St. Patrick Banished Snakes from Ireland

 
Friday's Urban Legend: FALSE

Connie Barlow describes A St. Patrick's Day Parable.

Ireland is a land of no snakes. It has no slithering serpents. There are no rat snakes in Ireland; there are no rattlesnakes; there are no garter snakes. There are no snakes at all.

The absence of snakes in Ireland seems to cry out for an explanation — but only if one regards or ventures to the island from outside: from England, say, or from continental Europe. To the indigenous Celts, there would, of course, have been nothing to explain. The Gaelic peoples no more needed to explain an absence of snakes on their island home than they needed to explain an absence of kangaroos. To those who came to Ireland from abroad, however, a dearth of serpents was a striking anomaly in need of an answer.

We humans must have answers. And so arose the legend of St. Patrick and the snakes. The reason Ireland has no snakes, the story goes, is that Patrick charmed all snakes on the island to come down to the seashore, slither into the water, and drown. So Ireland did once have snakes, but it has them no more. Patrick charmed them all into the sea.

She goes on to explain why there are no snakes in Ireland but I prefer to swtich to the website of the Smithsonian National Zoological Park for their explanation of Why Ireland Has No Snakes.

Now snakes are found in deserts, grasslands, forests, mountains, and even oceans virtually everywhere around the world. Everywhere except Ireland, New Zealand, Iceland, Greenland, and Antarctica, that is.

One thing these few snake-less parts of the world have in common is that they are surrounded by water. New Zealand, for instance, split off from Australia and Asia before snakes ever evolved. So far, no serpent has successfully migrated across the open ocean to a new terrestrial home. As the world's oceans have risen and fallen over the millennia, land bridges have come and gone between Ireland, other parts of Great Britain, and the European mainland, allowing animals and early humans to cross. However, any snake that may have slithered it's way to Ireland would have turned into a popsicle when the ice ages hit.

The most recent ice age began about three million years ago and continues into the present. Between warm periods like the current climate, glaciers have advanced and retreated more than 20 times, often completely blanketing Ireland with ice. Snakes, being cold-blooded animals, simply aren't able to survive in areas where the ground is frozen year round. Ireland thawed out for the last time only 15,000 years ago. Since then, 12 miles of icy-cold water in the Northern Channel have separated Ireland from neighboring Scotland, which does harbor a few species of snakes. There are no snakes in Ireland for the simple reason that they can't get there.

[The book cover is from a book by Sheila MacGill Callahan (Author) and Will Hillenbrand (Illustrator). You can buy it on Amazon.com.]

War is Not Healthy for Children and Other Living Things

For the longest time we had a poster on our wall that said "War Is Not Healthy for Children and Other Living things" [War Is Not Healthy: The True Story].

The sentence seems trite if you didn't live though the 60's but it's taking on more and more significance every day. The point is that war is hell. People die. Innocent people. We better not forget that.

But there are people who do want to forget. They want to purge war of all of it's ugliness and remember only the bravery and the glory. In Canada the movement to glorify a deadly First World War battle—the battle of Vimy Ridge—is gaining ground. In this battle there were 30,000 casualties and the front advanced a few miles. There was no strategic gain. This was a war that should not have happened and a battle that wasted thousands of lives. It was not glorious and it should be something to be embarrassed about, not celebrated.

But there's an even more important illustration of our tendency to forget the horrors and the mistakes of war. Tuesday's Globe and Mail has an article about veterans protesting a sign at the Canadian War Museum in Ottawa. The issue concerns strategic bombing in World War II and it's a hot button issue in Canada because of a documentary televised several years ago.

The goal of Bomber Command during World War II was to destroy German cities and reduce Germany's will to continue the war. Nobody was under any illusions about the consequences because London and other British cities had been bombed in 1940. They knew that flower gardens would be wiped out and so would little children [Strategic bombing during World War II]. The image below is of bombed out apartment buildings in Hamburg in 1944. People used to live in those buildings. Thousands and thousands died during the firestorms created by massive bombing raids by British and American forces during 1944 and 1945.

These are facts. The controversy is about whether the bombing raids were effective. There are many who say they weren't; in fact, there seems to be a consensus among historians that strategic bombing of Germany did not have as much negative effect as the High Command believed.

Thousands of Allied airmen died in planes over Germany. Many of them were Canadians. The Canadian War Museum has a display dedicated to those airman. I have seen it. I have shown it to my children. My father was a pilot during World War II.

There are plaques and pictures describing the planes and the crews. One of the plaques is titled An Enduring Controversy. It reads,

The value and morality of the strategic bombing offensive against Germany remains contested. Bomber Command's aim was to crush civilian morale and force Germany to surrender by destroying its cities and industrial installations.

Although Bomber Command and the American attacks left 600,000 Germans dead and more than five million homeless, the raids resulted in only a small reduction in German war production until late in the war.

This is what the controversy is all about. The Royal Canadian Legion objects to this plague because it calls into to question the morality of strategic bombing and the morality of bomber crews who served during World War II.

Last year, the veterans complained that the panel made them look like war criminals. Art Smith, a veteran leading the attack, said, "Ten thousand crewmen didn't make it back. It really distresses me that people want to knock their memory." A former member of Parliament, he lobbied for a private member's bill to force a rewrite of the text.

Guess what? War is hell. War is immoral. You can't pretty it up by ignoring the truth. Bombs killed women and children. Lots of them. Their lives may have been wasted because nothing was gained by their deaths.

We owe it to our sons and daughters to leave that plaque just the way it is. We need to remind them that war isn't healthy for children and other living things. The children of Iraq and Afghanistan know this.

The Web of Life

Regular readers of Sandwalk will recall a series of articles on the death of the Three Domain Hypothesis. One of them covered the ideas of W. Ford Doolittle from Dalhousie University in Nova Scotia [If the Tree of Life Fell, Would We Recognize the Sound?]. He advocates a web of life with numerous exchanges of genes during the early years.

The figure below is taken from Doolittle's Scientific American article "Uprooting the Tree of Life" (February 2000). © Scientific American


Doolittle has a new paper out in PNAS (Doolittle and Bapteste, 2007). In that paper he restates his ideas about the web of life and emphasizes the fact that most of us are making unsubstantiated assumptions about the treelike structure of life. This is not a criticism of evolution—far from it—but as you might expect it has attracted the attention of anti-science writers such as Casey Luskin.

Doolittle and Bapteste (2007) are opposed to the bifurcating tree of life such as the one shown on the Dept. of Energy (USA) Joint Genome Initiative website [JGI Microbial Genomes]. They say,

The meaning, role in biology, and support in evidence of the universal "Tree of Life" (TOL) are currently in dispute. Some evolutionists believe (i) that a single rooted and dichotomously branching representation of the relationships between all life forms is appropriate (at all levels above species), because it best represents their history; (ii) that we can with available data and methods reconstruct this tree quite accurately; and (iii) that we have in fact done so, at least for the major groups of organisms. Other evolutionists question the second and third of these beliefs, holding that data are as yet insufficiently numerous and phylogenetic models as yet insufficiently accurate to allow reconstruction of life's earliest divisions, although they do not doubt that some rooted and dichotomously branching tree can in principle represent the history of all life. Still other evolutionists, ourselves included, question even this most fundamental belief, that there is a single true tree. All sides express confidence in their positions, and the debate often seems to be at an impasse.

The argument is long and complex but the essence is that we need to abandon our assumption that the tree of life can be represented by: (i) a unique hierarchical pattern, (ii) the historical record can be best represented by a branching pattern, and (iii) natural selection is the primary cause of speciation.

We've pretty much abandoned the third point ...

As to this third possibility, modern evolutionists accept the uncoupling of selection from divergence, not only at the molecular level (the neutral theory) but in certain models for speciation, without seeing the Darwinian (or at least the neo-Darwinian) theory as refuted (21, 22). We have come to appreciate the plurality of evolutionary processes of lineage diversification. But most of us hold on to the first two tenets, that there is a real and universal natural hierarchy, and that descent with modification explains it, in much the same way as Darwin did. We may be process pluralists, but we remain pattern monists.

This brings us to the title of their paper Pattern Pluralism and the Tree of Life Hypothesis. Doolittle and Bapsiste want us to not only be pluralists with respect to the mechanism of evolution but also with respect to the pattern of evolution.

Doolittle maintains that lateral gene transfer (LGT) is so common that it's impossible to construct a reliable bifurcating tree to represent the actual history of life. In other words, a Tree of Life is not only technically difficult but impossible in theory as well. This problem extends to all branches of the prokaryotic tree including the major divisions. Even the existence of two prokaryotic domains is questionable. Rooting the tree of life is out of the question.

I'm a big fan of Ford Doolittle—after all, he's an honorary Canadian! I certainly agree with him about the demise of the Three Domain Hypothesis. (Most people seem to have missed the death announcement.) I also agree with him that early evolution is more like a web of life than a tree of life. Nevertheless, I think he goes too far. Lateral gene transfer is an important, and common, phenomenon but I don't think it's quite as prevalent as he makes out. I still think that a bifurcating tree can be used to represent most species evolution after about 2.5 billion years ago.

Doolittle, W.F. and Bapteste, E. (2007) Pattern pluralism and the Tree of Life hypothesis. Proc. Natl. Acad. Sci. (USA) 104:2043-2049. [PubMed]

More on Cellphones in Hospitals and How Doctors Deal with Evidence

 
Last Friday I mentioned a study done at the Mayo Clinic where they looked at the practice of banning cellphone use in hospitals [Cell Phones Can Cause Death in Hospitals]. The study concluded that there is no scientific evidence to support such a ban. Cellphones and BlackBerry's do not interfere with hospital equipment, according to the study.

Tuesday's Globe and Mail had a skeptical front page article on banning cellphones in hospitals [Hole Poked in Hospital Cellphone Shroud].

Cellphone use does not interfere with medical equipment and should be allowed in hospitals, according to a study that turns years of warnings on its head.

The study comes amid a sharp debate within the medical profession, with some institutions beginning to loosen their rules while others stick to the view that the devices can be dangerous to patients.

Among the people interviewed was Chris O'Conner at Mississauga Trillium Health Centre. This large teaching hospital is part of the University of Toronto Medical School. It's my local hospital and I've been there many times, both as a patient and a visitor.

Trillium lifted their ban on cellphones two years ago. Not only that, the staff is encouraged to communicate with each other using BlackBerrys and other devices. According to O'Conner, this has not only improved efficiency but also enhanced patient safety by avoiding communications lapses.

So, why are cellphones banned at other hospitals? Is this a problem? I don't know whether you could say the ban is a serious "problem," but it sure is an inconvenience. For parents sitting in an emergency waiting room for 6 hours it is frustrating to have to rely on a pay phone to keep others informed of what's happening. For those of us who are picking up someone from a hospital, it is annoying to not know when a patient is about to be discharged. (We recently had to pick up a patient from a large downtown teaching hospital. Fortunately they don't ban cellphones so we were able to keep in touch with the patient and find out when he was going to be released.) For patients in a hospital bed it is sad that they can't use their cellphones to talk to friends and relatives.

These concerns are real enough but my main interest is the conflict between rationalism and superstition. The Globe and Mail also interviewed spokeswoman Brandy Delves from a major Vancouver hospital.

A spokeswoman for Vancouver Coastal Health said last night that cellphones and other handheld communication devices continue to be banned near sensitive equipment there, including ventilators and incubators.

While a few hospitals have begun to buck the trend, conventional wisdom supports the VCH's view that these devices could interfere with crucial equipment.

Typical of this concern were warnings from the U.S. Federal Communications Commission that electromagnetic waves from cellphones could shut down electronic devices in hospitals.

These fears were firmly enough entrenched to have made their way into popular legend.

According to an e-mail that made the rounds in 2003, a young girl died during a routine operation because "some idiot" used a cellphone near the operating theatre.

"Be compassionate," this e-mail went on to urge. "Do not use your hand phone at any hospital or places where you are told not to use it. You might not be caught in the act, but you might have killed someone without knowing it."

That message was later debunked by snopes.com (an Internet site about urban legends), and, according to a study released by the Mayo Clinic, the fears it addresses are groundless.

The article goes on to note some of the findings of the Mayo Clinic study then returns to a comment from the Vancouver Hospital.

But the policy-makers at VCH are not convinced. Spokeswoman Brandy Delves said the hospital has had the same policy since 1996, banning cellphones and other hand-held communication devices in key areas. "We have reviewed all the recent literature and have decided to keep our current policy," she said last night.

This is interesting. It's very hard to prove a negative so one can't expect absolute "proof" that cellphones are harmless in a hospital setting. Once the idea of possible danger has been planted it always seems better to be safe than sorry. Nevertheless, all of the so-called evidence of danger has been refuted and there are hospitals that have lifted the ban. Those hospitals do not seem to be losing patients due to unexpected equipment failures. In light of data like this why would "policy-makers," many of whom are doctors, not make a rational decision to lift the ban?

What is it about our psychology that causes some people to reject scientific/rational evidence when it conflicts with their superstitions? Even people who are trained in "evidence-based" medicine seem to be incapable of applying the methodology in real life.

The Molecular Basis of Roundup® Resistance

Recall that glyphosate inhibits the enzyme EPSP synthase, an enzyme that catalyzes the following reaction in the chorsimate biosynthesis pathway [How Roundup® Works].

Funke et al. (2006) explored the molecular basis of this inhibition by looking at the structure of EPSP synthase from the C4 strain of Agrobacterium sp. This is the resistant form of the enzyme that has been genetically engineered into Roundup Ready® plants [Roundup Ready® Transgenic Plants].

Note that the structure of glyphosate resembles one of the substrates of the reaction; namely phosphoenolpyruvate (PEP). It was already known that glyphosate binds tightly to the active site of the enzyme and inhibits the reaction by preventing PEP binding. As it turns out, the site for glyphosate binding is exactly the same as the site for PEP binding and this explains the inhibition.

Funke et al. (2006) looked at the C4 EPSP enzyme with and without one of the other substrates: namely, shikimate-3-phosphate (sometimes called shikimate-5-phosphate). The results reveal the precise location of the active site of the enzyme at the base of a cleft between two domains. This form of the enzyme is called class II EPSP synthase because it is distantly related to the class I enzymes in other bacteria and eukaryotes (30% amino acid sequence identity). This is the first paper to examine the structure of a class II enzyme.

As an aside, notice that the enzyme closes up a little bit when the substrate binds—sort of like a Pacman icon. This mechanism of substrate binding is called induced fit and it's proving to be more common than most people realized.

The glyphosate resistant (Roundup Ready®) mutation in C4 EPSP synthase is a substitution of Alanine (A) for Glycine (G) at amino acid position 100. The glyphosate molecule fits nicely into the wild type G100 form of the enzyme (lower image) and it excludes PEP binding completely. Note that glyphosate (green) is in an extended configuration when it is bound. The dotted lines represent non-covalent interactions between the enzyme and the glyphosate molecule. The blue dots are "frozen" water molecules embedded in the active site.

In the mutant form of the enzyme the extra methyl group on alanine is just big enough to cause glyphosate to distort so it can no longer lie in the optimal extended configuration (top image). This means that glyphosate binds much more weakly and doesn't inhibit enzyme activity.

The important point is that the active site can still accommodate phosphoenolpyruvate because it is smaller than glyphosate. What this means is that the overall activity of the enzyme in the absence of glyphosate is unaffected. There are lots of EPSP synthase mutants that don't bind glyphosate but in almost all cases the rate of the reaction is drastically reduced because PEP binding is also weakened. For example, if you mutate the glycine to alanine at the equivalent position in other bacterial or plant enzymes you abolish PEP binding along with glyphosate binding.

What's special about the class II enzymes in general and the Agrobacterium sp. enzyme in particular, is that the amino acids surrounding the PEP binding pocket are positioned just right so that a slight shift can exclude glyphosate without affecting phosphoenolpyruvate. This is mostly due to the positions of the charged amino acid side chains that form weak interactions with the oxygen atoms and the nitrogen of glyphosate; for example, arginines (R) at 128, 357, and 405; lysine (K) at 28; and glutamate (E) at 354.

The results of this study not only shed light on the mechanism of glyphosate resistance but they also help explain the lack of Roundup® resistant plants. Apparently, the class I enzymes in plants have a binding pocket that is difficult to mutate in a way that excludes glyphosate while still allowing PEP binding. Nevertheless, some examples of Roundup® resistant plants are known. I'll describe them tomorrow.

(Funke et al. had to do a bit of sleuthing and reconstruction in order to solve the structure of the C4 EPSP synthase. The C4 strain of Agrobacterium sp. has, naturally enough, not been given out to scientists outside of Monsanto laboratories. So Funke et al. got the amino acid sequence from US Patent 5633435 and reverse engineered the nucleotide sequence of the gene. They synthesized the nucleotide sequence and amplified the fragments by PCR. They then tacked on a promoter and a transcription termination signal and cloned the articfial gene into an E. coli plasmid. The artificially reconstructed protein was then expressed in E. coli, isolated, purified, and crystallized.)

Funke, T., Han, H., Healy-Fried, M,L., Fischer, M., and Schonbrunn, E. (2006) Molecular basis for the herbicide resistance of Roundup Ready crops. Proc. Natl. Acad. Sci. (USA) 103:13010-13015. [PubMed]

Jim Watson Comments on GM Crops and Recombinant DNA Technology

 
Watch this clip of Jim Watson commenting on recombinant DNA technology and its uses in making genetically modified plants [Dr. James Watso]. The video is produced by Monsanto so those of you with a bias can easily dismiss it without a second thought.

The rest of you should pause to think about what Watson is saying. He's definitely outspoken but is he right? He says ...

Recombinant DNA is the safest technology I’ve ever heard.

Read Nobel Laureate: Paul Berg for information about Asilomar and the recombinant DNA controversy of the 1970's. Read the comments to that article for other points of view and references to Watson. Hsien Hsien Lei has an opinion and so does Jeremy.

The Great Muffin Joke Debate

 
Check out The Great Muffin Joke Debate at Cosmic Variance. I think it's funny. It's not ROTFLMFHO funny, but it does make me smile. John Tierney does not think it's funny. Is there a correlation between whether you think the joke is funny and whether you "get" irony and sarcasm?

A New Understanding of the Early Evolution of Flowering Plants

 
The folks over at the UBC Botanical Gardens have written an easy-to-understand summary of the recently published Nature paper on Hydatellaceae [A New Understanding of the Early Evolution of Flowering Plants].

Turns out that Hydatellaceae, a family of flowering plants, diverged from other flowering plants before the monocot-dicot split. They are related to water lilies, another group that branches deep in the tree of flowering plants. There are some pretty pictures of various species in the Hydatellaceae family over on the Botany Photo of the Day website. The one shown here is Trithuria submersa a species from Western Australia. These are very small plants and most of them are only found in Australia and New Zealand.

Proof That God Exists from a Prestigious Journal

 
EukekAlert! reports proof that God exists [Does God answer prayer? ASU research says 'yes'].

The answer, according to a new Arizona State University study published in the March journal Research on Social Work Practice, is “yes.” David R. Hodge, an assistant professor of social work in the College of Human Services at Arizona State University, conducted a comprehensive analysis of 17 major studies on the effects of intercessory prayer – or prayer that is offered for the benefit of another person – among people with psychological or medical problems. He found a positive effect.

“There have been a number of studies on intercessory prayer, or prayer offered for the benefit of another person,” said Hodge, a leading expert on spirituality and religion. “Some have found positive results for prayer. Others have found no effect. Conducting a meta-analysis takes into account the entire body of empirical research on intercessory prayer. Using this procedure, we find that prayer offered on behalf of another yields positive results.”

Hodge’s work is featured in the March, 2007, issue of Research on Social Work Practice, a disciplinary journal devoted to the publication of empirical research on practice outcomes. It is widely recognized as one of the most prestigious journals in the field of social work.

Hmmmm ... "one of the most prestigious journal in the field of social work." Well, that does it for me. Where's the nearest church? Pray for me.

Roundup Ready® Transgenic Plants

By the late 1990's it was apparent that recombinant DNA technology [see Nobel Laureate: Paul Berg] had advanced to the point where it was feasible to consider the production of genetically modified crops. One of the first targets was the creation of plants that were resistant to the herbicide glyphosate or Roundup® [How Roundup® Works].

Surprisingly, in spite of extensive spraying with Roundup® no resistant plant species had been detected. Since the target of glyphosate, EPSP synthase (EC 2.5.1.19), is also present in bacteria, a search for resistant bacteria was undertaken. The idea is that if a glyphosate-resistant enzyme from bacteria could be transferred to plants it might make the plants resistant to the herbicide. Such Roundup Ready® transgenic plants be an enormous advantage for farmers since a crop of, say Roundup Ready® soybean, could be sprayed with Roundup® to kill all weeds without affecting the crop.

Coincidently , it would be of enormous advantage to Monsanto, the manufacturer of Roundup®, especially if they could control the distribution of the genetically modified plants.

The C4 strain of Agrobacterium sp. proved to be just the thing. This is a species of bacteria that was found growing in the waste-fed column at a factory that made glyphosate. The EPSP synthase enzyme from this bacterium (C4 EPSP synthase) was almost completely insensitive to glyphosate.

The C4 EPSP bacterial gene was cloned and inserted into a bacterial plant vector in order to prepare for cloning into plants. The details of one of the Monsanto C4 EPSP cloning vectors are shown in the first patent filed on September 13, 1994 [US Patent 05633435].

This is a modifed bacterial plasmid vector designed to be propagated in E. coli (for cloning and construction) and Agrobacterium tumefaciens (for transforming plants). Ori-322 is an origin of replication from plasmid pBr322. It is used in E. coli to replicate the plasmid. Ori-V is an origin from plasmid RK2, a plasmid that can propagate in a wide variety of gram negative bacteria, including Agrobacterium tumefaciens. Rop is a small gene that encodes a protein requried to maintain plasmid copy number in bacteria.

There are two selectable markers. SPC/STR encodes a protein conferring spectinomycin/streptomycin resistance. The gene is derived from transposon Tn7. AAC(3)-III encodes bacterial gentamycin-3-N-acetyl transferase type III allowing selection for gentamycin resistance in plants. The bacterial AAC(3)-III gene has to be modified in order to allow effient expression in plant cells. A plant promoter (P-35S) is inserted at the 5' end. This promoter is the 35S promoter from cauliflower mosaic virus (CaMV). The 3' end of the gene is modified by inserting the polyadenylation site (NOS 3') from the nopaline synthase gene of the tumor-inducing (Ti) plasmid from Agrobacterium tumefaciens.

Similarly, the bacterial C4 EPSP gene was modified to have a strong plant promoter (P-e35S, related to P-35S) and a polyadenylation site (NOS 3'). One additional modification is necessary because the plant EPSP synthase is in chloroplasts where synthesis of chorimsate takes place. The bacterial gene has to have an N-terminal leader sequence that targets the protein to the chloroplast. This is supplied by CTP2, the chloroplast transit peptide from the Arabidopsis (wall cress) EPSP synthase gene.

The shuttle plasmid is built in E. coli then purified plasmid DNA is used to transform Agrobacterium tumefaciens. This bacterium infects plants and injects DNA from a Ti-like plasmid into plant cells where it enters the nucleus and becomes incorporated into the plant chromsomes. Under normal circumstances Agrobacterium tumefaciens causes gall tumors in plants but in this case the recombinat DNA is transferred and no tumors are formed. The transformation is mediated by cutting the plasmid at the RIGHT BORDER to produce a linear DNA molecule. Defective Ti plasmids in the bacterial cell are required to promote the transfer of the recombinant DNA.

The interesting feature of this transformation is that it is mediated by the bacteria. All you need to do is expose the plant cells to the bacteria under the right conditions and your gene of interest will end up in a plant chromsome.

The complete process begins with the isolation of small bits of plant tissue. They are grown on nutrient plates before being exposed to the bacteria carying the recombinant DNA plasmid.

Transformed cells will start to grow and they can eventually be isolated and transferred to a liquid that promotes shoot growth. After a few weeks you end up with an entire plant carrying the recombinant DNA. This plant is then propagated to produce thousands of genetically modified plants and seeds.

Roundup Ready® soybean was the first crop plant produced by Monsanto. Today, 90% of the soybean crop in the USA consists of Roundup Ready® plants. You can't buy soybean products that don't come from genetically modified plants.

Two thirds of the cotton and a quarter of the corn crop are Roundup Ready® plants. There is some resistance to growing Roundup Ready® wheat.

Nobel Laureate: Paul Berg

 
The Nobel Prize in Chemistry 1980.

"for his fundamental studies of the biochemistry of nucleic acids, with particular regard to recombinant-DNA"


Paul Berg won the Nobel Prize in 1980 for his work on developing recombinant DNA technology. This is the only Nobel Prize that has been awarded for that achievement.

Berg is credited with creating the first recombinant DNA molecule back in 1972 (Jackson et al. 1972). He combined a fragment of a bacterial plasmid with a piece of DNA from a simian virus (SV40). The goal was to understand the structure and organization of the small SV40 virus—the main focus of research in Berg's laboratory. Berg was hoping to create a recombinant DNA vector that would introduce foreign DNA into mammalian cells where it could be expressed. Here's part of the original press release ...

Berg was the first investigator to construct a recombinant-DNA molecule, i.e. a molecule containing parts of DNA from different species, e.g. a chromosome from a virus combined which genes from a bacterial chromosome. His pioneering experiment has resulted in the development of a new technology, often called genetic engineering or gene manipulation, which has already had important practical applications, e.g. the manufacture of human hormone with the aid of bacteria. Berg performed his experiment, however, as part of an incisive analysis of the chromosome of an ape virus (called SV 40) Viruses contain DNA (or sometimes RNA, another nucleic acid). They cause disease by introducing foreign genetic information in a cell and in this way disturbing its chemical machinery. As DNA molecules from viruses are relatively small, they are excellent objects of investigation for the study of the relationship between the chemical structure and biological function of DNA.

Following the creation of the first recombinant DNA molecule—but after a lag of a few years—Paul Berg was successful in his attempt to construct mammalian cloning vectors. His lab was the first to express a cloned foreign gene in mammalian cells. In this case it was the recently cloned rabbit β-globin gene.

The original recombinant DNA molecule constructed in 1972 was not immediately propagated in living cells out of safety concerns. At the time, it was unclear whether the cloning of a potential cancer causing virus (SV40) presented a health hazard. Berg and others voluntarily stopped research in this field until they could sort out the safety issues.

The voluntary moratorium in 1973-74 led to the famous Asilomar Conference where the issue was debated by a group of prominent scientists. This was such an important event that a 2004 article by Paul Berg on the Asilomar Conference is included in the Nobel Prize website [Asilomar and Recombinant DNA]. The result of the debate was a decision to proceed with caution and a number of safety protocols for working with recombinant DNA were put in place.

Almost all of the safety concerns proved to be exaggerated and the recombinant DNA regulations have been quietly dropped over the years. Even in 1980, when Berg received his Nobel Prize, he was able to express some frustration at how the concerns of scientiests were perceived. Nevertheless, there's a common perception among scientists that their behavior in the mid-1970's was not only ethical but highly successful. That point of view is expressed in the 2004 article ...

What did the actions taken by the scientific community achieve? First and foremost, we gained the public's trust, for it was the very scientists who were most involved in the work and had every incentive to be left free to pursue their dream that called attention to the risks inherent in the experiments they were doing. Aside from unprecedented nature of that action, the scientists' call for a temporary halt to the experiments that most concerned them and the assumption of responsibility for assessing and dealing with those risks was widely acclaimed as laudable ethical behavior. If the Asilomar exercise was a success, it was because scientists took the initiative in raising the issue rather than having it raised against them; that initiative engendered considerable credibility instead of cynical suspicion of what was to follow. The public's trust was undeniably increased by the fact that more than 10% of the participants were from the news media. They were free to describe, comment on and criticize the discussions and conclusions at the end of the conference. All the deliberations, bickering, bitter accusations, wavering views and the arrival at a consensus were widely chronicled by the reporters that attended and subsequently by the rest of the media and subsequent commentators.

While much of that may be true, it tends to ignore the consequences that we had to live with for a decade. By 1980 it was clear that recombinant DNA posed no danger but by then all the strict rules and regulations were in place and compliance was enforced by law. At that point the opinions of the experts didn't matter. The public was scared and they were determined to ignore scientific evidence in order to restrict research. We've also forgotten the serious attempts by uninformed governments to stop recombinant DNA research altogether.

The cynical point of view is that the public's trust in science declined in the 1970's because scientists were pushing ahead with highly dangerous research that could destroy the world.

So, what are the lessons of Asilomar? Here's how Berg describes it in 2004 ..

Is "the Asilomar model" appropriate for resolving or contributing to some of the "hot button" issues confronting scientists and the public today? For example, are the deep divisions about fetal tissue and embryonic stem cell research, somatic and germ-line gene therapy and directed genetic modification of food crops amenable to deliberation and resolution? I believe the Asilomar model would not succeed in dealing with those issues today to the extent it did 30 years ago with recombinant DNA for the following reasons. First, the public's awareness of the recombinant DNA breakthrough was sudden and unanticipated. It was more than just another interesting scientific advance because it brought with it potential dangers to public health. Furthermore, the implications of risk came from the scientists conducting that research, not from some investigative reporter or disaffected scientist; that was most unusual, even historic. There seemed to be an urgent need for consensus on how to proceed and a plausible plan on how to deal with issues, both of which were provided by the scientific community. Action was prompt and seen by the public to have been achieved by transparent deliberations and with considerable cost to their own scientific interests. The issue and its resolution were complete before an entrenched, intransigent and chronic opposition developed. Attempts to prohibit the research or reverse the actions recommended by the conference threatened but never generated sufficient traction to succeed.

By contrast, the issues that challenge us today are qualitatively different. They are often beset with economic self-interest and increasingly by nearly irreconcilable ethical and religious conflicts and challenges to deeply held social values. An Asilomar type conference trying to contend with such contentious views is, I believe, doomed to acrimony and policy stagnation, neither of which advances the cause of finding a solution. There are many forums for airing opposing views but emerging with an agreed upon solution from such an exercise is elusive and discouraging.

The Asilomar decisions emerged from a consensus of opposing views. Although the recommendations were clearly "inconvenient", the participants had a stake in having the science move forward and not in leaving the rules for conducting the research to be set by others. By contrast, there is little prospect for consensus in our society on the ethical issues concerning fetal tissue and embryonic stem cell research, genetic testing, somatic and germ-line gene therapy, and engineered plant and animal species and hence little incentive to seek a compromise. Compromise in those instances may only be achievable by political means, where majority rule prevails.

In other words, the lesson of Asilomar is that when politicians and the general public learn enough about an issue to start forming an opinion, the views of scientists are usually ignored or rejected. It's better to keep them ignorant until you can get some reasonable laws passed. Not a very happy lesson.

Jackson, D.A., Symons, R.H., and Berg, P. (1972) Biochemical method for inserting new genetic information into DNA of Simian Virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli. Proc. Natl. Acad. Sci. (USA) 69:2904-2909 [PubMed]

Please Tell Me This Is a Joke

 
From Biology News Net comes this crazy article [Why aren't humans furry? Stone-Age moms could be the answer.

Medical Hypotheses, an Elsevier publication, has announced the winner of the 2006 David Horrobin Prize for medical theory. Written by Judith Rich-Harris, author of The Nurture Assumption and No Two Alike, the article, "Parental selection: a third selection process in the evolution of human hairlessness and skin color" was judged to best embody the spirit of the journal. The £1,000 prize, launched in 2004, is awarded annually and named in honour of Dr. David Horrobin, the renowned researcher, biotechnology expert and founder of Medical Hypotheses who died in 2003.

Harris' paper describes Stone Age societies in which the mother of a newborn had to decide whether she had the resources to nurture her baby. The newborn's appearance probably influenced whether the mother kept or abandoned it. An attractive baby was more likely to be kept and reared.

Harris' theory is that this kind of parental selection may have been an important force in evolution. If Stone Age people believed that hairless babies were more attractive than hairy ones, this could explain why humans are the only apes lacking a coat of fur. Harris suggests that Neanderthals must have been furry in order to survive the Ice Age. Our species would have seen them as "animals" and potential prey. Harris’ hypothesis continues that Neanderthals went extinct because human ancestors ate them.

This year's prize judge was Professor Jonathan Rees FMedSci of Edinburgh University, Scotland – co-discoverer of the 'red hair gene'. Professor Rees said: "This paper is an excellent example of the kind of bold thinking and theorizing which David Horrobin intended to encourage when he began Medical Hypotheses. I hope that Judith Rich Harris' idea provokes debate and further investigation of this topic."

This can't be correct, can it? An apparently respectable organization giving a prize to someone who postulates that stone-age women killed off their hairy children and kept the hairless ones and that's why we don't have hair? It's a joke, right?

"Bold thinking" indeed. I can think of better words to describe that "theory."

Genome Size in Birds

 
The Animal Genome Size Database is maintained by T. Ryan Gregory of the University of Guelph in Ontario. Gregory has collected data on genome size in animals from the scientific literature and from work in his own lab. He is interested in several projects on genome evolution.

There are several ways of reporting genome size. The most common is to give the C-value (haploid genome size) in picograms (pg) because a lot of the data simply measures the amount of DNA in a nucleus using a DNA-specific stain. The range of C-values for different groups of organisms is shown in the figure (above right). As the legend states, there's no special significance to the order of the groups (from top to bottom) other than the fact that it's easy to understand if mammals are at the top.

One of the things that Gregory works on is the correlation between cell size and genome size. It turns out that the size of the nucleus is related to the size of the cell, such that large genomes give rise to large nuclei and large cells. This is particularly evident when you look at red blood cells and Gregory has a remarkable image showing this correlation on his website [Gregory Lab].

It has been known for some time that birds have smaller genomes than reptiles and mammals. This has natually given rise to an adaptionist explanation;namely, that the small genome is due to selection for small cells in birds because they exert a lot of energy in flight. In other words, small genomes are an adaption for flight.

A recent News article on the Nature website raises an important question concerning this adaptionist explanation. If birds have smaller genomes than other vertebrates then is that a derived trait or did birds inherit a small genome from their dinosaur ancestors? [Did a 'light' genome help birds take flight?].

A study of dinosaur genomes hints that the early evolution of a smaller genome might have been necessary for later vertebrates to take to the skies.

Birds have long been known to have much smaller genomes than mammals and reptiles living on the ground. And a small genome has been linked to both small cell size and high metabolic rate: the lower volume-to-surface ratio of small cells, which don't have much DNA to pack inside, can allow for faster transport of nutrients and signals across the membrane. Thus, some suggest that the energetic demands of flight require birds to have a 'light' genome.

But which came first: flying birds or the smaller genome?

The paper by Organ et al. (2007) looked at genome size in extinct dinosaurs with a view to discovering whether the bird ancestors had large or small genomes. Obviously, they couldn't measure genome size directly in fossils. What they did was measure the size of fossilized cells, having previously established that there's a correlation between the size of cells and the size of the nucleus. The size of the nucleus, in turn, depends on the amount of DNA in the genome.

The result is shown below. Red and purple lines indicate species with small genomes. You can see that the bird lineages (Aves) all have smallish genomes. So do the theropods that cluster with the birds on the right-hand group within Dinosauria. What this means is that the entire group of dinosaurs that descended from theropods had small genomes. It means that birds, which didn't arise until later, inherited their small genomes from ancestral theropods.

The result indicates that small genome size in birds is not an adaptation for flight. Perhaps it is not an adaptation at all but simply an accident due to the fact that the ancestor of sauropods just happened to have a reduced genome.

Before I had a chance to prepare this article, Carl Zimmer had not only done the work and interviewed Gregory, but he had published the review on the Science website [Jurassic Genome]!!! Please read Zimmer's excellent article for a more complete story.

Organ, C.L., Shedlock, A.M., Meade, A., Pagel, M., and Edwards, S.V. (2007) Origin of avian genome size and structure in non-avian dinosaurs. Nature 446:180-184. [PubMed]

How Roundup® Works

This week's molecule is N-(phosphonomethyl) glycine better known as glyphosate, the active ingredient in the herbicide Roundup® [Monday's Molecule #17]. Glycophosate is a potent inhibitor of one of the key enzymes in the pathway for synthesis of the aromatic amino acids, tryptophan, phenylalanine, and tyrosine [How Cells Make Tryptophan, Phenyalanine, and Tyrosine].

Specifically, the herbicide blocks the activity of EPSP synthase, the enzyme that catalyzes one of the steps leading to chorismate. Chorismate is the precursor of all three aromatic amino acids so by blocking this enzyme, the synthesis of three plant amino acids is prevented.


Plants need to synthesize all 20 amino acids so this blockage causes plants to die. The glyphosate mechanism is well known from studies of the homologous bacterial versions of EPSP synthase. An example of glyphosate bound to the active site of the E. coli enzyme is shown on the right. When glyphosate is bound, the enzyme is incapable of catalyzing any reaction.

As pointed out earlier in "How Cells Make Tryptophan, Phenyalanine, and Tyrosine," animals have lost the ability to synthesize chorismate and the aromatic amino acids. They require tryptophan, phenyalanine, and tyrosine in their diet. What this means is that the potent herbicide, glyphosate, has no effect on animals since they have already dispensed with the EPSP synthase enzyme. That's one of the reasons why Roundup® is so safe for humans.

Those of you who have used Roundup® on your driveways and walkways know that it kills all plants indiscriminately. You'd better not get it on your wife's favorite roses (... not that I'm admitting anything, mind you).

You can't spray it on crops, such as soybeans, corn, cotton, granola, and wheat to get rid of weeds because it kills the crops as well as the weeds. Wouldn't it be nice to have Roundup® resistant crops so you could spray them to control weeds?

Monsanto makes Roundup® and and they thought so too. Now, how do you genetically modify plants to make them resistant?

Immigration Critical to Canada

 
All Canadians know how important immigration is to our future. Not only do we benefit from an influx of new ideas and new faces, we also benefit from the increase in population that is so important to maintaining our present high standard of living.

An article on cnews makes the case [Census: Immigration critical to Canada].

Canada saw its native-born populace climb by a modest 400,000 souls between 2001 and 2006. It was the addition of 1.2 million immigrants that helped push the country’s enumerated population total to 31.6 million.

The 2006 census data, released Tuesday by Statistics Canada, shows overall population growth of 5.4 per cent — the highest among the Group of Eight industrialized nations. Canadian growth was up from four per cent in the previous five-year census period, which had been the slowest half-decade in modern Canadian history.

Thank immigration for Canada’s relatively robust growth. An average 240,000 newcomers per year more than compensated for the country’s flat fertility rate.

Canada's immigration rate is the highest in the industrialized world, higher by far than that of the United States, although the US has more immigrants in terms of total numbers (not counting Mexicans, I assume).

Canada’s net migration, per capita, is among the highest in the world. According to the OECD, Canada’s net migration of 6.5 migrants per 1,000 population between 2000-2004 put it at the head of the international pack. Australia, another immigration juggernaut, accepted 6.2 migrants per 1,000 population during the same period.

Canada’s influx offsets a flacid national birthrate of about 1.5 kids per woman, well below the replacement rate of 2.1 and just below the OECD average.

The United States, by way of example, accepts only 4.4 immigrants per thousand but has a fertility rate 25 per cent higher than Canada.

I don't know why the US birth rate is so much higher than Canada's or Europe's. Does anyone have an answer?