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?

Apple Computer Unveils the New iRack

 



[Hat Tip: Sunbeams from Cucumbers]

Roll Up the Rim

 
There's always a long line at my regular Tim Horton's on the first floor of my building. The lines are even longer at this time of year because it's "Roll-up-the-rim" time. Timmy's has a special contest where you can win prizes by simply rolling up the rim of your coffee cup. I'm just about to do it right now ......

Rats! It says, "PLEASE PLAY AGAIN/RÉESSAYEZ S.V.P" (Remember, we're a bilingual country so we get to be disappointed in two languages.) Back in 1993 I won a stereo system by rolling up the rim and I'm hoping for a big screen TV next time.

Believe it or not, some people have trouble rolling up the rim. Apparently, there's an epidemic of broken fingernails and other serious injuries during the Tim Hortons promotion in March and April. That's prompted an Ottawa inventor to come up with a nifty tool to help out [Ottawa invention makes it easy to play again... and again... and...]. I guess they don't have anything better to do up in Ottawa.

The Rimroller tool is marketed by Lee Valley Tools. Now, you may be wondering why a company like Lee Valley would be involved in marketing a tool to roll up the rim of Tim Hortons coffee cups. You weren't? Well I was, so I looked on their website and read what the President had to say.

When we were first shown the Rimroller many months ago, we recognized immediately that this was an elegant, well-designed, and well-manufactured product at a very reasonable price. It was one of those products that just delighted people when they used it. We also recognized that the inventor, Paul Kind, had plowed a ton of time and capital into bringing the product to the point where it was ready to market. So, while Lee Valley is clearly not the most appropriate retailer of this product, we could only stand by for so long watching Mr. Kind work hard to sell this product without success.

That certainly explains it.

Want to know how it works? ....... Okay, I can respect that; but for the rest of you, here are the simple instructions.

This is an easy-to-use product. Essentially a curved clip with two integral (covered) blades, it slices the cup rim twice (1-1/8" apart) when pushed down, and an internal lip unrolls the paper edge when it’s pulled up. Push, pull and you’re done. 2" high, 1-1/2" wide, with an attached split-ring.

Invented and manufactured in Ottawa, Canada.

You can buy them wherever you find a Lee Valley Tools store for $1.95 (+tax). Personally, I'd rather save money on the Rimroller and buy another coffee. I really need that TV 'cause the World Curling Championships are coming up next month.

Kieffer Sutherland In Toronto

 
Here's a picture from the weekend Toronto Star with an interesting caption. Lots of people are upset about torture on "24".

Less Torture in "24"


More on "24" Torture

How Cells Make Tryptophan, Phenyalanine, and Tyrosine

 
Most species have to synthesize all of their amino acids from simple compounds. Several of the metabolic pathways are quite complicated, especially those leading to the complex aromatic amino acids like tryptophan, phenyalanine, and tyrosine. Many animals, including humans, have lost the ability to make these aromatic amino acids. We assume that the loss was not lethal because it was easy to get adequate amounts in the diet. The fact that we can't make them means that tryptophan, phenylalanine, and tyrosine are essential amino acids.

The other essential amino acids also have complicated biosynthesis pathways. We have also lost the ability to synthesize lysine, methionine, threonine, valine, leucine, isoleucine, and histidine.

Let's look at the pathway for the synthesis of tryptophan, phenylalanine, and tyrosine as seen in bacteria, plants, fungi, and protists. These are species that cannot get adequate supplies of pre-formed amino acids so they have to make all of the amino acids needed for protein synthesis de novo.

The first part of the pathway begins with a simple three carbon compound (phosphoenolpyruvate) and a simple carbohydrate derivative (erythrose 4-phosphate). These are combined in a series of four reactions to produce shikimate, a common metabolite in bacteria and most eukaryotes. Shikimate is then phosphorylated by shikimate kinase to make shikimate 5-phosphate.

The next step is very important. A three carbon addition to shikimate yields the complicated product 5-enolpyruvylshikimate 3-phosphate. The addition to the ring will eventually become the core part of the amino acid. This reaction is catalyzed by the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSP synthase) an enzyme that we'll hear more about very soon.

The final step in the first part of the pathway is the removal of the phosphate group to produce chorismate. Chorismate is another common metabolite in all species except animals.


The three aromatic amino acids are all made from chorismate (see below). The pathway to tryptophan is complicated but those leading to phenylalanine and tyrosine are much simpler. In addition to the pathway shown, tyrosine can also be made directly from phenylalanine by hydroxylation, in a reaction catalyzed by phenylalanine hydroxylase. That's why tyrosine is sometimes not listed as an essential amino acid; it's not essential if there are adequate supplies of phenylalanine in the diet. (Defects in phenylalanine hydroxylase are responsible for phenylketonuria.)

The important point for later on is the chorismate pathway. It is absolutely crucial for life in most species but it isn't even present in most animals. Blocking that pathway with a herbicide in plants will be lethal but the herbicide will have no effect on animals.

Douglas Adams Speaks About Religion

 
Coturnix reminds us that yesterday was the birthday of Dougls Adams [Happy Birthday Douglas Adams]. Most of us remember the funny Douglas Adams and, in that vein, Coturnix posted a number of humorous quotations.

But there was a serious side to Douglas Adams and I'm going to post an extended quotation of Adams that I first saw in A Devil's Chaplain by Richard Dawkins. As most of you know, Douglas Adams and Richard Dawkins were friends—Adams introduced Dawkins to his current wife. [Lament for Douglas]

The quotation in A Devil's Chaplain is taken from a speech that Adams gave in Cambridge in 1998. The complete text of the speech is at [Is there an Artificial God?]. You can also listen to a podcast of Douglas Adams giving the speech. Here's what Douglas Adams says about our attitude toward religion.

Now, the invention of the scientific method and science is, I'm sure we'll all agree, the most powerful intellectual idea, the most powerful framework for thinking and investigating and understanding and challenging the world around us that there is, and that it rests on the premise that any idea is there to be attacked and if it withstands the attack then it lives to fight another day and if it doesn't withstand the attack then down it goes. Religion doesn't seem to work like that; it has certain ideas at the heart of it which we call sacred or holy or whatever. That's an idea we're so familiar with, whether we subscribe to it or not, that it's kind of odd to think what it actually means, because really what it means is 'Here is an idea or a notion that you're not allowed to say anything bad about; you're just not. Why not? — because you're not!' If somebody votes for a party that you don't agree with, you're free to argue about it as much as you like; everybody will have an argument but nobody feels aggrieved by it. If somebody thinks taxes should go up or down you are free to have an argument about it, but on the other hand if somebody says 'I mustn't move a light switch on a Saturday', you say, 'Fine, I respect that'.

The odd thing is, even as I am saying that I am thinking 'Is there an Orthodox Jew here who is going to be offended by the fact that I just said that?' but I wouldn't have thought 'Maybe there's somebody from the left wing or somebody from the right wing or somebody who subscribes to this view or the other in economics' when I was making the other points. I just think 'Fine, we have different opinions'. But, the moment I say something that has something to do with somebody's (I'm going to stick my neck out here and say irrational) beliefs, then we all become terribly protective and terribly defensive and say 'No, we don't attack that; that's an irrational belief but no, we respect it'.

It's rather like, if you think back in terms of animal evolution, an animal that's grown an incredible carapace around it, such as a tortoise—that's a great survival strategy because nothing can get through it; or maybe like a poisonous fish that nothing will come close to, which therefore thrives by keeping away any challenges to what it is it is. In the case of an idea, if we think 'Here is an idea that is protected by holiness or sanctity', what does it mean? Why should it be that it's perfectly legitimate to support the Labour party or the Conservative party, Republicans or Democrats, this model of economics versus that, Macintosh instead of Windows, but to have an opinion about how the Universe began, about who created the Universe, no, that's holy? What does that mean? Why do we ring-fence that for any other reason other than that we've just got used to doing so? There's no other reason at all, it's just one of those things that crept into being and once that loop gets going it's very, very powerful. So, we are used to not challenging religious ideas but it's very interesting how much of a furore Richard creates when he does it! Everybody gets absolutely frantic about it because you're not allowed to say these things. Yet when you look at it rationally there is no reason why those ideas shouldn't be as open to debate as any other, except that we have agreed somehow between us that they shouldn't be.

We've discussed this issue many times. What is it about religion that makes us bend over backwards to avoid offense? We wouldn't hesitate to criticize those who fall for "The Secret" or those who are taken in by Sylvia Browne. We challenge those people who claim that the moon landings were faked. We debunk urban legends. We question homeopathy.

But if a man says he can't turn on a light switch because it's Saturday we say nothing. Why is that? Is it because the orthodix Jew is expressing a personal belief that's none of our business? If that's it then what about conspiracy buffs or those who think they've been abducted by aliens? Aren't those harmless personal beliefs as well? Is Adams correct to assume that it's "religion" that's out-of-bounds?

Monday's Molecule #17

 
Name this molecule. You must be specific. We need the correct scientific name and in this case we need the generic and brand names as well.

As usual, there's a connection between Monday's molecule and this Wednesday's Nobel Laureate. This one's a bit of a stretch. Extra bonus points for guessing Wednesday's Nobel Laureate(s).

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