academy of Sciences has decided to confer upon you this year's Nobel Prize in Chemistry.

On behalf of the Academy, I convey to you our warmest congratulations and I now ask you to receive the Prize from the hands of His Majesty the King.


Monday, September 08, 2008

Monday's Molecule #87

 
This could be difficult so I'll give you a few clues. This molecule is secreted and it's function is to degrade nucleic acid. I want the name of the molecule and also a brief description of the image you see on the left. What is it showing?

There's a indirect connection between the image of today's molecule and a Nobel Prize. We are looking for the single person most responsible for the particular kind of image you see here.

The first person to correctly identify the molecule and name the Nobel Laureate, wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are four ineligible candidates for this week's reward. You know who you are.

THEME:

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

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

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

UPDATE: This week's winner is Dima Klenchin of the University of Wisconsin. The molecule is bovine ribonuclease and the image depicts the different conformations of the molecle in solution as solved by NMR. The Nobel Laureate is Kurt Wüthrich. Congratulations Dima!


Saturday, September 06, 2008

Denyse O'Leary Is a "Top-flight Science Journalist"

 
Now that I've got your attention, let me explain.

Deborah Gyapong—that's her on the right—has a blog called Deborah Gyapong (of course). According to her profile ...
Deborah Waters Gyapong’s journalism career spans more than 20 years in television, print and radio, including 12 years as a producer for the Canadian Broadcasting Corporation’s television news and current affairs programming. Deborah now covers religion and politics primarily for Roman Catholic and Evangelical newspapers.
In a recent posting, Denyse O'Leary takes Rob Breakenridge to task, she comments on the op-ed article that Denyse published in the Calgary Herald (See Intelligent Design Creationism Is Just Anti-Evolutionism). Here are two quotations about Denyse O'Leary written by Deborah Gyapong.
Denyse, who is an expert on the various theories of evolution and intelligent design and a top-flight science journalist, ...

Denyse is the EZ [Ezra Levant] of intelligent design, i.e. she is well-informed, rational, and will eat you for breakfast if you don't have a logical, well-presented, well-researched factual argument.
No comment is necessary except to note that science journalism is in even worse shape that I imagined.


[Hat Tip: Eamon Knight in the comments section of The Big Tent Springs a Leak.]

Teaching Both Sides of the Controversy

 
I found this on Sneer Review [Teach Both Sides Of The Controversy - part 2]. It's an accurate portrayal of the weight of evidence for evolution and for Intelligent Design Creationism. So, what are we afraid of?


What we're afraid of is that the controversy won't be taught properly. I think we need to make this clear. Scientists aren't the least bit afraid of going head-to-head with any form of creationism. Teaching critical thinking and analyzing controversies is a valid part of science education and, if done properly, it can be a wonderful way to learn.

But that's not what's going to happen when creationist teachers cover evolution. They are not going to teach the controversy. They are going to teach lies about science. Teaching the controversy only applies to qualified teachers who are knowledgeable about their subject.

Let's not get trapped into opposing critical thinking and controversy. Let's focus on making sure that teachers are qualified to teach the curriculum.


The Big Tent Springs a Leak

 
It doesn't happen very often but every now and then some of the Intelligent Design Creationists slip up by not keeping on message. Here's an example of Denyse O'Leary revealing that there's a wee bit of difference between "Evolutionary Creation" and "Intelligent Design Creation" [ Evolutionary Creationism? I am supposed to promote THAT?].

She refuses to promote a book called Evolutionary Creation: A Christian Approach to Evolution by Denis Lamoureux because he had the audacity to criticize Michael Behe.
I have had several conversations with Lamoureux, and he has struck me as a typical fatuous sellout of the decaying “evangelical Christian” culture that currently helps to deform Canada.

Earth to Lamoureux: Darwin is not the answer to any problem we now have. There is NO need to figure out how to incorporate him into our life together.

Just forget him and start figuring out what really happened in the history of life. Stop attacking people who know that Darwinism - and all its works - is false.
Hmmm ... many the wedge strategy is working after all.


Friday, September 05, 2008

Science Writers Need Science History

 
Carl Zimmer does it again! This time he shows why he's the best science writer by getting three things right in the same article: (1) junk DNA, (2) the existence of regulatory sequences isn't news, and (3) history is important [Science Writers Need Science History].

I bet he reads the blogs [What's Wrong wiht Modern Science?] [Junk in Your Genome: Protein-Encoding Genes] [Stop the Press!!! ... Genes Have Regulatory Sequences!].


Into the Textbooks It Goes

 
This week's issue of Science contains an important paper.
Maier, T,, Leibundgut, M. and B. Nenad (2008) The Crystal Structure of a Mammalian Fatty Acid Synthase. Science 321:1315-1322.
We've known for a long time that this is a very important enzyme and that it's a classic example of a little protein machine combining the activities of may different enzymes in order to carry out the complex reactions of fatty acid synthesis. Here's how I described it in the last edition of my book ...
In bacteria, each reaction in fatty acid synthesis is catalyzed by a discrete monofunctional enzyme. This type of pathway is known as a type II fatty acid synthesis system (FAS II). In animals, the various enzymatic activities are localized to individual domains in a large multifunctional enzyme and the complex is described as a type I fatty acid synthesis system (FAS I). The large animal polypeptide contains the activities of malonyl/acetyl transferase, 3-ketoacyl-ACP synthase, 3-ketoacyl–ACP reductase, 3-hydroxyacyl–ACP dehydratase, enoyl–ACP reductase, and thioesterase. It also contains a phosphopantetheine prosthetic group (ACP) to which the fatty acid chain is attached. Note that the malonyl CoA:ACP transacylase enzyme shown in Figure 16.3 is replaced by a transferase activity in the FAS I complex. This transferase catalyzes a substrate loading reaction where malonyl CoA is covalently attached to the ACP-like domain on the multienzyme polypeptide chain. The eukaryotic enzyme is called fatty acid synthase.
The structure (shown below) will be going right into the textbooks.




Citation Classic: Recombinant DNA

 
Read John Dennehy's citation classic for this week at This Week's Citation Classic: Genetic Engineering. The paper is one of the first examples of genetic engineering and recombinant DNA technology. Before you go, try and guess when the paper was published. Was it before you were born or after?


[Photo Credit: Protesters at the National Academy of Sciences Forum on Recombinant DNA from The Maxine Singer Papers]

Sue Blackmore on Teaching Critical Thinking

 
Susan Blackmore is an interesting person. According to her Website ...
Sue Blackmore is a freelance writer, lecturer and broadcaster, and a Visiting Lecturer at the University of the West of England, Bristol. She has a degree in psychology and physiology from Oxford University (1973) and a PhD in parapsychology from the University of Surrey (1980). Her research interests include memes, evolutionary theory, consciousness, and meditation. She practices Zen and campaigns for drug legalization.

Sue Blackmore no longer works on the paranormal.
Yesterday she published an article in The Guardian (UK) [Opening Minds].
Should science teachers in Britain challenge their students' religious beliefs? Is it their right? Is it even their duty?

I say yes. This is (amongst much else) what education is for; to teach children how to think for themselves. And thinking for yourself is challenging, especially if your previous beliefs were based on dogma and ancient books.
This may illustrate one of the ways that education in the UK differs from that in the USA.
I don't mean that science teachers should belittle religious beliefs, or scoff at them, or even tell students they are wrong. They need not even mention religion or creationism. What they must do is explain so clearly how natural selection works that those students, like one or two in Dawkins' series, begin to feel the terrifying impact of what Darwin saw. This realisation will change them. It will challenge what mummy and daddy told them, it will cry out against what they heard in chapel or synagogue or mosque. It will help immeasurably in their ponderings on human nature, the origins of life and the meaning of existence. This is growing up. This is learning. This is the process that skilful science teachers need to initiate, encourage, and help sensitively to guide.

They should never shy away from challenging their students' religious beliefs and opening their minds, because understanding the world through science inevitably does just that.
I'm all for challenging students to think. Problem is, you'd better make sure you know what you're talking about. I'd like to challenge Sue Blackmore to stop thinking about Darwin, Dawkins and natural selection and start thinking about the 21st century version of evolution.

Next question is, how do we evaluate students in such a course? Can they still pass if they reject evolution and critical thinking?


[Hat Tip: RichardDawkins.net]

The Earth's Axis Has Shifted by 26°!

 
Friday's Urban Legend: FALSE

Today's dose of non-critical thinking comes from the August 9th issue of New Scientist [Tilting Earth Cover up].
WORRIED by hurricanes, earthquakes and volcanoes? Wondering what to blame? Would you believe that these have all been linked to the Earth's axis shifting by 26 degrees in two stages, one in late 2004 and one in early 2005?

How is it, you may well ask, that you didn't notice? It's because the US government covered it up, as you will learn at http://axischange.wordpress.com. Apparently the Global Positioning System broke down at these times and it was kept secret.
Even bigger laughs can be had at Divulgence.net.

Apparently Phil Plait of Bad Astronomy dealt with this issue some time ago.
Bad Astronomy points out that if the Earth's axis had shifted that much, we would have been in sunlight at midnight, whereas in fact it was quite definitely dark. What's more, even if we didn't look out of the window, we would surely have spotted the satellite TV blinking off as the satellite dishes ceased to point to where the satellites are.
I'd like to link to Phil's posting on this issue—does anyone have a URL? Here's the link to Bad Astronomy [Tilt!]


Knowing How to Learn

The August 9, 2008 issue of New Scientist contains an important commentary by A.C. Graying on The importance of knowing how.

The key point is in the third paragraph ...
So although everyone coming out of an educational system should at least know the periodic table, the salient dates of world history, the fundamentals of geography, and other kinds of basic information, they are much more in need of knowing how to find things out, how to evaluate the information they discover, and how to apply it fruitfully. These are skills; they consist in knowledge of how to become knowledgeable.
I agree with this statement. The most important goal of a university education is, in my opinion, to teach students how to think. An important part of that goal is teaching students how to acquire reliable information.
Knowing how to evaluate information, therefore, is arguably the most important kind of knowledge that education has to teach. Some schools offer courses in it, and there are a number of books about it on the market. But only the International Baccalaureate makes critical thinking ("theory of knowledge") a standard requirement, and in this as in so many ways it leads the field, because critical thinking and evaluation of claims to knowledge should always be right at the centre of the educational enterprise.
I'm not so sure that the IB program is the only one that teaches critical thinking but I agree with the general idea here. I think every university should require that students take certain courses on logic and knowledge. These courses should be taught by philosophers.
I wonder whether the need for critical thinking lessons is more urgent in the humanities than the sciences because the latter, by their nature, already have it built in. The science lab at school with its whiffs, sparks and bangs is a theatre of evaluation; the idea of testing and proving is the natural order there, and the habits of mind thus acquired can be generalised to all enquiry.

When we talk of scientific literacy, one thing we should mean is acquisition of just this mindset; without it, too much rubbish gets through.
Hmm ... I don't think I would have had the gumption to claim that science students may be better at critical thinking than humanities students. I may think it, but writing it is a different story.

If true, the problem may be related to what passes for "postmodernism" in the humanities. Believe it or not, there are humanities Professors whose ideas about critical thinking are quite bizarre. I've met some of them. They think it's wrong to pick a side in an intellectual dispute because all sides are equally valid. They think that we can't really "know" anything. For them, I guess "knowing how to learn" is an oxymoron.


[Photo Credit: Professor A.C. Grayling, Professor of Philosophy, Birkbeck, University of London UK.]

Is Your Name Steve or Stephanie?

 
If you answered "yes" to that question then you are one third of the way toward winning a huge prize. All you have to do is answer "yes" to two more questions: (1) do you have a Ph.D., (2) do you agree with the following statement ...
Evolution is a vital, well-supported, unifying principle of the biological sciences, and the scientific evidence is overwhelmingly in favor of the idea that all living things share a common ancestry. Although there are legitimate debates about the patterns and processes of evolution, there is no serious scientific doubt that evolution occurred or that natural selection is a major mechanism in its occurrence. It is scientifically inappropriate and pedagogically irresponsible for creationist pseudoscience, including but not limited to “intelligent design,” to be introduced into the science curricula of our nation’s public schools.
Check out Panda's Thumb for more details about Project Steve [Looking for Dr. 900].1



1. You don't have to be American (I think).

Thursday, September 04, 2008

Critical Thinking Skills in Science

 
I start teaching a course next week on misconceptions and controversies in science. One of the goals is to teach critical thinking skills. I think we'll start out by discussing the objectives of the recently passed law in Louisiana. It looks like a good description of what we should be trying to do in university and it has the added advantage that we can segue right into creationist lies, cynicism, and hypocrisy.
AN ACT


To enact R.S. 17:285.1, relative to curriculum and instruction; to provide relative to the teaching of scientific subjects in public elementary and secondary schools; to promote students' critical thinking skills and open discussion of scientific theories; to provide relative to support and guidance for teachers; to provide relative to textbooks and instructional materials; to provide for rules and regulations; to provide for effectiveness; and to provide for related matters.

Be it enacted by the Legislature of Louisiana:

Section 1 R.S. 17:285.1 is hereby enacted to read as follows:

285.1 Science education; development of critical thinking skills

A. This Section shall be known and may be cited as the "Louisiana Science Education Act."

B. (1) The State Board of Elementary and Secondary Education, upon request of a city, parish, or other local public school board, shall allow and assist teachers, principals, and other school administrators to create and foster an environment within public elementary and secondary schools that promotes critical thinking skills, logical analysis, and open and objective discussion of scientific theories being studied including evolution, but not limited to evolution, the origins of life, global warming, and human cloning.

     (2) Such assistance shall include support and guidance for teachers regarding effective ways to help students understand, analyze, critique, and objectively review scientific theories being studied, including those enumerated in Paragraph (1) of this Subsection.

C. A teacher shall teach the material presented in the standard textbook supplied by the school system and thereafter may use supplemental textbooks and other instructional materials to help students understand, analyse, critique and review scientific theories in an objective manner, as permitted by the city, parish, or other local public school board.

D. This Section shall not be construed to promote any religious doctrine,promote discrimination for or against a particular set of religious beliefs, or promote discrimination for or against religion or nonreligion.

E. The State Board of Elementary and Secondary Education and each city, parish, or other local public school board shall adopt and promulgate the rules and regulations necessary to implement the provisions of this Section prior to the beginning of the 2008/2009 school year.
I ain't no lawyer but to me it looks like this is going to be a hard law to challenge in court. We all know its purpose—to promote religion—but its authors may have done a good job of phrasing it in a way that avoids a challenge.

Any lawyers out there?


Why Is ATP an Important Energy Currency in Biochemistry?

For many years the answer to this question seemd obvious. As described by Fritz Lipmann, ATP has "high energy" bonds. When these bonds are cleaved by hydrolysis a large amount of free energy is released and this energy can be captured and used to perform useful work.

By the mid-1960s this concept was being challenged by biochemists with a deeper appreciation of thermodynamics and chemistry. For example, Albert Lehninger1 wrote in Bioenergetics (1965).
The High-Energy Phosphate Bond—a Misnomer

Those phosphorylated compounds having a relatively high free energy of hydrolysis, such as ATP, phosphocreatine, and phosphopyruvate, are often spoken of as having high-energy phosphate bonds, and such bonds are universally designated by the symbol ~P. These expressions have been very useful and handy to biochemists, but they can be very misleading to the beginner. The term "high-energy phosphate bond" is an unfortunate misnomer because it implies that the energy spoken of is in the bonds and that when the bond is split, energy is set free. This is quite wrong. In the ordinary usage of physical chemistry, bond energy is defined as the energy required to break a given bond between two atoms. Actually relatively enormous energies are required to break chemical bonds, which would not exist if they were not stable. The term "phosphate bond energy" thus does not refer to the true bond energy of the covalent linkages between the phosphorus atom and the oxygen or nitrogen atom. The term "high energy phosphate bond" means only that the difference in energy content between the reactants and the products of hydrolysis is relatively high: the free energy of hydrolysis is not localized in the actual chemical bond itself. It is regrettable that this use of these terms is so deeply ingrained by long usage, but it will not matter if we keep this true meaning in mind.
Lehninger goes on to explain why the standard Gibbs free energy of ATP hydrolysis is such a large negative number. His version is out-of-date so I'll give the modern view from a textbook that I'm very familiar with2 ...

We're discussing the following reaction

ATP + H2O → ADP + Pi          ΔG°′ = -32 kJ mol-1
Several factors contribute to the large amount of energy released during hydrolysis of the phosphoanhydride linkages of ATP.
  1. Electrostatic repulsion among the negatively charged oxygen atoms of the phosphoanhydride groups of ATP is less after hydrolysis. (In cells, ΔG°′hydrolysis is actually increased [made more positive] by the presence of Mg2+ which partially neutralizes the charges on the oxygen atoms of ATP and diminishes electrostatic repulsion.)
  2. The products of hydrolysis, ADP and inorganic phosphate, or AMP and inorganic pyrophosphate, are better solvated than ATP itself. When ions are solvated, they are electrically shielded from each other. The decrease in the repulsion between phosphate groups helps drive hydrolysis.
  3. The products of hydrolysis are more stable than ATP. The electrons on terminal oxygen atoms are more delocalized than those on bridging oxygen atoms. Hydrolysis of ATP replaces one bridging oxygen atom with two new terminal oxygen atoms.
The three contributions are: electrostatic repulsion; solvation effects; and resonance stabilization. The one most responsible for the large negative Gibbs free energy change is the solvation effect. The energies of solvation of ADP and inorganic phosphate are much greater than that of ATP, making hydrolysis to its products a more favorable state.

UPDATE:Under standard conditions the concentrations of substrates and products are equal (1M). Under those conditions, the reaction will proceed to the right until the concentration of ADP is very much higher than that of ATP. When the reaction reaches equilibrium the rates of the forward and reverse reactions are equal and ΔG = 0. At that point, there is no net free energy gain from hydrolysis of ATP. The only reason ATP is an energy currency inside cells is because the system is maintained (regulated) far from equilibrium. In fact, the concentration of ATP inside cells is higher than than that of ADP and the actual free energy change is even more negative than -32 kJ mol-1 [see The Demise of the Squiggle].


1. See Good Science Writers: Albert Lehninger.

2. Horton, H.R., Moran, L.A., Scrimgeour, K.G., perry, M.D. and Rawn, J.D. (2006) Principles of Biochemisty. Pearson/Prentice Hall, Upper Saddle River N.J. (USA)

The Demise of the Squiggle

Fritz Lipmann is often credited with discovering ATP but that's not correct. He won his Nobel Prize for discovering Coenzyme A [The Nobel Prize in Physiology or Medicine 1953].

However, it's fair to say that Lipmann made some of the most important contributions to our understanding of ATP as an energy currency. His classic 1941 paper in Advances in Enzymology was entitled "Metabolic Generation and Utilization of Phosphate Bond Energy." In that paper he introduced the concept of an energy-rich phosphate bond designated by a squiggle (~). Thus ATP could be represented as

AMP~P~P

to show that it had two such high energy bonds. The cleavage of either bond is accompanied by a large release of energy that's available to do work. The idea that ATP contained some special bonds with high energy was very attractive and the concept ruled in biochemistry textbooks for several decades. Indeed, there are still many courses and websites that still use the squiggle.

The concept is extremely misleading and came under attack by many biochemists in the 1950s and 60s. According to these biochemists, the correct way of looking at ATP as an energy currency is to recognize that the overall reaction of hydrolysis is associated with a large negative Gibbs free energy change.

ATP + H2O → ADP + Pi          ΔG°′ = -32 kJ mol-1


It's the system, including reactants and products, that is associated with the large negative free energy change. The only reason ATP is useful as an energy currency is because the concentration of ATP is maintained at high levels relative to ADP + Pi inside the cell. As a matter of fact, the actual Gibbs free energy change in vivo is closer to -48 kJ mol-1.

If the system were allowed to reach equilibrium then ΔG°′ = 0. Think about what this means. At equilibrium those ~P "high energy" bonds are still being broken but there's no useful energy being produced.

Does this mean that the strength of a chemical bond depends on the relative concentration of reactants and products? Of course not. What it means, in the words of someone who knew Friz Lipmann, is that his understanding of basic thermodynamics was rudimentary.

The arguments over the proper way to think about ATP raged back and forth in the scientific literature for over thirty years. For the most part Lipmann did not participate in the squiggle debates, he left his defense to others. It's fair to say that there was no knock-out blow that ended the fight. Gradually people began to realize that the squiggle—and the concept of a high energy bond—were unfortunate at best and possibly misleading to the point of being counter-productive. The squiggle has been dropped from most (all?) textbooks.

So, how do we explain the fact that ATP hydrolysis is associated with a large release of energy under conditions found inside the cell? If it's not because of some special "high energy" bond, then what is it? See Why Is ATP an Important Energy Currency in Biochemistry?.


Here's a couple of articles on the history of the squiggle:

Fritz Lipmann

Power, Sex, Suicide: Mitochondria and the Meaning of Life: The elusive squiggle (p.80>)

Here are some websites that still refer to "high-energy" bonds and still use the squiggle. It's interesting that most of these sites include a modest disclaimer, stating that there's no such thing as a "high-energy bond" but they then go on to talk about high energy bonds using the squiggle notation.

Rensselaer Polytechnic Institute

Columbia University

University of Connecticut

Online Textbook: Department of School Education, Govt. of Tamil Nadu, India

[I am indebted to my colleague Byron Lane for explaining the history to me. He was a post-doc in the Lipmann lab during the 1950s where he was in a position to observe the debate first-hand. Byron kindly gave me copies of the relevant papers. Our discussion began when we realized that the kinds of scientific debates that were common in the past are no longer occurring even though there are many controversies bubbling beneath the surface. We don't know why. Does anyone?]

Tangled Bank #113

 
The latest issue of Tangled Bank has been published on En Tequila Es Verdad [The Tangled Bank #113: A Labor Day Carol].
Blogging across the parallel universes brings not only rewards but a burden of responsibilities. I learned this to my chagrin one day in 2112, on Tangled Bank #113, a beautiful little terraformed world in Parallel U. Gamma, named in honor of the great Charles Darwin. Certain theories of time travel had recently been overturned. My physicist friend Yoo Chung burst in my door shortly after creating a time travel device that utilized the wormholes he once doubted.

"Dana! Grab your Smack-o-Matic and hurry!" he shouted, arms flailing like dear little windmills. "Darwin never published Origin in Parallel U. Cappa. Now the backward denizens of that universe have stolen a U-Skipper from the anthropologists sent to observe them and are planning to unleash ignorance bombs throughout the multiverse! There's no time to lose!"


Send an email message to host@tangledbank.net if you want to submit an article to Tangled Bank. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.