Ethidium Bromide Is a Dangerous Chemical

 
Friday's Urban Legend: PROBABLY FALSE

Monday's Molecule #35 from last month was ethidium. The salt, ethidium bromide, is used as a dye to stain DNA [Ethidium Bromide Binds to DNA].

Most of us have heard that ethidium is a potent mutagen so you need to be very careful when using it in the lab. Wear gloves at all times and dispose of any excess ethidium solutions in the proper containers.

According to Rosie Redfield, a microbiologist at the University of British Columbia (Canada), this may have been an overreaction to the presumed dangers of ethidium bromide [Heresy about Ethidium Bromide].

THEME

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Deoxyrobonucleic Acid (DNA)Apparently ethidium is regularly used as a drug to treat African Sleeping Sickness and it shows no significant ill effects when used at doses that are 1000 times what we use in a typical laboratory.

Creationist Delusions about Transitional Fossils and Information

 
As expected, the IDiots are gloating over the widespread media misrepresentation of human evolution based on a recent Nature paper [The Ileret Skulls: My Two Cents] [Man Bites Dog].

Over on Uncommon Descent, one of our favorite IDiots has jumped on the bandwagon [Paleoanthropologists bungle again…]. The sycophants that are allowed to post comments on that blog have raised the old issue about the presumed lack of transitional fossils. As usual, they demonstrate their lack of understanding of evolution although, in this case, they have lots of company in the media and even among some scientists.

One person has posted this video of Richard Dawkins being interviewed by Creationists. The sycophants are delighted because it supposedly shows Dawkins being stumped by the demand that he give an example of the increase in genetic information in the genome. They ignore the second part of the video where he explains why we don't see the kinds of transitional fossils that the Creationists demand.



Look at the first part of the video. This is a very famous incident and Dawkins has written about it several times, most notably in a lengthy article on Australian Skeptics [The Information Challenge]. The article also appears in A Devil's Chaplain. Here's how Dawkins describes the incident.

In September 1997, I allowed an Australian film crew into my house in Oxford without realising that their purpose was creationist propaganda. In the course of a suspiciously amateurish interview, they issued a truculent challenge to me to "give an example of a genetic mutation or an evolutionary process which can be seen to increase the information in the genome." It is the kind of question only a creationist would ask in that way, and it was at this point I tumbled to the fact that I had been duped into granting an interview to creationists - a thing I normally don't do, for good reasons. In my anger I refused to discuss the question further, and told them to stop the camera. However, I eventually withdrew my peremptory termination of the interview as a whole. This was solely because they pleaded with me that they had come all the way from Australia specifically in order to interview me. Even if this was a considerable exaggeration, it seemed, on reflection, ungenerous to tear up the legal release form and throw them out. I therefore relented.

My generosity was rewarded in a fashion that anyone familiar with fundamentalist tactics might have predicted. When I eventually saw the film a year later, I found that it had been edited to give the false impression that I was incapable of answering the question about information content. In fairness, this may not have been quite as intentionally deceitful as it sounds. You have to understand that these people really believe that their question cannot be answered! Pathetic as it sounds, their entire journey from Australia seems to have been a quest to film an evolutionist failing to answer it.

With hindsight - given that I had been suckered into admitting them into my house in the first place - it might have been wiser simply to answer the question. But I like to be understood whenever I open my mouth - I have a horror of blinding people with science - and this was not a question that could be answered in a soundbite. First you first have to explain the technical meaning of "information". Then the relevance to evolution, too, is complicated - not really difficult but it takes time. Rather than engage now in further recriminations and disputes about exactly what happened at the time of the interview (for, to be fair, I should say that the Australian producer's memory of events seems to differ from mine), I shall try to redress the matter now in constructive fashion by answering the original question, the "Information Challenge", at adequate length - the sort of length you can achieve in a proper article.

Now that I've provided the link, I'm certain all the IDiots over on Uncommon Descent will read the Dawkins article and learn how new information gets into the genome. That should be the end of this little episode, right?

Dawkins on the Sandwalk

 
Somebody else has walked the walk [90% True]. They took a picture of Dawkins' book but if they have pictures of themselves on the Sandwalk I'd be happy to post them.

T. Ryan Gregory on the Sandwalk

John Wilkins on the Sandwalk

Walk the Sandwalk

[Hat Tip: PZ Myers]

Oklahoma Specialty License Plates

 
You can buy a whole bunch of different specialty license plates in Oklahoma like the one below [Oklahoma Specialty License Plates]. I looked through the list but I didn't find any that said "I Support Abortion" or "Atheist" or "Socialized Medicine" or "Cut and Run" or "Gay Marriage" or "Screw Oklahoma." I wonder why?


[Hat Tip: John Lynch]

Creationism Continuum

In an earlier posting [What Is Creationism?] I took issue with Denyse O'Leary and fellow blogger Mike Dunford who agree that Intelligent Design isn't creationism. My position is that there are various definitions of creationism and I prefer the definition that includes all believers in a Creator God.

The posting prompted considerable discussion about the meaning of the word "creationism." There are many commentators who insist that Creationism means only one thing—a belief in Special Creation as described in the Bible. Jonathan Badger of T. TAXUS (photo on left) expressed his disapproval of my definition by writing,

I am not "choosing" a definition of creationism, Larry -- you are. Or perhaps it would be truer to say that you are trying to *invent* a new definition. Please show a dictionary definition of "creationism" that doesn't mention the bible if you disagree with me. Both Old Earth Creationists and Young Earth Creationists believe that the events of Genesis literally happened -- the only difference between the two is the Old Earth types think their god defines "days" differently than people do, and so 7 "days" could be millions of human years.

I understand what you are trying to do -- most sane people (even mainstream theists) agree that creationists are nut cases, and so redefining "creationist" to mean "theist" is a cute rhetorical trick, much like how some right-wingers want to redefine "socialist" to mean anyone who wants a government providing social services. But such word games are pretty childish on any side.

This deserves a more extensive response than my comments on the earlier thread. There are several different points that I'd like to address so here goes.

Another Definition of Creationism

Jonathan accuse me of "inventing" a new definition of creationism—one that's not found in standard dictionaries. He quoted several dictionary sources that were similar to the one in the American Heritage Dictionary,

Creationism: Belief in the literal interpretation of the account of the creation of the universe and of all living things related in the Bible.
                        ...American Heritage Dictionary

Nobody denies that this is one of the definitions in common usage. That's not the point. The point is rather that it's not the only definition and if you choose this one, as Denyse O'Leary and the some of the IDiots do, then you are obligated to make that clear. Jonathan disagrees because he claims that this is the only legitimate definition. He is wrong.

When I open a page of Darwin I immediately sense that I have been ushered into the presence of a great mind. ... When I read Phillip Johnson, I feel that I have been ushered into the presence of a lawyer.

Richard Dawkins (1996)Phillip Johnson is one of the founders of Intelligent Design Creationism. His position has been very clear from the beginning and it's a legitimate philosophical stance in spite of Dawkin's dislike of lawyers.

Johnson maintains that creationists are anyone who believes in a Creator and he rejects the narrow definition of Duane Gish and the Young Earth Creationists.

I am not interested in any claims that are based on a literal reading of the Bible, nor do I understand the concept of creation as narrowly as Duane Gish does. If an omnipotent Creator exists He might have created things instantaneously in a single week or through gradual evolution over billions of years. He might have employed means wholly inaccessible to science, or mechanisms that are at least in part understandable through scientific investigation.

The essential point of creation has nothing to do with the timing or the mechanism the Creator chose to employ, but with the element of design or purpose. In the broadest sense, a "creationist" is simply a person who believes that the world (and especially mankind) was designed and exists for a purpose. With the issue defined that way, the question becomes: Is mainstream science opposed to the possibility that the natural world was designed by a Creator for a purpose? Is so, on what basis?
                        Phillip Johnson (1993)

Johnson is attempting to draw a line between religion and science and between creationism and naturalism, where naturalism is defined as the belief that supernatural beings play no role in creating or maintaining the universe. In addition, Johnson maintains that evolution, properly understood, is entirely naturalistic and therefore inconsistent with a Creator. Thus, according to Johnson there is a shape line between creationism and evolutionism. If you believe in a Creator, as all Christians do, then you cannot believe in evolution.

Ironically, Johnson's position is similar to that of many atheists a fact that has been gleefully pointed out by Theistic Evolutionists who want to distance themselves from both the philosophical naturalist position and the Young Earth Creationist position. In an earlier essay, I've tried to explain why this "middle ground" is an illusion ["Theistic Evolution: The Fallacy of the Middle Ground"].

The broad definition of creationism is shared by many religious scholars who are unhappy with the narrow definition that's confined to a literal belief in the Bible. The position of the Roman Catholic Church, for example, is strongly in favor of a creationist viewpoint [Creation]. This is a view that's shared by many religious scientists as well. For example, Howard J. Van Till, a Professor of Physics and Astronomy (and an evolutionist) writes,

All Christians are authentic "creationists" in the full theological sense of that term. We are all committed to the biblically-informed and historic Christian doctrine of creation that affirms that everything that is not God is part of a creation that has being only because God has given it being and continues to sustain it. As a creation, the universe is neither a divine being nor a self-existent entity that has its being independent of divine creative action. This theological core of the doctrine of creation sets Judeo-Christian theism in bold distinction from both pantheism (all is God) and naturalism (all is nature).
                        Howard J. Van Till (1998)

Now, as it turns out, most of these theologians and scientists are perfectly aware of conflicting definitions of "creationism," which is why they take pains to define their terms. They don't want to cede to the religious right a perfectly good word that describes their belief in a Creator God. That's why Theodosius Dobzhansky says the following in his famous article Nothing in Biology Makes Sense Except in the Light of Evolution (1973).

I am a creationist and an evolutionist. Evolution is God's, or Nature's method of creation. Creation is not an event that happened in 4004 BC; it is a process that began some 10 billion years ago and is still under way.

In some cases, the stigma of Young Earth Creationism is too much to bear and scientists go out of their way to avoid the creationist label. This is explained by Francis Collins in his book The Language of God.

Few religious of scientific views can be neatly summed up in a single word. The application of misleading labels for particular perspectives has regularly muddied the debate between science and faith throughout the modern era. Nowhere is this more true than in the case of the "creationist" label, which has featured so prominently in the science-and-faith debates over the past century. Taken at face value, the term "creationist" would seem to imply the general perspective of one who argues for the existence of a God who was directly involved in the creation of the universe, In that broad sense. many deists and nearly all theists, including me, would need to count themselves as creationists.

Over the past century, however, the term "Creationist" has been hijacked (and capitalized) to apply to a very specific subset of such believers, specifically those who insist on a literal reading of Genesis 1 and 2 to describe the creation of the universe and the formation of life on earth.
                        Francis Collins (2006)

I still maintain that there are at least two definitions of creationism. The narrow definition, often referred to as Creationism with a capital "C" or Special Creationism, is widely accepted in American society. A recent survey reveals that 53% of Americans had heard of the term and, of those, 59% believed the narrow definition [Evolution and Creationism in Public Education].

The second definition is the broad definition that is frequently used in serious discussions about science and religion. I did not make it up. Whenever one attempts to comment on creationism it is incumbent upon the user to disclose the definition being used. In my case, I try to distinguish between the various forms of creationism by referring to Young Earth Creationism, Intelligent Design Creationism, etc. in order to avoid confusion.

Denyse O'Leary and some of her friends (but not Phillip Johnson) say there's a difference between Young Earth Creationism and Intelligent Design Creationism. I see the distinction, but I don't think it's as clear cut as she imagines.

One reason that it is appropriate for a Professor of Law to comment upon the philosophy of biology is that so many of the philosophers and biologists want to be litigators.
Phillip Johnson (1996)Finally, it's worth noting that the definition of "creationism" is tied up with legal issues in the United states of America. In Edward v. Aguillard (1987) the plaintiffs were successful in overturning Lousiana's "Creationism Act" on the grounds that it promoted religion. In this case, the judge declared that, "The Act impermissibly endorses religion by advancing the religious belief that a supernatural being created humankind."

In Tammy Kitzmiller, et al. v. Dover Area School District, et al. Judge Jones listened to evidence presented by the plaintiffs that Intelligent Design was just another name for creationism. Since the teaching of creationism had already been declared religious, and illegal, it was important to define creationism in such as way as to include Intelligent Design.

The plaintiffs were successful. In his final ruling, Judge Jones said, "The evidence at trial demonstrates that ID is nothing less than the progeny of creationism." The legal definitions of creationism are interesting but they seem to have had little effect on the general public, many of whom continue to believe that the only legitimate definition of creationism is the one requiring a belief in the Biblical Genesis story.

Are Old Earth Creationists and Young Earth Creationists the only Kind of Creationists?

That's what some people are saying. In his criticism of me Jonathan Badger strongly implies that the only legitimate creationists are the Young Earth Creationists (YEC's) and the Old Earth Creationists (OEC's) who still follow the sequence of events in Genesis. He would agree with Denyse O'Leary that Intelligent Design proponents (IDiots) are not creationists because they don't necessarily adopt a belief in the truth of Genesis.

Many would disagree and that's why you often hear people refer to Intelligent Design as Intelligent Design Creationism. There seems to be little doubt that the intelligent design movement grew out of the (capital C) Creationist movement in the 1980's. This has been well-documented by Barbara Forrest (left), most prominently at the Dover trial in 2005 and in a lengthy article in Intelligent Design Creationism and Its Critics (Forrest, 2001). In that article she examines the strategy of the Discovery Institute's Center for Renewal of Science and Culture (CRSC) and concludes that it is stealth creationism in spite of what its proponents might claim. The goal of Intelligent Design Creationists is make creationism more acceptable by introducing it on university campuses. This is part of the wedge strategy.

The accomplishment of these goals is especially important to the CRSC's strategy to advance theri brand of creationism; indeed, it is critical because they are the only creationists who stand a chance of pulling it off. The old-style creationism represented by Henry Morris, Duane Gish, and others is unlikely to be tolerated on mainstream campuses, even religious ones like Baylor. The CRSC creationists have taken the time and trouble to acquire legitimate degrees, providing them a degree of cover both while they are students and after they join the university faculties.

Whether you agree with the very broad definition of creationism or not, you are being incredibly naive if you think that Intelligent Design isn't creationism. There's more to creationism than just YEC's and OEC's.

Robert T. Pennock, a philosopher at Michigan State University and a leading opponent of Intelligent Design Creationism testified at the Dover trial that intelligent design was just warmed-over creationism—using a broad definition of creationism that equates it to religion. For Pennock, one of the defining tenets of creationism is the rejection of evolution, or at least some forms of evolution. He also tends to agree with Johnson that any belief in a Creator is a form of creationism. (He does not agree that evolution is incompatible with creationism.)

No attempt to discuss creationism would be complete without looking at the work done by the National Center for Science Education (NCSE). Eugenie Scott, the Executive Director of NCSE, has published several articles on the subject and has recently put out a book called Evolution vs. Creationism. Let's look at the Creation/Evolution Continuum published by NCSE and see how it conforms to various definitions of creationism.

Before starting, let me say that the distinction between "creationism" on the one hand and "evolution" on the other seems strained to me. It has led to much confusion—I have contributed to some of it. It would be far better to make the extremes "creationism" and "naturalism" since what we are usually looking at it is a continuum representing the strength of belief in God.

Nevertheless, you can see from the diagram that Eugenie Scott and NCSE recognize many different degrees of creationism ranging from the most extreme examples, such as Young Earth Creationism, down to far less extreme examples such as Evolutionary Creationism. She does not recognize Theistic Evolutionism as a version of creationsm: instead, she refers to it as "the theological view in which God creates through the laws of nature" (Scott, 2004). To me this is a quibble. I include Theistic Evolution as a form of creationism in the same sense as Theistic Evolutionists Francis Collins and Theodosius Dobzhansky (see above).

Intelligent Design Creationism covers a range of views as indicated on the graph.

The dotted line represents the split between literal belief in the Bible and a more liberal interpretation of scripture. This is the dividing line between (captial C) Creationsm or Special Creationism and other forms of creationism. To many people it is the difference between "creationism" (top) and something that is not creationism (bottom). (What is that something below the line? It appears to represent belief in a Creator God and a partial rejection of the full implications of evolution while studiously avoiding the creationist label. Are they Creator Godists?) I find it hard to justify that particular definition of creationism but as long as its proponents make their preference known it shouldn't be a problem. Naturally, the rest of us don't have to agree.

Is the Broad Definition of Creationist Just a Cute Rhetorical Trick?

I'm accused of using the broad definition as a "rhetorical trick" to tarnish the theists who reject a literal belief in the Bible. This reminds me of a similar accusation from Bill Dembski as reported by Robert Pennock (2000).

Dembski chides me for never using the term "intelligent design" without conjoining it to "creationism." He implies (though never explicitly asserts) that he and others in the movement are not creationists and that it is incorrect to discuss them in such terms, suggesting that doing so is merely a rhetorical ploy to "rally the troops."

Pennock goes on to demonstrate beyond a shadow of a doubt that Dembski is a creationist by the broad definition.

I don't resort to the cheap trick of using the word "creationist" as a pejorative label. I use "IDiots" for that purpose. Whenever I refer to creationists I qualify it with other descriptors such as Young Earth Creationism or Intelligent design Creationism. If I'm trying to make an important point about religion and science then I try and make it clear that I'm using a broad definition of creationism.

Jonathan Badger is not religious. His attack on my use of the word "creationst" falls into the category of accommodationist. (formerly appeaser). He thinks it's insulting to theists to be called creationists. My position is that Theistic Evolutionists are trying to pull the wool over our eyes by distancing themselves from the fringe creationists while allying themselves with the atheist evolutionists. When I say that theists are creationists I mean that in the same sense as many other theists such as Dobzhansky and Van Till (and the Pope). I do it in order to emphasize the fact that they do believe in a Creator God even though they accept most of the scientific evidence for evolution and common descent. It's not a rhetorical trick. I'm being as open and obvious as I know how.

Over on the comments thread of my earlier posting, there are even more interesting statements. Let me close by addressing one more. This one is from Pete Dunkleberg.

Using words like "definition" for one's preference is a bit political. So you want to put down theists by calling them creationists. But those are different words for good reason.

The main characteristic of creationists is that they claim scientific arguments against geology and or biology. Sometimes this has been called (by creationists) scientific creationism, abbreviated SciCre (not by creationists). Lately the term ID has been used for SciCre.

I hope I've demonstrated to your satisfaction that there is a legitimate second definition of "creationism" that's used by people who call themselves creationists. I didn't make it up and it's not political.

I do not put down theists by calling them Young Earth Creationists—the only kind of creationists you seem to recognize. If I'm putting down theists I do it very openly by criticizing their belief in a Creator God in spite of the fact that they accept most of science. I fail to see why Ken Miller would be upset if I "accused" him of believing in a Creator God. He doesn't disguise this fact in his book (Miller, 1999).

As a scientist, I know very well that the earth is billions of years old and that the appearance of living organisms was not sudden, but gradual. As a Christian, I believe that Genesis is a true account of the way in which God's relationship with the world was formed. And as a human being, I find value in both descriptions. In order to reveal Himself to a desert tribe six thousand years ago, a Creator could hardly have lectured them about DNA and RNA, about gene duplication and allopatric speciation, He spoke to them in the direct and lyrical language of Genesis.

Wouldn't it be fun if God came back to visit us in 2007 and gave us a lecture about gene duplication and allopatric speciation? I'd pay to hear that although I'd probably wonder if he(?) wasn't just pulling our legs in the same way he did with the desert tribe 3000 years ago. Was Genesis the ultimate example of framing?

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[Photo/Image credits: The photograph of Jonathan Badger is taken from the ASM video made when he was here in Toronto for the American Society of Microbiology meeting in May 2007 (see Bloggers in Toronto and Bacteria, Bloggers, and Toronto). Jonathan is in a phone booth on Baldwin St. where we had dinner. The photograph of Barbar Forrest is taken from her website [Dr. Barbara Forrest]. The Creation/Evolution Continuum is from The Creation/Evolution Continuum by Eugenie C. Scott]

Collins, F. (2006) The Language of God. Free Press, New York (USA).

Dawkins, R. (1996) Reply to Phillip Johnson. Biology & Philosophy 11:539-540. reprinted in Intelligent Design Creationism and Its Critics Robert T. Pennock ed. MIT Press, Cambridge MA (USA) (2001).

Johnson, Phillip (1993) Darwin on Trial Regnery Gateway, Washington DC (USA).

Johnson, P. (1996) Response to Pennock. Biology & Philosophy 11:561-563. reprinted in Intelligent Design Creationism and Its Critics Robert T. Pennock ed. MIT Press, Cambridge MA (USA) (2001).

Scott, E. (2004) Evolution vs. Creationism. University of California Press, Berkeley CA (USA).

Van Till, H. J. (1998) The Creation: Intelligently Designed or Optimally Equipped? Theology Today 55:344-364. reprinted in Intelligent Design Creationism and Its Critics Robert T. Pennock ed. MIT Press, Cambridge MA (USA) (2001).

Is Barack Obama Dangerously Naive?

 
Today's National Post had a comment about Barak Obama [Presidential hopeful Obama ‘promotes’ PM to president].

U.S. presidential hopeful Barack Obama, already under fire from fellow Democratic candidates for his supposed inexperience and unguarded comments on American foreign policy issues, is raising eyebrows again after vowing to telephone the "president of Canada" if elected to the White House to begin renegotiating terms of the NAFTA trade deal.

The titular miscue came Tuesday night during a discussion of trade and labour issues at a Democratic debate in the Illinois senator's home base of Chicago.

"I would immediately call the president of Mexico, the president of Canada, to try to amend NAFTA, because I think that we can get labour agreements in that agreement right now," Mr. Obama said. "And it should reflect the basic principle that our trade agreements should not just be good for Wall Street; it should also be good for Main Street."

Most of the fuss is about the fact that Obama doesn't know we have a parliamentary system of government with a Queen, but no President. That's pretty bad for a Senator from a northern state but it's not the only thing that troubles me.

We don't need a lecture from the US President on the proper way to treat workers. If there are any "labor issues" that separate Canada and the USA then it's the way the American Congress kowtows to special interest groups, like farm workers and workers in the softwood lumber industry, in violation of NAFTA. A really sore spot for Canada is the way American ignores the parts of the treaty that it doesn't like whenever it feels like it.

There are many Canadians—I'm not one—who would gladly terminate the treaty if the American government wanted to re-open it. It would mean that Canada would be free to sell its gas and oil to other countries at the full market price. Under "free trade" we are obligated to supply a certain set amount of oil and gas to America every year [Article 605].

Here's a list of current disputes (2006-2007, see below) under NAFTA [Canadian NAFTA Secretariat]. They all involve countervailing duties or import restrictions imposed by the US Congress on Canadian goods in spite of "free trade." In most cases, the Canadian goods can be sold cheaper in the USA than similar goods produced in America by American workers. As far as I know there are no disputes involving Canadian restrictions on American goods. Also, I believe that the USA has lost every single case that has come before the dispute resolution panel.

I wonder if Barak Obama knows this?

• Magnesium from Canada (Five-Year Reviews of the Countervailing Duty and Antidumping Duty Orders)
• Softwood Lumber from Canada (Dumping - 2002)
• Softwood Lumber from Canada (Countervailing Duty - 2002)
• Durum Wheat and Hard Red Spring Wheat from Canada (Countervailing Duty)
• Pure and Alloy Magnesium from Canada (Countervailing Duty)
• Softwood Lumber from Canada (Final Results of Countervailing Duty Administrative Review and Rescission of Certain Company-Specific Reviews - 2005)
• Softwood Lumber from Canada (Determination under Section 129(a)(4) of the Uruguay Round Agreements Act - 2005)
• Softwood Lumber from Canada (antidumping duty determination under Section 129 of the Uruguay Round Agreements Act - 2005)
• Softwood Lumber from Canada (Final Results of Antidumping Administrative Review - 2006)
• Softwood Lumber from Canada (Final Results of Countervailing Duty Administrative Review - 2006)
• Carbon and Certain Alloy Steel Wire Rod from Canada (Final Results of Antidumping Duty Administrative Review)

Nobel Laureate: Svante August Arrhenius

 
 
The Nobel Prize in Chemistry 1903.

"in recognition of the extraordinary services he has rendered to the advancement of chemistry by his electrolytic theory of dissociation"


Svante August Arrhenius (1859-1927) won the Nobel Prize in Chemistry for working out the theory of dissociation. Monday's Molecule #38 illustrates the fundamental concept. Some compounds like NaCl can dissociate in water to form separate charged ions (Na⁺ and Cl^-.

Today, more than 100 years after the Nobel Prizes were first awarded, there are very few winners who make fundamental contributions to our understanding of chemistry and biology. It was more common back in the olden days—probably because there were more fundamental discoveries to be made. It's difficult to compare the genius of a man like Arrhenius with the 2006 Nobel Laureate Roger Kornberg, for example. Kornberg never had the chance to discover the theory of dissociation or any other fundamental theorem.

The Presentation Speech was given by Dr. H.R. Törnebladh, President of the Royal Swedish Academy of Sciences, on December 10, 1903.

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

During the first year of the last century Volta made the first electric pile. By studying the chemical actions of the electric current thus obtained Davy in Britain and Berzelius and Hisinger in Sweden arrived at the conclusion that the relationship between electrical and chemical phenomena was one of cause and effect. On the basis of this idea Berzelius established his well-known electrochemical theory, which reigned supreme until the middle of the century; however, new discoveries showed that this theory would not stand up to examination, and chemical phenomena ceased to be explained as being due to electricity. It was generally accepted that chemical changes of matter were due to a certain affinity, though the origin of this affinity was absolutely unknown. Then came the heyday of thermochemistry, when it was believed that the explanation of the transformation of chemical energy during chemical reactions lay in the heat phenomena occurring during chemical processes.

Around 1880 Svante Arrhenius - then studying for a doctorate in science - arrived, as a result of his researches into the movement of electric current through solutions, at a new explanation of the causes of chemical phenomena, i.e. he attributed them to electrical charges contained in the constituents of reacting substances. Electricity was thus introduced as a decisive factor into the theory of chemistry, in other words the basic notion of the theory of Berzelius had come back into favour, although in a greatly modified form.

In the time of Berzelius this notion rested on a qualitative basis only, whereas Arrhenius's theory determined it quantitatively, thus allowing it to be treated mathematically. In his doctor's thesis, twenty years ago, Arrhenius had deduced from this principle all known laws governing chemical changes, but despite this the new theory was very little understood. It so conflicted with current ideas as to disprove them. According to this theory, for instance, common salt, sodium chloride, when dissolved in water splits up to a varying extent, in other words it is dissociated into its constituent parts which are diametrically opposed but charged with electricity, i.e. into ions of chlorine and of sodium, the only chemically effective substances in a solution of common salt. The theory also claimed that when an acid and a base react upon one another, water is the primary product and salt the secondary, and not reversely, as was then generally believed. Ideas so contrary to those current at that time could not be accepted immediately. A struggle lasting more than ten years and an enormous number of new experiments were required before the new theory was accepted by everyone. During this long battle over Arrhenius's theory of dissociation tremendous advances were made in chemistry and ever closer links were established between chemistry and physics - to the great benefit of both sciences.

One of the most important consequences of Arrhenius's theory was the completion of the great generalizations for which the first Nobel Prize for Chemistry was awarded to Van't Hoff. Without the support of Arrhenius's theory that of Van't Hoff would never have gained general recognition. The names of Arrhenius and Van't Hoff will go down in history of chemistry as marking the modern period of this science and it is for this reason that the Academy, despite the fact that the experimental basis of the theory of dissociation belongs to physics, did not hesitate to award the Nobel Prize for Chemistry to Arrhenius.

The Academy of Sciences counts itself fortunate in being able to award the Nobel Prize for Chemistry this year to the compatriot of Berzelius who rehabilitated the fundamental notion of his theory, and its task is made even more pleasant by the fact that its choice is supported by the most outstanding scientific authorities of our day.

Doctor. The world of science already recognizes the importance and value of your theory, but its lustre will continue to increase in the days to come, as you yourself and others use it to advance the science of chemistry. Physical research has contributed to your discovery and this fact throws new light on the relationship - more sensed than proved - between the different natural sciences, the common objective of which is to solve the riddles of life.

Success spurs us on to new endeavours - a fact realized by the generous Maecenas, whose name is now linked with your own. May your future work bear ever more abundant fruit and, when champions of the spirit and of learning advance along the trail that you have blazed, may your name be remembered in the proud words: Ille fecit.

Does anyone know the meaning for the last two words? I think it means something like "it will be done."

A Beautiful Parasite

 


This is Psittacanthus sp. or parrot-flower mistletoe from Botany Photo of the Day [August 08, 2007 : Psittacanthus sp.].

The plant normally grows as a parasite on conifers.

Hype and Reality in an Important Transcription Paper

An important paper has just been published in Nature Structural & Molecular Biology. The work examines the in vivo kinetics and dynamics of transcription in mammalian cells and it confirms some important parameters derived from in vitro studies (Darzacq et al., 2007).

Before looking at the results, let's see what the press release has to say. The experiments were mostly done in Robert Singer's lab at the Albert Einstein College of Medicine in New York. The college issued a press release that was relayed on the ScienceDaily site [Scientists Discover The Dynamics Of Transcription In Living Mammalian Cells]. Here's the hype ...
THEME:
Transcription

Transcription — the transfer of DNA’s genetic information through the synthesis of complementary molecules of messenger RNA — forms the basis of all cellular activities. Yet little is known about the dynamics of the process — how efficient it is or how long it takes. Now, researchers at the Albert Einstein College of Medicine of Yeshiva University have measured the stages of transcription in real time. Their unexpected and surprising findings have fundamentally changed the way transcription is understood.

Actually, a great deal is known about the dynamics of transcription including how efficient it is and how long it takes. There's nothing in the paper that's particularly unexpected or surprising. The results do not fundamentally change the way transcription is understood.

Theme: Transcription

 
Transcription is one of the key steps in the flow of information from gene to protein. Transcription is the process by which information in double-stranded DNA is copying into a molecule of RNA.

The postings listed below describe the various steps of transcription and the structure of RNA polymerase.

March 19, 2007
Monday's Molecule #18. The molecule is α-amanitin, an important inhibitor of RNA polymerase.

March 19, 2007
Gene and Transcription Orientation. This article describes the relationship between a gene and its RNA.

March 19, 2007
Transcription. Covers the essentials of transcription: initiation, elongation, termination.










March 20, 2007
Mushrooms for Dinner. How Julia Agrippina disposed of her husband and put her son, Nero, on the throne.

March 20, 2007
Eukaryotic RNA Polymerases. Describes the five different kinds of RNA polymerase in eukaryotic cells.






March 21, 2007
Nobel Laureate: Roger D. Kornberg (Chemistry 2006) "for his studies of the molecular basis of eukaryotic transcription"

March 21, 2007
How RNA Polymerase Works: The Chemical Reaction. This posting explains the chemical reaction of RNA polymerization.

March 22, 2007
How RNA Polymerase Works: The Topology of the Reaction and the Structure of the Enzyme. The structure of RNA polymerases is illustrated using the yeast and E. coli enzymes as examples. How RNA polymerase succeeds in unwinding RNA from it's DNA template is described.

March 25, 2007
RNA Polymerase Genes in the Human Genome. This article was written for Gene Genie. It describes the locations of the human genes for RNA polymerase subunits.



August 7, 2007
Hype and Reality in an Important Transcription Paper. A discussion of a recent paper demonstrating the actions of RNA polymerases in mammalian nuclei.

September 27, 2007
Transcription of the 7SL Gene. How the 7SL gene is transcribed by RNA polymerase III and the significance of internal promoters in creating junk DNA.

February 7, 2008
Junk RNA. Much of the mammalian genome may be transcribed by accident and the resulting RNAs are quicky degraded.

February 7, 2008
Regulation of Transcription. An overview of the main forms of transcriptional regulation.

February 12, 2008
Repression of the lac Operon. This is a description of the binding properties of lac repressor, used as an introduction to DNA binding proteins.

February 12, 2008
Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm. Transcription factors bind to thousands of sites on the Drosophila genome. Many of the sites appear to be non-functional.

What Is the Cause of Genetic Differences in Domesticated Rice Varieties?

 
There are two main varieties of domesticated rice (Oryza sativa). One variety, O. sativa indica can be found in India and Southeast Asia while the other, O. sativa japonica, is mostly cultivated in Southern China.

Extensive studies of the varieties has demonstrated that they were independently derived from the wild rice species Oryza rufipogon (left). The domesticated varieties show much less variation (polymorphism) than the wild species. This is not unexpected since they were presumably bred from a small number of plants when rice first began to be cultivated more than 10,000 year ago. This phenomenon of restricted variation after a speciation event is called the bottleneck effect because it represents a severe reduction in the number of different individuals that contributed to the new species. This bottleneck effect is thought to be a major factor in reducing variation in domesticated strains as well. In this case, the "speciation" event is man-made.

Bottleneck effects are similar to founder effects and both of them are forms of random genetic drift. The changes in the frequency of alleles within the new populations are due to chance and not to adaptation.

Caicedo et al. (2007) have recently explored the patterns of nucleotide polymorphisms in rice. They looked at SNP's, or single nucleotide polymorphisms, in 111 different regions of the genome. The idea was to see if certain polymorphisms tended to cluster together to form distinct patterns. If one genetic locus had a particular nucleotide "A" at site SNP-32, for example, it would be interesting to see whether the nearby regions of the genome were similar or different. If the same pattern, say SNP-32(A), SNP-33(G), and SNP-34(T), occurred at a high frequency then it indicates that there hasn't been enough time for recombination to separate the three distinctive variations.

When such patterns are found, there's a tendency to attribute the pattern to "selective sweeps." In a selective sweep the pattern becomes rapidly fixed in the genome due to selection for one of the markers. Assume, for example, that the presence of nucleotide "G" at site SNP-33 conferred some selective advantage on the plant. As this allele is rapidly selected, the nearby alleles (SNP-32(A) and SNP-34(T)) will be swept up in the adaptive event. Their frequency in the population will increase because they are hitchhiking on the SNP-33(G) allele. It's important to remember that the fixation of the flanking alleles are accidents—they are not being selected for their own phenotype.

But selective sweeps are not the only way that specific patterns of alleles can become widespread in a population. It can also happen if the population goes though a bottleneck where much of the variation was eliminated by chance. If the bottleneck occurred relatively recently then the pattern can look very much like a rapid fixation due to adaptation and hitchhiking.

The pattern of evolution in domestic rice varieties compared to Oryza rufipogon shows many examples of associated alleles, or haplotypes. The O. japonica variety has only 19% of the total polymorphism of the wild type genome and the other main variety, O. indica, has only 43%. The authors note that such patterns are often associated with selected sweeps but there are other possibilities.

An excess of high-frequency derived SNPs is often interpreted as a result of genetic hitchhiking during recent selective sweeps [26]. Because the site-frequency spectrum in rice varieties is observed from randomly selected loci, and the loci contributing high frequency derived SNPs are distributed across the genome (Fig. S4), this pattern suggests that strong linkage to positively selected mutations occurred within most of the genome. However, demographic forces may have also played a role in shaping the rice genomes. We developed several demographic models and a multiple selective sweeps model to test which evolutionary processes may best explain the observed patterns of polymorphism in rice.

In addition to a selective sweep model, the authors tested a neutral population bottleneck model defined as,

The most widely accepted demographic model for crop domestication is a neutral bottleneck model [27-29]. In this model, rice domestication is assumed to be a result of recent population divergence, with one of the two daughter populations experiencing a reduction in population size at divergence associated with the founder effect at the time of domestication, followed by population growth as cultivation of the crop increases.

The other models were combinations of bottleneck and migration between populations, and bottleneck plus selection.

It isn't easy to test these models, even with an extensive database such as the one from rice genomes. The mathematics is complicated and many simplifying assumptions have to be made. Nevertheless, Caicedo et al. (2007) conclude from their analysis that bottlenecks alone are not sufficient to explain the SNP patterns they see in domesticated rice. They conclude that the patterns result from a combination of drift (bottlenecks) and adaptation (selective sweeps).

A more complex demographic scenario involving very strong bottlenecks that led to the fixation of alternate alleles during the two rice domestication events (with concurrent gene flow between variety groups) can explain the site-frequency spectrum of indica and O. rufipogon. However, this pure demography model requires a bottleneck four-fold stronger in indica and twice as strong in tropical japonica relative to the model that incorporates selection (Table 2; Figure 5), and a relatively high migration rate between domesticated rice and wild O. rufipogon populations. It is also important to note that the model is a poor fit to the observed frequency distribution of alleles in tropical japonica.

Domestication, however, is characterized by strong directional selection on a suite of traits that lead to the establishment of cultivated species as distinct entities from their wild progenitors within agricultural settings. We show that, in contrast to the complex demographic model, a simple bottleneck with sweeps model fits data from both tropical japonica and indica well without requiring an extremely strong domestication bottleneck. Since domesticated Asian rice has been subject to artificial selection, the selection plus demography model is a very plausible explanation for the observed strong excess of high frequency derived alleles in domesticated rice varieties, and is consistent with recent reports about domestication genes in rice [45,46].

The lesson here is that it is very difficult to distinguish selection from drift and one should be cautious in attributing results to only one of these mechanisms of evolution.

---

Caicedo, A., Williamson, S., Hernandez, R.D., Boyko, A., Fledel-Alon, A., et al. (2007) Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice. PLoS Genet. In press. [doi:10.1371/journal.pgen.0030163.eor]

[The drawing of Oryza rufipogon is from Naples, M.L. (2005). The middle photograph is of Japanese short grained rice from the Wikipedia article on rice. The lower figure is Figure 3 from Caicedo et al. (2007)]

Monday's Molecule #38

 
Today's molecule is actually several molecules. In order to win the reward you have to identify what's going on and make the connection to Wednesday's Nobel Laureate(s).

The reward (free lunch) goes to the first person who correctly identifies the molecules and the Nobel Laureate(s) when comments are unblocked.^*

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

^*Previous free lunch winners are ineligible for one month from the time they first collected the prize. There's only one (Marc) ineligible candidates for this Wednesday's reward since many recent winners haven't collected their prize. The prize is a free lunch at the Faculty Club.

What Is Creationism?

Denyse O'Leary recently posted some comments on the Creation Museum funded by Answers in Genesis [ Creationism and popular culture: A friend visits Kentucky's Creation Museum]. It's a typical comment from an Intelligent Design Creationist. She does not speak out against the false science in the museum; instead, she tries to draw a distinction between her own personal beliefs and those of the Young Earth Creationists. According to Denyse O'Leary, Intelligent Design Creationism is not Creationism. (Why is it that the moderate Intelligent Design Creationists can be so hard on scientists while turning a blind eye to the blatant stupidity of the Young Earth Creationists?)

Mike Dunford agrees with Denyse O'leary in The Big Difference Between Creationism and Intelligent Design. He says,

It's extremely uncommon for me to find myself in agreement with Denyse on anything (and it's not a comfortable feeling), but in this case I do think she's got a good point. Creationism is certainly explicitly based on the Bible, and Intelligent Design certainly is not.

There are several different ways of defining "creationism." I prefer the definition that refers to "creationists" as people who believe that the universe was created by God. In some cases God just set up the original universe with all its laws of physics and chemistry, while in other versions of creationism he/she did some meddling after the initial creation event.

Young Earth Creationists are those who take the Bible literally. Old Earth Creationists are creationists who accept some parts of science and reject a literal interpretation of Genesis. Intelligent Design Creationists are creationists who believe that there is scientific evidence to support the creation event(s). Some Intelligent Design Creationists are also Young Earth Creationists while others are Old Earth Creationist and still others are closer to Theistic Evolutionists.

The supporters of Theistic Evolution are also creationists because they believe in a creator who created some part of the existing universe while, at the same time, accepting most of evolution. Deism is the softest version of creationism and the one most compatible with science.

I think the Wikipedia article on Creationism has it right when it says,

Creationism is the belief that humanity, life, the Earth, and the universe were created in their entirety by a deity or deities (typically God), whose existence is presupposed.[1] In relation to the creation-evolution controversy the term creationism (or strict creationism) is commonly used to refer to rejection of evolution. The wide spectrum of such beliefs includes young Earth creationism holding a very literal interpretation of Genesis, while old Earth creationism accepts geological findings but rejects evolution. The term theistic evolution has been coined to refer to beliefs in creation which are compatible with scientific findings on evolution and the age of the Earth.

On this day in 1945 ....

 
At 8:15 AM on August 6, 1945 an atomic bomb was detonated over Hiroshima, Japan. Approximately 78,000 civilians were killed on that day. Six months later the death toll had risen to about 140,000 people.

There are many arguments in favor of dropping the bomb just as there are many arguments against it. What's clear is that in the context of 2007 we are not in a good position to judge the actions of countries that had been at war for many years.

The most important lesson of Hiroshima is that war is hell and many innocent people die. It's all very well to enter into a war with the best of intentions—as the Japanese did on December 7, 1941—but it's foolish to pretend that when you start a war there won't be any suffering. When you do that you can really say that the victims of Hiroshima died in vain.

The killing and maiming of civilians is an inevitable outcome of war, no matter how hard you might try to restrict your targets to military objectives. Before going to war you need to take the consequences into account and decide whether the cost is worth it.

One of the many mistakes in Iraq was the naive assumption that it would be a clean war with few casualties and no long-term consequences for the Iraqi people. Yet today, the numbers of innocent lives lost in Iraq is comparable to the numbers lost in Hiroshima and Nagasaki. And what is the benefit for Iraq that outweighs the cost in human lives? Is it "freedom" and "democracy"?

Hiroshima was not a glorious victory. It was ugly, heartbreaking, and avoidable. War is not an end in itself, it is the failure of peace. War is not an instrument of your foreign policy—it is an admission that you don't have a foreign policy.

[The top photograph shows the mushroom cloud over Hiroshima on the morning of August 6, 1945 (Photo from Encyclopedia Britanica: Hiroshima: mushroom cloud over Hiroshima, 1945. [Photograph]. Retrieved August 7, 2007, from Encyclopædia Britannica Online. The bottom image is taken from a Japanese postcard (Horoshima and Nagassaki 1945). It shows victims of the attack on Hiroshima.]

A Citation Classic: Nirenberg & Matthaei

 
John Dennehy has described a classic paper on cracking the genetic code. Read about the Nirenberg & Matthaei experiment and how it was received at [This Week's Citation Classic] on The Evilutionary Biologist.

John also likes my description of the experiment but he thinks I should delete my posting now that he has put up a better one. Ain't gonna happen.