While poking around on YouTube I stumbled across this performance by Arlo Guthrie of one of the best songs ever. I just had to share it with the one or two other people who might agree with me. The song was written by Steve Goodman in 1970.
Thursday, January 15, 2009
Arlo Guthrie: City of New Orleans
While poking around on YouTube I stumbled across this performance by Arlo Guthrie of one of the best songs ever. I just had to share it with the one or two other people who might agree with me. The song was written by Steve Goodman in 1970.
Meat Loaf: Would you let your daughter listen to "Paradise by the dashboard light?"
I have a confession to make. I've been fan of Meat Loaf ever since Rocky Horror Picture Show.1
It was fun watching Meat Loaf on this FOX news clip—thanks to Greg Laden for posting it.
At six minutes and ten seconds into the video the moderator says that he doesn't want his daughter, when she become 14, listening to "Paradise by the dashboard light." Them's fighting words.
Would you let your daughter see this video and listen to the lyrics? If not, what are you afraid of? Do you think that 14 year old girls (and boys) don't know about sex?
Here's one of my favorites ("I Would Do Anything for Love"). I seem to recall that it was my daughter—when she wasn't much older than 14—who first started playing it on our car trips. Incidentally, Ms. Sandwalk isn't a big fan of Meat Loaf. She has a stack of 20 or 30 CDs that we play on our car trips and I don't think there's a single song by Meat Loaf. There are lots of songs by dudes I never heard of, like Tchaikovsky and The Rolling Stones.
1. I'm also a fan of Susan Sarandon
Wednesday, January 14, 2009
Nobel Laureates: Sir Henry Hallett Dale and Otto Loewi
The Nobel Prize in Physiology or Medicine 1936.
"for their discoveries relating to chemical transmission of nerve impulses"
Sir Henry Hallett Dale (1875 - 1968) and Otto Loewi (1873 - 1961) won the Noble Prize in 1936 for discovering the role of chemicals, especially acetycholine, in transmitting nerve impulses. Today we take it for granted that chemicals are involved at the synapses but in the beginning of the 20th century this wasn't obvious. The impact of this work is apparent from the Presentation Speech.
THEME:
Nobel Laureates
It was generally thought that impulses in the nerves act directly on the muscles or glands bringing about a change in their activity. But as early as 1904, Elliott presented a different interpretation. From the medulla of the adrenal glands, which, as embryonic development shows, is related with the sympathetic nervous system, a substance can be produced, i.e. adrenaline, the effect of which is remarkably similar to that produced by increased activity in the sympathetic system. Elliott therefore supposed that the impulses in the sympathetic nerves produced a release of adrenaline in the nerve endings which would then be the real vehicles of the stimulation effect. Ten years later, Dale published a comprehensive investigation of another substance, acetylcholine, for which he found a corresponding conformity with the effect of the parasympathetic stimulation. As, however, at that time acetylcholine had not been met with in the body, there was not sufficient basis for a discussion as to whether it normally transmitted impulses.
The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.
[Photo Credits: Henry Hallett Dale: Jamd; Otto Loewi: ©Copyright Encyclopedia of Austria]
Dr. Larry Moran Flunks Philosophy
It wouldn't be fair for me to ignore Michael Egnor's devastating put-down demonstrating my ignorance and bigotry [Dr. Larry Moran Flunks Philosophy].
I especially like being called a Darwinian fundamentalist.
The "discussion" is all about Mary's Room. Here's the synopsis from the Wikipedia site.
Mary is a brilliant scientist who is, for whatever reason, forced to investigate the world from a black and white room via a black and white television monitor. She specializes in the neurophysiology of vision and acquires, let us suppose, all the physical information there is to obtain about what goes on when we see ripe tomatoes, or the sky, and use terms like ‘red’, ‘blue’, and so on. She discovers, for example, just which wavelength combinations from the sky stimulate the retina, and exactly how this produces via the central nervous system the contraction of the vocal cords and expulsion of air from the lungs that results in the uttering of the sentence ‘The sky is blue’. [...] What will happen when Mary is released from her black and white room or is given a color television monitor? Will she learn anything or not?The answer, by the way, is "yes." Mary will learn something when she actually experiences how photons of different wavelengths impinge upon her retina and are interpreted by her brain.
Isn't that profound?
Falling into a pit
Falling into a pit may be a much better analogy for evolution than adaptive peaks and climbing Mt. Improbable. To find out why read Chris Nedin's blog Ediacaran [Climbing Pit Improbable].Atheist Buses in Genoa
"The bad news is that God does not exist. The good news is that you do not need him."I wonder how long it will take until these signs show up on buses in the major cities of North America? Anyone want to takes bets on when we'll see an atheist bus sign in Vancouver, Toronto, Montreal, or Calgary?
[Hat Tip: Friendly Atheist]
The taste of MSG
Discount Thoughts has posted a wonderful description of how we taste the glutamate in monosodium glutamate [How we taste umami]. The taste is called "umami" and it's distinct from the four standard tastes of sweet, sour, salty, and bitter. The figure shows a glutamate molecule (yellow) bound to the umami receptor with inosine monophosphate (IMP) (green). You need both glutamate and IMP in order to get the umami taste.
Theme
A Sense of Smell
I know lots of people who can taste MSG but that's not the problem. There appear to be some other effects of this chemical that are much less pleasant.
The umami flavor is common in meats, cheese, seafood, and lots of other foods that are rich in protein. Vegetarians don't know what they're missing!
Do you know what this is?
If you can't identify the organism in the photograph then read The Beautiful Angel of Death on Catalogue of Organisms. Life is stranger than most of us realize.
Tuesday, January 13, 2009
ScieneOnline '09: Things to do in Durham
ScienceOnline '09 is being held in the Research Triangle, North Carolina (USA) this weekend. For those of you who aren't familiar with the region, the "triangle" consist of Chapel Hill, Raleigh, and Durham. I've spent a lot of time there over the past 25 years but unfortunately I can't make it this weekend.Chapel Hill is one of the best places in America for all kinds of reasons. Raleigh is a pretty decent city.
Abel Pharmboy has the unenviable task of promoting Durham. You can read his attempt at: General cool stuff to do in Durham, NC, during ScienceOnline'09.
He did about as good a job as someone from Durham could possibly do.
2008 Weblog Awards
Voting for the best science blog will close tonight. Pharyngula is in the running and so is Bad Astronomy.
The current leader in the voting is a climate change denialist blog called Watt's Up with That?.
Do NOT, repeat DO NOT, rush over and vote for Pharyngula or Bad Astronomy, or any other real science blog. PZ is not asking you to do that. Many science bloggers (including me) want the anti-science blog to win in order to completely discredit the whole notion of online voting for best blog.
It's about time we put an end to this nonsense and letting an anti-science blog win for "Best Science Blog" is an excellent way to send a message.
Paleobet and Cambrian Fossils
PZ has discovered palaeobet1 so, naturally, I had to post my initials as well.
Some of you may not recognize "laggania." It's Laggania cambria, one of several species related to Anomalocaris. Collectively they are known as Anomalocarids. Here's a fossil of Laggania cambria from the Burgess Shale (right). It just so happens that I was looking at this very fossil on Saturday during our visit the the Royal Ontario Museum. The Burgess Shale fossils are stuck in a corner of the museum where they can easily be missed by people entering the dinosaur rooms. That's a shame since these are unique fossils and very few museums have such a wonderful collection of Cambrian fossils.
Most of you are probably more familiar with Anomalocaris canadensis, a much more fierce-looking cousin of L. cambria (see below). A comparision of the two species can be found on The Anomalocaris Homepage.
Anomalocaris and Laggania were among the species made famous by Stephen Jay Gould in his excellent book Wonderful Life. Gould pointed out that these species so not fit neatly into any of the existing phyla, although they have some of the characteristics of arthropods and onychophora (velvet worms).Lumpers will now include them in Arthropoda and splitters assign them to a separate, extinct, phylum called Dinocaridida. What's clear is that there are no modern species that can trace their ancestry directly to the anomalocarids. They represent a body plan that has not survived and this lends support to Gould's idea that there were more fundamentally different kinds of animals in the past that we see today. As he put it on page 208 ...
The Burgess Shale includes a range of disparity in anatomical design never again equaled, and not matched today by all the creatures in the world's oceans. The history of multicellular life has been dominated by decimation of a large initial stock, quickly generated by the Cambrian explosion. The story of the last 500 million years has featured restriction following by proliferation within a few stereotyped designs, not general expansion of range and increase in complexity as our favored iconography, the cone of increasing diversity, implies. Moreover, the new iconography of rapid establishment and later decimation dominates all scales, and seems to have the generality of a fractal pattern.Scientists have been chipping away at Gould's thesis over the years since the publication of Wonderful Life in 1989. Several problematic species have been reliably assigned to existing phyla and others have been tentatively squeezed into the standard animal phyla. The goal is to discredit the idea that life was more diverse (disparate) during the Cambrian and the conclusion that the evolution of animals is characterized by the extinction of major lines.
I think Gould's main point is still valid and I don't understand why so many people find it troubling. It may have something to do with people's perception of evolution as progress.
1. Fossil animals for each letter of the alphabet.
[Hat Tip: P (pteraspis) Z (zalambalestis) Myers]
Monday, January 12, 2009
Trouble with Blogger Is Over
Blogger has finally fixed the problems with RSS feeds. As I mentioned earlier [Trouble with Blogger] this is a problem that the blogger team seem to have created back on December 19th. It was fixed on January 9th—21 days later.The most obvious change is in the recent comments in the left sidebar. You can now actually see recent comments instead of comments from June 2007.
I suppose we shouldn't complain, after all Blogger is free and it's pretty good most of the time.
I'm sorry if I missed any of your comments during the outage. I was able to keep up with all comments on recent postings but if you commented on an old posting chances are I missed it.
Drift vs. Selection
Daniel MacArthur of Genetic Future weighs in on the ongoing debate over the important of random genetic drift vs natural selection during human evolution [Genetic differences between human populations: more drift than selection?].
Daniel MacArthur seems to be a smart guy. Here's a teaser ....
I should emphasise that there's little doubt that at least some recent population-specific selection has occurred in humans (the signal around the lactase gene in Europeans is about as unambiguous as it gets) - but perhaps it has not been anywhere near as pervasive as some researchers (e.g. John Hawks) have argued.
Monday's Molecule #103
Name this molecule. We need a biochemically accurate name and the formal IUPAC name. The role of this molecule in biological systems was discovered by one or more Nobel Laureate(s) almost one hundred years ago. Your task is to correctly identify the molecule and name the Nobel Laureate(s). The first one to do so wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize.
There are three ineligible candidates for this week's reward: Timothy Evans of the University of Pennsylvania, John Bothwell of the Marine Biological Association of the UK in Plymouth, UK and Dima Klenchin of the University of Wisconsin.
John, Dale (twice), and a previous winner (Ms. Sandwalk) have offered to donate their free lunch to a deserving undergraduate so the next two undergraduates to win and collect a free lunch can also invite a friend. Since undergraduates from the Toronto region are doing so poorly in this contest, I'm going to make a special award this week. In addition to the normal winner, the first undergraduate student who can accept a free lunch will win a second prize. Please indicate in your email message whether you are an undergraduate and whether you came make it for your free lunch (with a friend). Mmmmmm .... poutine. Good luck.
THEME:
Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.
Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.
UPDATE: The molecule is acetylcholine (2-acetoxy-N,N,N-trimethylethanaminium). The Nobel Laureates are Sir Henry Hallett Dale and Otto Loewi.
The winner is Bill Chaney of the University of Nebraska who was the first one to correctly identify the molecule and the Nobel Laureates. The undergraduate winner is Maria Altshuler of the University of Toronto. She can bring a friend to lunch.
Postdoc Salaries: Foreigners vs Americans
Check out Biocurious for a discussion stimulated by Lou Dobbs on CNN. Watch the YouTube video.
A typical graduate student in our department gets $25,000 per year. A typical post-doc gets $40,000 per year (range 36-45) and a typical Assistant Professor is hired at about $80,000 per year (range 70-100, depending on the university).
What should a post-doc earn? Would salaries be higher if you couldn't hire any foreigners as post-docs?
Sunday, January 11, 2009
Homeschooling and Creationism
Not all homeschoolers are Creationists but for strong Biblical literalists homeschooling does offer an easy way of "protecting" children from evil ideas in the real world. Such ideas may cause them to doubt their religion.If you are a Young Earth Creationist there are some problems associated with the anti-science approach to education. If would be nice to have some helpful advice in case your children ever have to deal with the real world outside the home.
The current issue of Home School Enrichment magazine comes to the rescue. They have an article called Creation and You that's available for free download. (You have to give them an email address.)
The main part of the article extols the virtues of the Answers in Genesis Creation Museum; "600,000 visitors have gone through its doors into an amazing experience demonstrating the power, creativity, and love of the Creator God." I suppose this is a good thing if you're into brainwashing. We just spent yesterday with two young girls in the Royal Ontario Museum in Toronto and there was very little evidence of the "power, creativity, and love of a Creator God." On the other hand, there was quite a bit of good science. Our two friends might have got a bad impression of Biblical literalism. If their parents had been Young Earth Creationists we would have been in big trouble for leading them astray.
Anti-science homeschoolers are right to keep their children away from real museums.
But that's not the only problem they face. What to do if your kids want to have a career in Creation Science? Hmmm ... that's a tough one, isn't it? Here's the answer ....
Preparing for a Career in Creation ScienceLife is tough if you are anti-science but want a career in science. Not only are the secular universities trying to persuade you that truth is important in science but even some of the Christian colleges are "compromised."
Answers in Genesis content developers Gary Vaterlaus and Roger Patterson agree that more researchers are needed in Creation Science, but warn that the path may not be easy. Several Christian colleges across the country offer science courses taught from a Young-Earth Creationist perspective, but few research positions are available to those with anything less than a Master’s degree in their field; more likely a Ph.D. And, Roger says, getting those degrees will likely require spending some time in a secular university.
Furthermore, Gary explains that the evolutionary teachings at these secular universities are only part of the problem—there is also a very real prejudice against Creationists who attempt to embark upon a career in any of the relevant branches of science. Aside from the strong possibility of a known-Creationist student receiving failing grades merely for believing God created the universe, Gary cited a case where evolutionists actually petitioned a university to revoke a graduate’s Ph.D. when it was discovered he was a Creationist.
There is a need for young, up-and-coming students to enter the realm of Creation Science, but Gary and Roger emphasize that a student must have an unshakable foundation on the reliability and truthfulness of the Bible, and then be ready, willing, and able to face unbelievably strong opposition while pursuing a degree that will qualify them for the research positions they wish to obtain.
While none of this should dissuade students from choosing such a career, it is important for students and their parents to recognize the potential difficulties and take steps early to ensure a successful and victorious outcome.
For students wishing to be involved in the area of Creation Evangelism, such as speaking at churches or writing about creation related topics, Roger believes a Bachelor’s degree in some branch of science is important for establishing credibility. Several Christian colleges offer science programs, taught from a Young-Earth Creationist perspective, in which students can earn their Bachelor’s degrees. However, many Christian colleges have compromised in the area of origins and evolution, so this is something that should be carefully investigated when researching options for collegebound Creationist students.
But you can succeed if you resist education and maintain "unshakable foundation on the reliability and truthfulness of the Bible." Incredible.
What about average students who venture out into the secular world? What happens if they happen to pick up a book written by a (gasp!) real scientist, or if they mistakenly enter a real museum?
Roger Patterson of Answers in Genesis has some advice.
Homeschool parents often wonder how to protect their children from evolutionary ideas. We brought this up to Roger Patterson, a former biology teacher in a public school who is now one of the main content-developers at Answers in Genesis, and were impressed by his answer:I can't imagine what it must be like to be constantly on the lookout for sneaky remarks about evolution and other scientific facts that challenge your religion. I can't imagine what it must be like to brainwash your kids into responding with, "We know that’s not true. Praise God He did create us, that He is the one who’s sustaining all this."
“As a ministry in general,” Roger explains, “we don’t say, ‘keep your kids isolated from evolutionary ideas.’We think that’s kind of a bad philosophy because when they do go out on their own, they’re going to face those things every day. Case in point: [my wife and I recently] got this space-age ant colony gel material. Flip open the book, and you’re reading through the instructions and all these fun facts about ants, [then] ‘Fossil ants have been found a hundred million years old.’ What we would hope parents can do through homeschooling is teach their kids how to spot those things, and then what the biblical response is for those things. Not to isolate them from those things, but to insulate them to some degree and then help them understand what the problems are there.
“Okay, this is a fun ant gel colony, [but] they didn’t need to throw that little tidbit [about millions of years] in there; it adds nothing to the product or your ability to enjoy and watch the ants. And when you look at it from the perspective that God created these creatures to do what they do, and it’s an amazing thing, it even gives an opportunity to give praise to God when you run across the idea of evolution. [We can say] ‘We know that’s not true. Praise God He did create us, that He is the one who’s sustaining all this.’ Rather than running away and hiding from all those things, let’s face up to it. And then if you’re with your friend, you can tell them about it if they don’t understand those things.
“So my encouragement is not to be afraid of going and getting the dinosaur book from the library, but [be sure to] teach your children as they go through it to understand that some parts [evolutionary statements] are made up, based on the idea of rejecting God in science, and other parts are facts—such as when it tells us what shape the egg was, what size it was, what food they probably ate. Those types of things, we can trust those; those are solid scientific ideas. It’s when we start adding our own assumptions into those things, and telling stories, that we run into trouble.”
Roger explains that there are certain “code words” that parents can teach their children to watch out for. Among these would be “millions or billions of years,” statements about kinds of animals changing into other kinds of animals, and questionable statements of what scientists “know.” Above all, Roger says, it’s important to make sure our children have a solid biblical foundation for
their education, and to help them stand firm on the full authority of scripture.
I not a huge fan of the idea that teaching your children to be Young Earth Creationists is a form of child abuse but there are times, like today, when Dennet and Dawkins seem to have a strong case.
Home schooling isn't always a good thing for children.
Friday, January 09, 2009
A Shocking Discovery
Almost all proteins in Escherichia coli begin with the amino acid N-formylmethionine (f-met), a modified version of methionine. N-formylmethionine is inserted at AUG codons at the beginning of the open reading frame in mRNA. The initiation mechanism requires a specific initiator tRNA called f-Met-tRNA (right).
Internal AUG codons are recognized by another tRNA and normal methionine is inserted at these positions. The observation that a single codon (AUG) can serve as the codeword for two different amino acids depending on their position was made over thirty-five years ago and it has been incorporated into the textbooks for decades.
You can imagine how surprised I was to read this in a press release written by Haley Stephenson of ScienceNOW Daily News. You can read it yourself on the Science website: Genetic Code Sees Double.
Call it the genetic version of a double-entendre. Scientific dogma dictates that various three-letter combinations of our genetic sequence each "mean" exactly one thing--each codes for a particular amino acid, the building block of proteins. But a protozoan named Euplotes crassus appears to be more versatile: One of its three-letter combinations has two meanings, coding for two different amino acids. Although the find may seem trivial, it poses a major challenge to more than 4 decades of scientific thinking.The idea that a protozoan might use UGA to encode both cysteine and a modified form of serine called selenocysteine is quite interesting. It has long been known that UGA is a normal stop codon that is also used to encode selenocysteine. It has also been known for a long time that some organisms can use UGA to encode cysteine.
But the idea that scientific dogma has been overturned by the discovery of a single codon that can encode two different amino acids is just plain silly. It doesn't pose a "major challenge to more than 4 decades of scientific thinking" unless your scientific thinking is flawed to begin with.
This must be an example of hyperbole. Such a claim would never make it into a scientific publication, especially in a prestigious journal like Science. Or so I thought.
Here's the opening sentence in the paper by Turanov et al. (2009).
Although codons can be recoded to specify other amino acids or to have ambiguous meanings (1, 2), and stop codons can be suppressed to insert amino acids (3), insertion of different amino acids into separate positions within nascent polypeptides by the same codeword is believed to be inconsistent with ribosome-based protein synthesis.It's enough to make me give up writing biochemistry textbooks. Apparently nobody reads them.
We seem to be producing a generation of scientists who don't know about the fundamentals of biochemistry and molecular biology that were elucidated in bacteria and bacteriophage in the mid-20th century. Doesn't anyone teach this stuff any more?
Turanov, A.A., Lobanov, A.V., Fomenko, D.E., Morrison, H.G., Sogin, M.L., Klobutcher, L.A., Hatfield, D.L., and Gladyshev. V.N. (2009) Genetic Code Supports Targeted Insertion of Two Amino Acids by One Codon. Science 323:259-261. [DOI: 10.1126/science.1164748]
John Pieret Issues a Challenge
John Pieret took the American Civil In his posting, Flunking At Being American, he reports that he scored 32/33 or 96.97%. Impressive.
He then asks, "I would be interested to know how non-US citizens score on the test."
Ask, and you shall receive. Here's my result.
You answered 30 out of 33 correctly — 90.91 %I didn't know which amendment was which, and what the Bill of Rights specifically prohibited. I'm too embarrassed to reveal the third question I got wrong.
Average score for this quiz during January: 74.2%
Average score: 74.2%
You can take the quiz as often as you like, however, your score will only count once toward the monthly average.
Here's one I got right.
27) Free markets typically secure more economic prosperity than government’s centralized planning because:I got it right by thinking like an American! (Ouch!) ;-)
A. the price system utilizes more local knowledge of means and ends
B. markets rely upon coercion, whereas government relies upon voluntary compliance with the law
C. more tax revenue can be generated from free enterprise
D. property rights and contracts are best enforced by the market system
E. government planners are too cautious in spending taxpayers’ money
It's a very strange "civil
What Could Be More Scary than the Flying Spaghetti Monster?
From the BBC News: Church removes 'scary crucifix'.A large sculpture of Christ on the cross has been removed from outside a church in West Sussex after its vicar said it was "scaring young children".Stainless steel crosses are also pretty scary.
The Reverend Ewen Souter said the 10ft crucifix was "a horrifying depiction of pain and suffering" which was also "putting people off".
The sculpture, located at the side of St John's Church in Broadbridge Heath, has now been given to Horsham Museum.
It will be replaced with a new stainless steel cross.
[Hat Tip: RichardDawkins.net]
Africans Need Jesus?
From RichardDawkins.net: Matthew Parris: As an atheist, I truly believe Africa needs God.
Now a confirmed atheist, I've become convinced of the enormous contribution that Christian evangelism makes in Africa: sharply distinct from the work of secular NGOs, government projects and international aid efforts. These alone will not do. Education and training alone will not do. In Africa Christianity changes people's hearts. It brings a spiritual transformation. The rebirth is real. The change is good.Read the comments. Some people aren't convinced that Christianity is the only way to change people's hearts for the better. Some people think it might be a wee bit condescending to imply that rationalism might be fine among Caucasians but Africans need superstition.
Changing Your Mind About Evolutionary Psychology
Every year John Brockman collects essay from his friends (I want to be one) and published them on his website and in a little book [The Edge Annual Question - 2009].This year's question was, "What game-changing scientific ideas and developments do you expect to live to see?" Last year's question was, "What Have You Changed Your Mind About? Why?" The book is now out.
There are far too many answers to these questions. I usually look at a few of them but it soon becomes boring.
Sharon Begley feels the same way but she has picked out a few interesting mind changes from the 2008 question. She writes in the Jan. 3, 2009 issue of Newsweek [On Second Thought ...].
The most fascinating backpedaling is by scientists who have long pushed evolutionary psychology. This field holds that we all carry genes that led to reproductive success in the Stone Age, and that as a result men are genetically driven to be promiscuous and women to be coy, that men have a biological disposition to rape and to kill mates who cheat on them, and that every human behavior is "adaptive"—that is, helpful to reproduction. But as Harvard biologist Marc Hauser now concedes, evidence is "sorely missing" that language, morals and many other human behaviors exist because they help us mate and reproduce. And Steven Pinker, one of evo-psych's most prominent popularizers, now admits that many human genes are changing more quickly than anyone imagined. If genes that affect brain function and therefore behavior are also evolving quickly, then we do not have the Stone Age brains that evo-psych supposes, and the field "may have to reconsider the simplifying assumption that biological evolution was pretty much over" 50,000 years ago, Pinker says. How has the view that reproduction is all, and that humans are just cavemen with better haircuts, hung on so long? "Even in science," says neuroscientist Roger Bingham of the University of California, San Diego, "a seductive story will sometimes … outpace the data." And withstand it, too.There are many reasons for changing your mind about the validity of evolutionary psychology but the idea that "human genes are changing more quickly than anyone imagined" isn't one of them.
As you might have guessed, John Hawks is really happy to encourage that kind of thinking. Hawks is a proponent of the idea that genes can be fixed in the entire human population by natural selection in only a few thousand years [Recent evolution in Newsweek].
An Unnecessary War?
Read what Jimmy Carter has to say about the current situation in Gaza [An Unnecessary War]. I wish Canadian politicians would be as rational as Carter and appreciate that this is a complex situation where nobody is totally right.
The one thing we can be sure about is that war is wrong.1
1. Firing rockets at your neighbors is war.
[Hat Tip: Runesmith's Canadian Content]
Thursday, January 08, 2009
Testing Natural Selection: Part 2
There are several interesting articles about evolution in the Januray 2009 issue of Scientific American. One of the most interesting is an article by H. Allen Orr of the University of Rochester (NY, USA). The magazine title is "Testing Natural Selection"1 and, as the title implies, the focus is on evolution by natural selection. Orr's article gives us an opportunity to compare and contrast the views of an adaptationist (Orr) and a pluralistic approach to evolution.
In Testing Natural Selection: Part 1 we discussed two of Orr's opinions: (1) random genetic drift is not as common as most people think, and (2) most (if not all) visible phenotypic change is driven by natural selection.
Here, we discuss Orr's ideas about speciation.
When we say "speciation" we're talking about the biological species concept. Speciation occurs when two formerly compatible populations evolve to the point at which they can no longer interbreed. The key question is what causes this reproductive isolation and how does it evolve?
To contemporary biologists, then, the question of whether natural selection drives the origin of species reduces to the question of whether natural selection drives the origin of reproductive isolation.Orr is correct to point out that random genetic drift is important in speciation. It's the mechanism described in many evolutionary biology textbooks, though it's not the mechanism that most people think about when they think about speciation.
For much of the 20th century, many evolutionists thought the answer was no. Instead they believed that genetic drift was the critical factor in speciation. One of the most intriguing findings from recent research on the origin of species is that the genetic drift hypothesis about the origin of species is probably wrong. Rather natural selection plays a major role in speciation.
Many biologists have always believed that natural selection plays a much more important role in speciation than random genetic drift. They aren't happy with the textbook description. Orr is one of these biologists. He now claims that the drift explanation is "probably wrong."
Let's think about what has to happen when two species become reproductively isolated. We'll use allopatric speciation as an example.2
We begin with a situation where two populations (races, subspecies) are geographically separated. There is very little gene flow between them so they evolve independently of each other. Over time, they may come to be different because each is adapting to different environments or they may just drift apart by accident. With respect to the actual speciation event, these differences don't matter.
From time to time, individuals from the two subspecies will interbreed to produce fertile offspring. This is responsible for limited gene flow between the subspecies and it proves that speciation has not occurred. If the barrier between the two populations breaks down they will merge back into a single population.
But if the two species have been separated for a long period of time, mutations that prevent interbreeding will accumulate and hybrids will become less and less viable until eventually no fertile hybrids are produced and speciation is complete. There are many ways that this can happen but a common hypothesis involves the build-up of post-zygotic genetic incompatibilities called Dobzhansky-Muller (D-M) incompatibilities.
How are D-M incompatibilites fixed in the population? If they interfere with the matings of individuals from the two populations then how come they don't contribute to infertility when individuals from the same population mate with each other? When the mutation first arises it seems to have a very strange property. It doesn't affect matings between an individual carrying the D-M allele and an individual not carrying that allele from the same population but it does affect matings between the individual carrying the new D-M allele and and an individual from the other population.
In order for this to happen there must already be some genetic differences between the two populations in terms of mating and reproduction. Those differences have accumulated in each of the populations but they must not have an effect on hybrid crosses. Presumably, the new D-M allele is not harmful in one genetic background but it is in the other.
Are these pre-existing potentiators neutral within a population, in which case they become fixed by random genetic drift? Or, are they beneficial in one of the populations, and not in the other, in which case they are fixed by natural selection? The general consensus has been that they are neutral within a population and they accumulate by accident. When enough of them become fixed the cumulative effect is to prevent hybridization. The last allele to arise, the D-M incompatibility allele, is the straw that breaks the camel's back.
Orr believes that the alleles are beneficial in one of the populations. Thus, according to him, reproductive isolation is driven by natural selection. He gives two examples.
The first one is the incomplete speciation in monkeyflower subspecies. I described this in an earlier posting [Speciation in Monkeyflowers], where I pointed out that the role of natural selection was not clear. The differences in flower color and pollinators could have arisen by selection if one postulates changes in the bee population but they could also be due to chance.
For an adaptationist like Allen Orr there's no doubt about what happened.
A good example is the evolutionary history of the two monkeyflower species mentioned earlier. Because their pollinators seldom visit the “wrong” species of monkeyflower, the two species are almost completely isolated reproductively. Even though both species sometimes occur in the same locations in North America, a bumblebee that visits M. lewisii almost never visits M. cardinalis, and a hummingbird that visits M. cardinalis almost never visits M. lewisii. Thus, pollen is rarely transferred between the two species. In fact, Schemske and his colleagues showed that pollinator differences alone account for 98 percent of the total blockage in gene flow between the two species. In this case, then, there can be no doubt that natural selection shaped the plants’ adaptations to distinct pollinators and gave rise to strong reproductive isolation.This is not a good example of speciation by natural selection. We simply don't know if the flower color mutation spread in one of the populations because it conferred a selective advantage on individuals within that population.
Besides, these two "species" will still form viable hybrids so they're not really species in the first place.
The other example of presumed speciation by natural selection comes from studies on Drosophila There are several example of D-M incompatibility alleles that have been identified. In some of them, there is evidence at the sequence level for rapid fixation. If correct, this is a good indication that the alleles have become fixed by natural selection. The resulting reproductive isolation is an epiphenomenon.3
One example is OdsH in Drosophila mauritiana. It appears to result in an increase in sperm production so it may have been selected in the early population of this species, before it became a species. Presumably, the allele was beneficial in the genetic background that had evolved up to that point and presumably it was detrimental in the genetic background of whatever subspecies it was related to.
The genetic background is obviously part of the speciation event. I suppose that if even one of the D-M alleles is selected then it's fair to say that speciation by natural selection took place.
The question is whether this is common or not. Shucker et al. (2005) looked at post-zygotic reproduction isolation in two populations of grasshopper and provided evidence that all the D-M incompatibilities could be adequately explained by random genetic drift. We'll need to have many more examples in order to decide whether natural selection explains most speciation events.
Personally, I find it easier to understand how reproductive isolation could arise by accidental accumulation of many neutral alleles that eventually lead to reproductive isolation. It's harder to envisage alleles that confer a selective advantage within one population but are extremely detrimental in the other.
Orr doesn't agree.
The studies of the monkeyflower and of hybrid sterility in fruit flies only begin to scratch the surface of a large and growing literature that reveals the hand of natural selection in speciation. Indeed, most biologists now agree that natural selection is the key evolutionary force that drives not only evolutionary change within species but also the origin of new species. Although some laypeople continue to question the cogency or adequacy of natural selection, its status among evolutionary biologists in the past few decades has, perhaps ironically, only grown more secure.I'm not an expert on speciation and I don't hang out with people who work in the field. However, my general impression from reading the scientific literature is that Orr's statements may be somewhat exaggerated. From what I can see, there are a great many evolutionary biologists who question the hegemony of natural selection. Their numbers seem to be growing, not shrinking.
I don't know where Orr is coming from when he implies that laypeople question the adequacy of natural selection. In my experience laypeople only think about natural selection. They have no idea that there are any other mechanisms of evolution.
1. The website title is "Testing Natural Selection with Genetics."
2. In allopatric speciation the two diverging populations are geographically separated. That's what makes them distinct populations. In sympatric speciation the two populations may exist in the same geographical and restricted gene flow between them is due to other factors. It's easier to visualize what's happening during allopatric speciation but the logic can apply to sympatric speciation as well.
3. I don't think Orr is actually proposing that there would be selection for reproductive isolation. How would that work?
Shuker, D.M., Underwood, K., King, T.M., and Butlin, R.K. (2005) Patterns of male sterility in a grasshopper hybrid zone imply accumulation of hybrid incompatibilities without selection. Proc. Roy. Soc. B 272:2491-2497. [DOI: 10.1098/rspb.2005.3242]
Buy a Dinosaur
Today's the day you can buy a dinosaur fossil. Maynards, in Vancouver, is auctioning off the complete collection of dinosaur fossils from the Seibu Museum in Tokyo, Japan [Auction Details: Dinosaurs].The collection includes ...
* Eusthenopteron foordi
* Bothriolepis
* Aspidorhynchus
* Araripichthys castilhoi
* Crinoids
* Tyrannosaurus rex
* Ankylosaur
* Dinosaur eggs
* Stegosaurus
* Edmontosaurus annectens
* Triceratops
* Whiteia
* Platecarpus
* Araucarites mirabilis
* Alethopteris
* ...and More
Haven't you always wanted a Stegosaurus in your living room? I think I'll bid on the T. rex. It would look great in my office. Do you think my students might be intimidated?
Wednesday, January 07, 2009
Nobel Laureate: Elias Corey
The Nobel Prize in Chemistry 1990.
"for his development of the theory and methodology of organic synthesis"
Elias James Corey (1928 - ) was awarded the Nobel Prize for his contributions to the synthesis of organic molecules. Here's the Press Release describing his achievements.Prize for masterly development of organic synthesis
The development of the art of organic synthesis during little over a hundred years has afforded efficient methods of manufacturing products such as plastics and other artificial fibres, paints and dyes, biocides and pharmaceutical products, all of which have contributed to the high standards of living and health, and the longevity, enjoyed at least in the Western world.
This year's Nobel Prize in Chemistry has been awarded to Professor Elias J. Corey, USA, for his important contributions to synthetic organic chemistry. He has developed theories and methods that have made it possible to produce a large variety of biologically highly active, complicated natural products, thereby making, among other things, certain pharmaceuticals commercially available. Corey's work has also led to new general methods of producing, synthesising, compounds in simpler ways.
The background to Elias J. Corey's successes lies in the fact that he has in a strictly logical way developed the principles of what is termed retrosynthetic analysis. This involves starting from the planned structure of the molecule one wishes to produce, the target molecule, and analysing what bonds must be broken, thus simplifying the structure step by step. One then finds that certain fragments are already known and their structure and synthesis already described. After working backwards in this way from the complex to the already known, it is possible to start building, synthesising, the molecule. This method has proved very amenable to data processing, which has entailed rapid developments in synthesis planning. Combining this synthesis planning with singular creativity, Corey has developed new methods of synthesis. He has produced some hundred important natural products, for example the active substance in an extract from the ginkgo tree, used in folk medicine in China.
Background information
Organic synthesis, that is, the production of complicated organic compounds using simple and cheap starting material, is one of the prerequisites of our civilisation. It is understandable that contributions in this field have often been rewarded with the Nobel Prize in Chemistry. Thus in 1902, only the second year that Nobel Prizes were awarded, the Chemistry Prize went to Emil Fischer for his work on synthesis within sugar and purine chemistry. In 1905 Adolf von Baeyer received the prize in recognition of contributions to the development of the chemical industry through his work on organic dyestuffs. Otto Wallach received the 1910 Prize for contributions to the development of the chemical industry. The 1912 prize went to Victor Grignard for his development of organic magnesium compounds, also termed Grignard reagents, into important intermediates in organic synthesis. In 1950 Otto Diels and Kurt Alder shared the Nobel Prize for discovering the preparatively very useful diene synthesis. Robert B. Woodward received the 1965 prize for his brilliant contributions to the development of the art of organic synthesis. In 1979 Herbert C. Brown and Georg Wittig were rewarded for developing boron compounds and phosphorus compounds, respectively, into important reagents in organic synthesis.
The synthesis of complicated organic compounds often shows elements of artistic creation, as for example architecture. Many earlier syntheses were performed more or less intuitively, so that their planning was difficult to perceive. Asking a chemist how he came upon precisely the starting materials and reactions that so elegantly led to the desired result would probably be as meaningless as asking Picasso why he painted as he did. The process of synthetic planning has been likened to a game of three-dimensional chess using 40 pieces on each side. But the problem may be even harder than this. Over 35,000 usable methods of synthesis are described in chemical literature, each with its possibilities and its limitations. During the synthesis, moreover, new methods appear which can modify the strategy.
Beginning in the 1960's, Corey coined the term, and developed the concept of, retrosynthetic analysis. Starting from the structure of the molecule he was to produce, the target molecule, he established rules for how it should be dissected into smaller parts, and what strategic bonds should be broken. In this way, less complicated building blocks were obtained, which could later be assembled in the process of synthesis. These building blocks were then analysed in the same way until simple compounds had been reached, whose synthesis was already described in the literature, or which are commercially available. Corey showed that strictly logical retrosynthetic analysis was amenable to computer programming. At present, synthesis planning with the help of computers is developing rapidly.
Through his brilliant analysis of the theory of organic synthesis, Corey has contributed in high degree to his own and other researchers' being able, during the last few decades, to complete total syntheses, hitherto impossible, of complicated, naturally-occurring, biologically active compounds, according to simple logical principles.
Elias J. Corey has himself synthesised about a hundred important natural products, of which only a few will be mentioned here. In 1978 he produced gibberellic acid (1), which belongs to a class of very important plant hormones of complicated structure. Recently, he has also synthesised (+)-ginkgolid (2), which owing to its complicated structure is a formidable challenge to anyone working in synthetic chemistry. (+)-ginkgolid is the active substance in an extract from the ginkgo tree, used as a folk medicine in China. The sales value of this natural product is believed to amount to $500 million annually. It is used in treatment of blood circulation disturbances in the elderly, and in asthma. Corey's most important total syntheses concern the medically very important eicosanoids such as prostaglandins, prostacyclins, thromboxanes and leucotrienes, which occur naturally in extremely small quantities. These frequently very unstable compounds answer for multifarious and vital regulatory functions of significance for reproduction, blood coagulation, normal and pathological processes in the immune system, etc. Their importance is witnessed by the award of the 1982 Nobel Prize in Physiology or Medicine to Sune Bergstrom, Bengt Samuelsson and Sir John Vane for the discovery of prostaglandins and closely related biologically active substances. Corey has with enormous skill carried out structural determination and total syntheses of a large number of compounds of many different types of eicosanoids such as prostaglandins and leucotrienes such as lipoxin A (3). It is thanks to Corey's contributions that many of these important pharmaceuticals are commercially available.To perform the total syntheses successfully, Corey was also obliged to develop some fifty entirely new or considerably improved synthesis reactions or reagents. It is probable that no other chemist has developed such a comprehensive and varied assortment of methods which, often showing the simplicity of genius, have become commonplace in the synthesising laboratory. His systematic use of different types of organometallic reagent has revolutionised recent techniques of synthesis in many respects. He has also in recent years introduced a number of very effective enzyme-like catalysts. These chiral catalysts give only one mirror isomer of the target product, in certain types of synthetically important reaction. The chiral catalysts are simple and easy to recover, and can in some cases be used in their own production.
The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.
[Photo Credit: NIH.]
A Primer on Skepticism
What more could you ask for than A Primer on Skepticism from Mike's Weekly Skeptic Rant? Here are some quotations from that posting to tempt you into reading the whole thing ....
If anyone can show me, and prove to me, that I am wrong in thought or deed, I will gladly change. I seek the truth, which never yet hurt anybody. It is only persistence in self-delusion and ignorance which does harm.
Marcus Aurelius
The invisible and the non-existent look very much alike.
Delos B. McKown
The statistics on sanity are that one out of every four Americans are suffering from some form of mental illness. Think of your three best friends. If they're ok, then it's you.
Rita Mae Brown
Democracy and Lawyers
In Canada we vote by marking a "X" on the ballot and putting it in a box. The person with the most "X's" wins.
If the vote is close, we count the ballots again and declare a winner.
It doesn't work that way in America as we learned in 2000. It took several truckloads of lawyers and many judges to count the ballots in Florida. Ultimately it was the US Supreme Court who decided that George Bush would be President.
Now they're doing it again, only this time it's a Senate race in Minnesota [Funny Business in Minnesota]. The lawyers and the judges will decide who actually won. Meanwhile, politicians in Washington will fight over which candidate they will put into the Senate while the court cases are being decided. Apparently the Senate doesn't have to accept the recount as long as the loser is unhappy.
This must be why they call America "the greatest democracy on Earth." It's because America has so many lawyers.
Probably?
In Britain there are 800 buses with the sign, "There’s probably no God. Now stop worrying and enjoy your life." [Atheists Send a Message, on 800 Buses]Apparently the British atheists wanted to leave out the word "probably" but that wouldn't conform to British advertising guidelines. I wonder if the guidelines apply across the board?
Are there bus and billboard signs that say, "Jesus probably loves you?"Has the British anthem been changed to, "God probably saves the Queen?"
And what about the coins? Will they be changed to read, "Queen, probably by the grace of God" (D.P.G.) in order to conform to advertising standards?
The best remark comes from an American tourist who spotted the sign on a bus. America is the bastion of free speech (according to some Americans) but only if it's speech that doesn't offend.
Spotting one of the buses on display at a news conference in Kensington, passers-by were struck by the unusual message.
Not always positively. "I think it’s dreadful," said Sandra Lafaire, 76, a tourist from Los Angeles, who said she believed in God and still enjoyed her life, thank you very much. "Everyone is entitled to their opinion, but I don’t like it in my face."
Denyse O'Leary and a Lesson on Irony
I was going to blog about this last weekend but I put it off until Monday, then I didn't get around to it yesterday. Now Canadian Cynic has used the exact same quotation that I was planning to highlight. His posting is funnier than anything I could have written. Read it at ... If the irony were any thicker ...
Tuesday, January 06, 2009
Mendel's Garden #27
The 27th edition of Mendel's Garden has just been posted on Another Blasted Weblog [Mendel’s Garden No. 27].Happy Befana from a freezing Rome. Got myself in a bit of a tizz with all this Blog Carnivalia stuff. I thought I was hosting Mendel’s Garden over at the Agricultural Biodiversity Weblog, but it seems I agreed to do it here instead. Not sure why, especially after my recent idleness. P’raps I’ll cross-post. Anyway, on with the show.
Hot Talks - Fact or Friction: The Continuous Tension Between Science and Religion
University of Toronto
Hart House, The Arbor Room
Wednesday, January 21st, 6:30 PM
Join us for an evening of open discussion on the topic of the tension between science and religion. There will be a reception following the event at 8:30pm. Speakers for the evening include:
Professor Jan Sapp
Professor Sapp is a professor of Biology and History at York University. His research is focused on the fields of cell and molecular biology, microbial phylogeny, symbiosis, genetics, evolution and ecology – all from an historical perspective. His historical research on evolutionary biology aims to enlarge the boundaries of that history from focusing solely on Mendelian genetics and the development of neo-Darwinian evolutionary theory.
Professor Yiftach Fehige
Professor Fehige is an assistant professor at St. Michael’s College and the Department of History and Philosophy of Science. His research focuses on Christianity and science, thought experiments, revelation, and research ethics. Professor Fehige is currently working elaborating a pragmatic account of thought experiments in terms of a naturalistic theory of intuition.
Professor Amanda Peet
Professor Peet is a fellow of Trinity College and teaches both within the college and across other disciplines including the Department of physics. She is a member of the Canadian Association of Physicists, the Canadian Institute for Particle Physics and the American Physical Society. She focuses on understanding the fundamental dynamics of all forces and particles seen so far in Nature, especially gravity.
Professor Michael Bourgeois
Professor Bourgoeis is an associate theology professor at Emanuel college. He focuses on constructive, historical, and contextual theologies — including both formative and alternative theological traditions. His particular interests include the relation of theology to the natural sciences, especially on questions of the origin and destiny of the universe and divine action; and expressions of religious ideas in popular culture.
Get a Job in Newfoundland
Memorial University: Departments of Computer Science and Biology
MEMORIAL UNIVERSITY
Tenure-Track Faculty Position in Bioinformatics
The Departments of Computer Science and Biology at Memorial University have each embarked on multi-year renewal programs. Each department currently has more than 20 tenure-stream faculty members, and supports M.Sc., Ph.D. and collaborative graduate programs. For more details, see http://www.mun.ca/biology/Home/ and http://www.mun.ca/computerscience/. Both departments invite applications for a tenure-track position in Bioinformatics, starting no later than September 1, 2009. This will be a joint appointment between the departments. The appointment will be made at the level of Assistant Professor, with the primary appointment in Computer Science, and equal responsibility in both departments, in accordance with the terms of Memorial’s Collective Agreement.
A Ph.D. in Computer Science, Computational Science, Biology, or related fields is required and postdoctoral or equivalent experience is desirable. Applicants should have experience in Bioinformatics, and be keen to do interdisciplinary work between the departments. Applicants should possess a strong research record with outstanding promise for future research, and be able to demonstrate the potential for excellent undergraduate and graduate teaching in Bioinformatics.
Applicants should submit a Curriculum Vitae, statements of research interests, teaching interests and philosophy, and up to three reprints of publications. The application should be accompanied by names of at least three referees of international standing, who are willing to provide letters of recommendation (include details on affiliations, plus phone numbers and email addresses). All material must be received by January 15, 2009; refer to position VPA-COSC-2007-001 in all correspondence, and submit materials to:
Dr. Wolfgang Banzhaf, Head
Department of Computer Science
Memorial University
St. John’s, NL, Canada, A1B 3X5
Email: chair@cs.mun.ca
Memorial University is the largest university in Atlantic Canada. As the Province’s only university, Memorial plays an integral role in the educational and cultural life of the Province of Newfoundland and Labrador. Offering diverse undergraduate and graduate programs to almost 18,000 students, Memorial provides a distinctive and stimulating environment for learning. St. John’s is a very safe and friendly city with great historic charm, a vibrant cultural life, and easy access to a wide range of outdoor activities.
Memorial University is committed to employment equity and encourages applications from qualified women and men, visible minorities, aboriginal people and persons with disabilities. All qualified candidates are encouraged to apply; however, Canadian citizens and permanent residents will be given priority. Partners of candidates for positions are invited to include their resumes for possible matching with other job opportunities.
Get Several Jobs in British Columbia
University of British Columbia: Departments of Botany and Zoology
Tenure track biology instructor positions
Closing date: January 15, 2009 at 5pm
The Departments of Botany and Zoology at the University of British Columbia (Vancouver, Canada) are seeking candidates to fill at least four tenure-track Instructor positions to teach in the Biology Undergraduate Program. At least two positions will be in cellular and molecular biology, with the remaining positions open to biologists in any area. Candidates must hold a PhD in Biology, have a broadly integrative perspective on the biological sciences, and be committed to the improvement of biology undergraduate teaching. Postdoctoral teaching and/or research experience is preferred.
Successful candidates will demonstrate 1) evidence of outstanding teaching, and 2) the ability to contribute to ongoing curriculum and course redevelopment.
Duties of the positions vary, but may include lecturing in introductory and advanced courses, teaching and administration of a large third-year undergraduate laboratory course in the area of specialty, participation in course and curriculum development, and the training and supervision of graduate student teaching assistants. There are also opportunities to work in collaboration with the Carl Wieman Science Education Initiative (www.cwsei.ubc.ca).
Interested candidates should submit a letter of application, a curriculum vitae, a statement of teaching philosophy, an outline of teaching interests, evidence of teaching effectiveness, and the names and contact information for at least three individuals who would be willing to provide letters of references to jobs@zoology.ubc.ca. Candidates are particularly encouraged to highlight previous experience in fostering the education of students from diverse backgrounds.
Review of applications will begin January 15, 2009 and continue until the positions are filled, with appointments anticipated to begin by July 1, 2009.
The University of British Columbia hires on the basis of merit and is committed to employment equity. All qualified persons are encouraged to apply; however, priority will be given to Canadian citizens and permanent residents of Canada.
Get a Job in Ontario
University of Western Ontario: Department of Biology
The University of Western Ontario
Faculty of Science
Department of Biology
Applications are invited for a 3-year Limited Term position in Biology commencing July 1, 2009. As a minimum, the preferred applicant will have a Ph.D. in Biology or a related field, and appropriate training in University level teaching. The successful applicant will be expected to contribute to the department’s commitment to excellence in teaching and provide evidence of his/her ability to teach at the undergraduate level. The successful candidate will be responsible for participating in the teaching of courses in cell and developmental biology as well as general biology.
Applications, including a curriculum vitae and names and addresses of three referees whom we may contact, should be submitted to:
Dr. M. Brock Fenton, Acting Chair
Department of Biology
The University of Western Ontario
London, Ontario
N6A 5B7
Applications for this position will be accepted until January 31, 2009 or until a suitable candidate is found.
Positions are subject to budget approval. Applicants should have fluent written and oral communication skills in English. All qualified candidates are encouraged to apply; however, Canadians and permanent residents will be given priority. The University of Western Ontario is committed to employment equity and welcomes applications from all qualified women and men, including visible minorities, aboriginal people and persons with disabilities.
Mendel's Stem Length Gene (Le)
The seven traits that Gregor Mendel worked with were: seed shape (R/r), cotyledon color (I/i), seed and flower color (A/a), pod shape (V/v), pod color (Gp/gp), flower position (Fa/fa), and stem length (Le/le). The last trait is also known as Tall (T) and short (t).The gene responsible for cotyledon color has been identified. It encodes an enzyme that degrades chlorophyll [Identity of the Product of Mendel's Green Cotyledon Gene (Update)]. The gene giving rise to the wrinkled phenotype (r) encodes the starch branching enzyme [Biochemist Gregor Mendel Studied Starch Synthesis].
The gene responsible for stem length has also been identified and cloned (Lester et al., 1997). It encodes an enzyme called 3β-hydroxylase. This enzyme is responsible for one of the last steps in the synthesis of the gibberallin GA1. See Monday's Molecule #102 for the structure of a similar gibberellin.
Gibberellins are plant growth hormones and GA1 is required to stimulate the grown of the stem in pea plants. The wild-type enzyme synthesizes GA1 from its substrate GA20. The pea gene (Le) is related to a similar gene in other flowering plants. Defects in those genes produce dwarf plants.
Lester et al. (1997) cloned the pea gene and identified a restriction length polymorphism that was associated with a mutant version of the gene (le). In the mutant, a single alanine residue was replaced by a threonine residue and this resulted in a 3β-hydoxylase activity that was 20-fold less than the wild type level. The reduced amount of gibberellin GA1 could account for the smaller plants.
The restriction length polymorphism was used as a genetic marker in crosses between Le/Le plants and le/le plants. It segregated with the le genotype as expected. This experiment establishes that the gene for 3β-hydoxylase is the Le gene that Mendel studied and the phenotype is due to differing levels of the plant hormone gibberellin GA1.
Lester, D.R., Ross, J.J., Davies, P.J., and Reid, J. (1997) Mendel’s Stem Length Gene (Le) Encodes a Gibberellin 3β-Hydroxylase. The Plant Cell 9:1435-1443. [PDF]
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