Getting Into Graduate School

 
Julianne Dalcanton is an astronomy professor at the University of Washington. She works on the evolution of galaxies which is sort of like real evolution, but not quite. She blogs at Cosmic Variance.

Julianne decided to enlighten students about the process of getting into graduate school [The Other Side of Graduate Admissions]. It's a very informative posting and I recommend it to anyone who will be applying to graduate school next year, or who is waiting to hear right now.

I think it's really important to give undergraduates the straight dope about getting into graduate school. It's not about grades, as Julianne says. It's about the complete package. In our department we look at five things and each one is important.

1. Grades in undergraduate courses: If your grades are below a minimum value you will need to have something extraordinary to compensate. If grades are too low then nothing will help you. Just because you have high grades doesn't mean you will be admitted.


2. Reference letters: This is much more important than you think. If you don't have good letters then your chances of being admitted are slim. If the letters say that you are passionately interested in becoming a physician but you'll seriously consider graduate school if you don't get into medical school, then you've got a problem. The letters need to tell us that science is your primary objective in life.


3. Courses: You should have taken the right undergraduate courses to prepare you for graduate school. What this means is that you need to have a number of upper level (4th year) courses in the field you're applying to. In some cases, your undergraduate studies may have been in a related field but you still need to demonstrate that you can handle the most difficult undergraduate courses. That means you're ready for graduate school. This can be a problem in our system here at the University of Toronto because we allow student to graduate with a B.Sc. even if they have only taken a few 400-level courses. Those students may not be acceptable candidates for some graduate schools.


4. Research Experience: We look for students who have already demonstrated that they can work in a laboratory. They will have completed a research project in their final year and they will have worked in research labs during the summer. They will have glowing letters from their research supervisors.


5. Motivation/Enthusiasm: This will come out in your letters of reference and in the choices you have made as an undergraduate. In some cases, we will conduct an interview to determine whether you are a suitable candidate for graduate school. We look for students who really want a career in science or who really want to learn more about science at an advanced level in order to pursue a related career (e.g., teaching). Remember, we're not interested in students who are picking graduate school as their second choice.

It's not as bad as it might seem to get an offer of admission. In our department we get about 135 applications in a typical year and we make offers to about 70 of the applicants for a success rate of 52%. About 30 students end up joining our graduate program because most students have multiple offers.

The best advice I can give undergraduates is to apply to many graduate schools in several different countries. If I recall correctly, I applied to 18 graduate departments and got five acceptances. This is not unusual.

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[Photo Credit: Graduate students in the Department of Biochemistry 2007-2008.]

Monday's Molecule #60

 
I'm a little pressed for time today 'cause my mid-term test is tomorrow. This is a molecule for all you hard-core biochemists out there.

You have to give me the common name of this molecule and explain what it's used for. You'll be pleased to know that I don't need the systematic IUPAC name for this one.

There's an indirect connection between this molecule and Wednesday's Nobel Laureate(s). Your task is to figure out the significance of today's molecule and identify the Nobel Laureate(s) who worked with it.

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). 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.¹ The prize is a free lunch at the Faculty Club.

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 the Nobel Laureate. Note that I'm not going to repeat Nobel Laureates so you might want to check the list of previous Sandwalk postings.

Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

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

UPDATE: The winner is Mike Fraser who correctly guessed that this is the tert-butyloxycarbonyl derivative of valine, also known as Boc-valine. The Boc group acts as a carboxy-terminal blocking group in the chemical synthesis of proteins. The most common peptide synthesizers are the solid phase peptide synthesizers originally developed by Bruce Merrifield. Merrifield received the Nobel Prize in 1984.

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1. Here's an interesting bit of trivia. How many ScienceBlog^TM authors have won the free lunch? How many have guessed the correct answer even though they weren't the first to do so? The answers might surprise you.

Quackery in Academia

 
Last night was lots of fun. A bunch of us went to the Centre for Inquiry for a pre-talk reception with David Colquhoun (pronounced "Ca-hoon"). There were light refreshments and lots of talk about atheism, blogs, science, and of course pseudoscience. About 30 friends of the centre showed up.

David Colquhoun is cool. He even agreed to pose with me for a picture. We look like two old curmudgeons but of course we're really not.

After the reception we all walked up to the campus were we heard Prof. Colquhoun talk about alternative medicine. In case, anyone is confused about alternative medicine, the definition is very simple. We all know about evidence-based medicine. That's the kind that's been shown to work. Everything else is "alternative" medicine—medicine that has not been shown to work.

In some cases we know that the "medicine" is not effective. This is the case with homeopathy, a scam that charges patients $2000/litre for water. In other cases, we don't know whether the treatment is helpful or harmful (e.g., some herbal remedies). What we do know is that the claims are wrong. (Because the claimants don't know whether they work either.)

You can find reviews of the talk at Mike's Weekly Skeptic Rant, The Frame Problem, and The Unexamined Life. The only thing I want to add is that Prof. Colquhoun made a strong case for academic quackery. He showed us a long list of universities that now have Departments of Alternative Medicine. The list included some Canadian schools like McMaster University in nearby Hamilton. Colquhoun pointed out that there are many legitimate academics who have fallen for the anti-science crap that is alternative medicine and he calls upon us to take notice and do something about it.

Fellow blogger Ron Brown (right)(The Frame Problem) and old friend Rob Day (left) were at the reception. Rob is a veteran of talk.origins and the creation/evolution controversy from way back—even before my time. It was fun to meet them and Mike (Mike's Weekly Skeptic Rant) again. I'm sorry I didn't get to meet the student behind The Unexamined Life. I guess he/she wanted to remain anonymous.

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Macromutations and Punctuated Equilibria

Olivia Judson has published a piece in The New York Times where she discusses "Hopeful Monsters" [The Monster is Back, and It’s Hopeful]. The basic idea here is that there can be single mutations that have a large effect on the phenotype of an organism. Think of a four-winged fruit fly, for example, that loses one set of wings.

The first organism to exhibit this new phenotype is a "Hopeful Monster." If it has aselective advantage, then the mutation will be passed down to its progeny and in a short time the species will be transformed in a single jump.

The term "Hopeful Monster" is associated with the views of Richard Goldschmidt. These views were thoroughly discredited in the 1940's at the time when the Modern Synthesis was being forged. The sudden leap in evolution due to macromutations was called "saltation" and we now know that this is not a common mechanism of evolution.

That does not mean that saltations never happen. Stephen Jay Gould wrote an essay in 1980 called Return of the Hopeful Monster in which he gave some examples of sudden changes. One of them is the acquisition of fertility by the axolotl of Lake Xochimilco. This amphibian never transforms into a normal-looking salamander but reproduces as a tadpole with external gills. The idea that mutations affecting development can have such effects is entirely in line with Gould's interest in the subject. His first book was Ontogeny and Phylogeny (1977).

Another example is the lobster Scyllus in which the second pair of antennae have been transformed into uropods in a manner highly reminiscent of homeotic mutations in Drosophila melanogaster (Dawkins, 1996 p. 252). Dawkins (1996 p. 103) also mentions the evolution of snakes, which have hundreds of vertebrae.

The number of vertebrae in different species of snakes varies from about 200 to 350. Since all snakes are cousins of each other, and since vertebrae cannot come in halves or quarters, this must mean that from time to time, a snake is born with at least one more, or one fewer, vertebra than it its parents. These mutations deserve to be called macro-mutations, and they have evidently been incorporated in evolution because all these snakes exist.

I think it's safe to say that the concept of macromutations and saltations is not ruled out in evolution although it is certainly rare. Gould makes the point in his essay that this kind of evolution, while dramatic, is Darwinian.

Jerry Coyne does not like macromutations or hopeful monsters and he has written a strong rebuttal of Olivia Judson's article. Carl Zimmer published it on his blog [Hopeless Monsters--A Guest Post from Dr. Jerry Coyne].

I don't want to get into the details of the Judson article. I think Coyne makes some very valuable points about the specific examples used in the article and I agree that the general tone of the New York Times piece is wrong. Macromutations are not common.

I want to make another point. Coyne says,

The idea of macromutational hopeful monsters, or "saltations," had a prominent resurrection in 1980 when Stephen Jay Gould, as part of his and Niles Eldredge's theory of punctuated equilibrium, proposed that macromutations could explain the "jumps" in the fossil record. After getting a severe drubbing from geneticists, Eldredge and Gould retreated in 1993, claiming that they never suggested the idea of saltations.

The idea that Gould's example of hopeless monsters was connected to punctuated equilibria is not correct. This is the same mistake that Greg Laden makes in his discussion of the topic [Hopeful Monsters and Hopeful Models]. Greg says,

The second reason is that the fossil record seems to have the property whereby many species stay roughly similar for long periods of time, then suddenly, there is lots of evolutionary change. You've heard of this, it's called "punctuated equilibrium." If hopeful monsters ... also called saltational (dancing, leaping) evolution ... occurred generally, we might postulate that these moments of dramatic change, these punctuations, are periods in time where for some reason a lot of hopeful-monstering was going on all at once. That would be cool.

Let's be very clear about what punctuated equilibria are and what they aren't. The pattern of punctuated equilibria show that speciation by splitting (cladogenesis) is associated with morphological change. The actual speciation event is relatively rapid (in geological time) and the end result is a morphologically distinct sibling species where the changes were not evident in the population before the split. The most common explanation is that variants in the larger population were enriched in a small founder population that went on to speciate. It's an example of random genetic drift, or possibly selection, but no new mutations have occurred.

What kind of changes are we talking about here? Very small changes. So small, in fact, that it often takes an expert to recognize them in the fossil record. We're talking about the differences between snails in the same genus, or different species of trilobites, or changes in the surface marking of diatoms. We aren't talking about saltations when we look at punctuated equilibria patterns. People who think that the normal pattern of punctuated equilibria represent big leaps in evolution are confusing two different aspects of evolution.

Daniel Dennet wrote a book in 1995 where he tried very hard to destroy the reputation of Stephen Jay Gould. One of the chapters in his book was "Punctuated Equilibria: A Hopeful Monster". Dennet lays out the case for confusion between saltation and puncturated equilibria as follows; "So it seemed to many biologists that Gould was arguing that punctuated equilibrium was a theory of Goldschmidtian speciation through macromutation" (Dennett 1995 p.288). When Gould (and Eldredge) denied any such thing these biologists "scoffed in disbelief. " After all, they knew what Gould had said. Dennet goes on to say,

But did they? I must admit that I thought they did until Steve Gould insisted to me that I should check all his various publications, and see for myself that his opponents were foisting a caricature on him.

Dennett checked, and found that Gould was right. To his credit, he reports that this claim about saltation being part of punctuated equilibria is wrong. Dennett concludes on p. 289-290.

"Punctuated equilibrium is not a theory of macromutation" (Gould 1982, p.88). Confusion on this score still abounds, however, and Gould has had to keep issuing his disclaimers [as has Eldredge, LAM]: "Our theory entails no new or violent mechanism, but only represents the proper scaling of ordinary events into the vastness of geological time" (Gould 1992b p.12).

So this was the false-alarm revolution that was largely if not entirely in the eyes of the beholders.

I'm quoting Dennett here instead of quoting Gould and Eldredge¹ directly because Dennett is one of Gould's fiercest opponents. If Gould's worst enemy can see the truth then why is this myth still being propagated?

I'll close with one of my favorite quotations from Eldgredge (1995 p.99).

Nonetheless, we were accused of being saltationists. Steve Gould wrote two consecutive essays in Natural History in 1977. Among other things, Steve speculated that the recent (sic) discovery of regulatory genes—genes that turn other genes on and off—raised the possibility that mutations in the regulatory apparatus might occasionally have the sort of effect Goldschmidt had in mind with his notion of 'macromutations.' These macromutations had the large-scale effects of the sort he posited for his 'hopeful monsters.' Nowhere in either article did Steve mention punctuated equilibria.

But it was enough, it seems, that he, champion of a new model positing bursts of relatively rapid change, would, a few years later, discuss Goldschmidt in favorable terms. Mayr was one of the first to level the charge that punctuated equilibria was nothing but old saltationism in new guise. Our debt to Mayr's concept of species and speciation, so central to the idea of punctuated equilibria, eventually induced him to do an about face. Mayr came to prefer taking credit for punctuated equilibria rather than seeing it linked to his old nemesis Goldschmidt.

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Dawkins, R. (1996) Climbing Mt. Improbable W.W. Norton & Company, New York.

Dennett, D. (1995) Darwin's Dangerous Idea. Simon & Schuster, New York.

Eldredge, N. (1995) Reinventing Darwin. John Wiley & SOns, Inc., New York

Was Charles Darwin an Atheist?

 
That's the question asked by Irwin Tessman in the January/February 2008 issue of Skeptical Inquirer. Tessman is a Professor Emeritus in the Biology Department at Purdue University. You can see a podcast of his lecture, "A Darwinian View of a Hostile Atheist" at [The Society of Non-Theists at Purdue University].

Tessman is interested in comparing the views of the so-called "militant atheist," Richard Dawkins with the religious views of Charles Darwin. He concludes that their views are not very different. The biggest difference between the two men is that Darwin choose to hide his lack of religion from the public in deference to his wife Emma, who was a devout Anglican.

With the publication of the compete text of Darwin's autobiography in 1958, we now have much greater insight into Darwin's thoughts about religion. Here's how Tessman puts it,

Where does Darwin stand on the matter of a personal God? "The old argument of design in nature, as given by Paley, which seemed so conclusive, fails now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by a man" (Darwin 1958, p.87). Darwin seems to reject the idea of a personal God and, therefore, theism too. His religious views are difficult to pin down (Browne, 2006, p.46), but something close to deism would seem to fit.

Theism is a belief in a personal God, one who responds to prayers and interferes in daily events; atheism is the opposite of theism. Deism is the belief in a God who set the universe in motion whit all the physical laws and both sacred and learned commentaries, but was absent after that. In practice, deism is much like atheism.

There seems to be general agreement that Darwin did not subscribe to the tenets of any organized religion. There is debate over whether he believed in supernatural beings. His Grandfather, father, and brother were non-believers so it's reasonable to suppose that Darwin was too.

He may have been comfortable with agnostic, a term that was invented by his friend Thomas Huxley. This would have been far more acceptable to Emma than atheist. I suspect that if Darwin were alive today he would be an atheist ... unless Emma were also alive.

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Browne, Janet (2006) Darwin's Origin of Species: A biography. Douglas & McIntyre Vancouver/Toronto.

Darwin, Charles (1958) The Autobiography of Charles Darwin, Nora Barlow ed. W.W. Norton and Company, New York.

Junk DNA Poll

 
Just a reminder to vote in the junk DNA poll seen in the left sidebar. Check out A Junk DNA Quiz and comments for more information.

Take the junk DNA quiz in the left sidebar to let me know what you think of your genome. How much of it could be removed without affecting our species in any significant way in terms of viability and reproduction? Or even in terms of significant ability to evolve in the future? In other words, how much is junk?

It's important to register your choice now. You'll get another chance to vote on a similar topic in February and it will be fun to compare the two polls.

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[Image Credit: The junk DNA icon is from the creationist website Evolution News & Views.]

Beware of Terrorists in Canada

 
Friday's Urban Legend: RIDICULOUS

Australia is a small country in the middle of the Pacific Ocean (see map). It is best known for its wild dogs that eat babies, race riots on public beaches, and for 1000 mile long rabbit-proof fences that don't work.

Judging by the buzz on radio stations in Canada, Australia is now becoming known for something else [Crikey! Be careful about Canada…]. It's getting a reputation for extreme stupidity.

The Australian government has a website to inform travelers about foreign countries. Here's what it says about Canada [Travel Advice for Canada].

We advise you to exercise caution and monitor developments that might affect your safety in Canada because of the risk of terrorist attack.

Pay close attention to your personal security and monitor the media for information about possible new safety or security risks.

We advise you to exercise caution and monitor developments that might affect your safety in Canada because of the risk of terrorist attack. Pay close attention to your personal security and monitor the media for information about possible new safety or security risks.

The rating for Canada is "Exercise Caution." This is the same rating that's given to Vietnam, Serbia, Malaysia, United States, United Kingdom, Belgium, Albania, France, and the Netherlands.

Countries receiving the safest rating ("Be Alert to Your own Safety") include: China, Ireland, Japan, New Zealand, Roumania, Hungary, Macau, Norway, and South Korea (Republic of Korea).

Apparently there are some Australians who might want to visit Canada in spite of the terrorists. Not to worry. The Australian government has some additional warnings that will discourage such a foolish trip. The weather in Canada is dangerous ...

Heavy snowfalls and ice in the winter can make driving dangerous. The wind-chill factor can also create dangerously cold outdoor conditions. Transport Canada provides detailed information on road conditions across Canada. You can also get tips for winter driving from the Canadian Automobile Association.

OK, so there's some truth to that statement. If tourists want to visit some parts of Canada in the winter (for skiing) then they should know how to cope with snow.

But the Australian government doesn't stop there. They need to inform their citizens about other common dangers in Canada.

The province of British Columbia in western Canada is in an active earthquake zone.

Alberta and British Columbia are also subject to avalanches. Information on avalanches is available from the Canadian Avalanche Association.

Tornadoes can occur in some areas of Canada between May and September. For more information on tornadoes see Environment Canada's website and the National Hurricane Centre. In the event of a Tornado you should monitor local and international weather on local television and radio.

Bush and forest fires can occur any time in Canada. You should consult local news reports and authorities before visiting forested areas and follow the advice of local authorities.

Scary stuff. I think I'll build a tornado shelter and prepare for bush fires in my neighbourhood. I wonder if there are any other countries where the threat of bush fires is severe? I seem to remember something about suburban houses being destroyed by fires in other countries but never in Canada, to the best of my knowledge.

Australians, you should be ashamed about the terrorist warning for Canada. On the other hand, the weather thingy isn't unusual. All countries have silly advisories about weather on their websites. Here's the one from Canada about Australia [Travel Advice: Australia].

Australia is located in a seismic zone. Canadians should know the address and telephone number of the High Commission of Canada in Canberra in the event of an emergency.

Severe flooding is affecting parts of the country, particularly New South Wales. Rising floodwaters may have an impact on transportation and other services. Travelers should be aware of the increased threat of water-borne disease and take appropriate precautions. Canadians should follow the advice of local authorities and maintain flexible travel plans.

The cyclone season extends from November to April. Cyclones may occur along the coastal areas of Queensland, Northern Territory, and Western Australia. Travellers should keep informed of regional weather forecasts and plan accordingly.

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Creationist Counties in Florida

 
The National Center for Science Education has been following the situation in Florida where the state board of education is revising the science standards. It looks like they will not only keep evolution in the curriculum but specifically mention the dreaded e-word and state that it is a "big idea" around which state standards in biology are organized.

That's the good news. The bad news is that nine country school boards have passed resolutions calling on the state board of eduction "to revise the new Sunshine State Standards for Science such that evolution is not presented as fact, but as one of several theories."

Here are some of the explanations for this bizarre behavior as reported in the St. Petersburg Times.

Dixie County school superintendent Dennis Bennett explained, "We just wanted to get it on the record that we're a Judeo-Christian community and we believe in academic freedom," and Ken Hall, a school board member in Madison County, commented, "We're not asking that evolution not be taught, just that it be taught as a theory, one of several. I'm a Christian. And I believe I was created by God, and that I didn't come from an amoeba or a monkey."

In case anyone wants to avoid those nine counties here they are: Baker, Clay, Hamilton, Holmes, Jackson, Madison, St. Johns, Taylor, and Washington. I've located them on a map for you.

If you live in one of those counties you have my deepest sympathy. Be sure to vote in the next school board elections. In case you're interested, the Canadian counties are all in the south on the west coat below St. Petersburg.

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Tangled Bank #97

 
The latest issue of Tangled Bank is #97. It's hosted at The Inoculated Mind [Tangled Bank 97: The Frozen Bank].

It is interesting to contemplate a frozen bank, clothed with ice of many kinds, with birds not singing on the bushes, with various insects nowhere to be seen, and with worms crawling under the earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have… aw hell, it’s fricken freezing and there’s nothing but ice, snow, and cold air on the banks of Madison, Wisconsin.

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

Science in an Age of Endarkenment

 
The University of Toronto Secular Alliance is one of the hosts of tomorrow's talk by David Colquhoun [University of Toronto Secular Alliance].

If you live anywhere near Toronto you should come and hear him speak and support the various groups that are sponsoring the event (University of Toronto Secular Alliance, Centre for Inquiry, Skeptics Canada)

U of T Secular Alliance Presents Professor David Colquhoun, FRS - Friday, January 25th, 2008

SCIENCE IN AN AGE OF ENDARKENMENT - SOME EXAMPLES FROM SCIENTIFIC FRAUD, QUACKERY, RELIGION AND UNIVERSITY POLITICS

Should complementary and alternative medicine be considered alongside evidence-based medicine? What role does it play in today's society? Should unscientific medicine be taught in universities? David Colquhoun tackles these issues and more.

Eminent UK scientist and noted skeptic David Colquhoun, FRS is a professor of Pharmacology at University College London, fellow of the Royal Society, and blogger (Improbable Science). He was recently the centre of controversy surrounding his popular blog, dedicated to exposing alternative medicine and pseudoscientific claims, after criticizing a herbal medicine practitioner about her questionable practices. This herbalist threatened legal action and Prof. Colquhoun was forced to remove his site from the UCL server. After much backlash from the scientific community, his website was revived. A leader in the skeptical community, Prof. Colquhoun will be speaking on issues surrounding alternative medicine, academia, and the intersection between the two.

Dr. Colquhoun's website: http://www.dcscience.net

Friday, January 25th 2008, 7pm-9pm
McLeod Auditorium, Medical Sciences Building, University of Toronto (1 King's College Circle, Toronto)
$7, $4 for students
Tickets available at the door.

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Nobel Laureate: Tom Cech

 

The Nobel Prize in Chemistry 1989.

"for their discovery of catalytic properties of RNA"



In 1989, Thomas R. Cech (1947 - ) was awarded the Nobel Prize in Chemistry for discovering that the ribosomal RNA precursor from Tetrahymena catalyzed its own self-splicing reaction. [Ribosomal RNA Genes in Eukaryotes]. He shared the prize with Sydney Altman who worked RNase P.

The presentation speech was delivered by Professor Bertil Andersson of the Royal Swedish Academy of Sciences.
THEME:

Nobel Laureates

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen,

The cells making up such living organisms as bacteria, plants, animals and human beings can be looked upon as chemical miracles. Simultaneously occurring in each and every one of these units of life, invisible to the naked eye, are thousands of different chemical reactions, necessary to the maintenance of biological processes. Among the large number of components responsible for cell functions, two groups of molecules are outstandingly important. They are the nucleic acids - carriers of genetic information - and the proteins, which catalyze the metabolism of cells through their ability to act as enzymes.

Genetic information is programmed like a chemical code in deoxyribonucleic acid, better known by its abbreviated name of DNA. The cell, however, cannot decipher the genetic code of the DNA molecule directly. Only when the code has been transferred, with the aid of enzymes, to another type of nucleic acid, ribonucleic acid or RNA, can it be interpreted by the cell and used as a template for producing protein. Genetic information, in other words, flows from the genetic code of DNA to RNA and finally to the proteins, which in turn build up cells and organisms having various functions. This is the molecular reason for a frog looking different from a chaffinch and a hare being able to run faster than a hedgehog.


Life would be impossible without enzymes, the task of which is to catalyze the diversity of chemical reactions which take place in biological cells. What is a catalyst and what makes catalysis such a pivotal concept in chemistry? The actual concept is not new. It was minted as early as 1835 by the famous Swedish scientist Jöns Jacob Berzelius, who described a catalyst as a molecule capable of putting life into dormant chemical reactions. Berzelius had observed that chemical processes, in addition to the reagents, often needed an auxiliary substance - a catalyst - to occur. Let us consider ordinary water, which consists of oxygen and hydrogen. These two substances do not react very easily with one another. Instead, small quantities of the metal platinum are needed to accelerate or catalyze the formation of water. Today, perhaps, the term catalyst is most often heard in connection with purification of vehicle exhausts, a process in which the metals platinum and rhodium catalyze the degradation of the contaminant nitrous oxides.

As I said earlier, living cells also require catalysis. A certain enzyme, for example, is needed to catalyze the breakdown of starch into glucose and then other enzymes are needed to burn the glucose and supply the cell with necessary energy. In green plants, enzymes are needed which can convert atmospheric carbon dioxide into complicated carbon compounds such as starch and cellulose.

As recently as the early 1980s, the generally accepted view among scientists was that enzymes were proteins. The idea of proteins having a monopole of biocatalytic capacity has been deeply rooted, and created a fundamental dogma of biochemistry. This is the very basic perspective in which we have to regard the discovery today being rewarded with the Nobel Prize for Chemistry. When Sidney Altman showed that the enzyme denoted RNaseP only needed RNA in order to function, and when Thomas Cech discovered self-catalytic splicing of a nucleic acid fragment from an immature RNA molecule, this dogma was well and truly holed below the waterline. They had shown that RNA can have catalytic capacity and can function as an enzyme. The discovery of catalytic RNA came as a great surprise and was indeed met with a certain amount of scepticism. Who could ever have suspected that scientists, as recently as in our own decade, were missing such a fundamental component in their understanding of the molecular prerequisites of life? Altman's and Cech's discoveries not only mean that the introductory chapters of our chemistry and biology textbooks will have to be rewritten, they also herald a new way of thinking and are a call to new biochemical research.

The discovery of catalytic properties in RNA also gives us a new insight into the way in which biological processes once began on this earth, billions of years ago. Researchers have wondered which were the first biological molecules. How could life begin if the DNA molecules of the genetic code can only be reproduced and deciphered with the aid of protein enzymes, and proteins can only be produced by means of genetic information from DNA? Which came first, the chicken or the egg? Altman and Cech have now found the missing link. Probably it was the RNA molecule that came first. This molecule has the properties needed by an original biomolecule, because it is capable of being both genetic code and enzyme at one and the same time.

Professor Altman, Professor Cech, you have made the unexpected discovery that RNA is not only a molecule of heredity in living cells, but also can serve as a biocatalyst. This finding, which went against the most basic dogma in biochemistry, was initially met with scepticism by the scientific community. However, your personal determination and experimental skills have overcome all resistance, and today your discovery of catalytic RNA opens up new and exciting possibilities for future basic and applied chemical research.

In recognition of your important contributions to chemistry, the Royal Swedish Academy of Sciences has decided to confer upon you this year's Nobel Prize for Chemistry. It is a privilege and pleasure for me to convey to you the warmest congratulations of the Academy and to ask you to receive your prizes from the hands of His Majesty the King.

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[Image Credit: Structure of the self-slicing ribosomal RNA precursor from Tom Cech Lab]

Ribosomal RNA Genes in Eukaryotes

 
The "genes" for ribosomal RNAs in eukaryotic genomes are found in separate clusters. One cluster consists of hundreds of copies of the 5S gene. These genes are transcribed by RNA polymerase III [Eukaryotic RNA Polymerases].

The other ribosomal RNA genes are found in an "operon"-like structure that's similar to the bacerial operons [Ribosomal RNA Genes in Bacteria]. Unlike bacterial transcription units, these ones are found in large tandem arrays on eukaryotic chromosomes. There can be hundreds of individual transcription units in a cluster and there can be several clusters. In humans, for example there are five clusters on five different chromosomes and each one has between 50 and 100 transcription units. The large eukaryotic ribosomal RNA genes are transcribed by RNA polymerase I.



There is considerable variation in the size of a transcription unit from one species to the next. This variation occurs in the length of the external transcribed sequences (ETS) that are found at either end of a cluster (open rectangles). There can also be substantial variation in the length of the internal transcribed sequences (ITS)—the ones that will be removed when the precursor is processed. The distance between transcription units can also vary. This region is referred to as the non-transcribed spacer (NTS).

Note that the order of the small (18S) and large (28S) RNAs is the same as in bacteria. Note also that the 5.8S eukaryotic ribosomal RNA is found at the 5′ end of the large RNA. The homologous part of the bacterial RNA is found at the end of the 23S RNA. What's happened in eukaryotes is that a new cleavage site has evolved so that the largest RNA is now expressed in two pieces.

RNA precursors derived from typical transcription units like the one shown above are processed by cutting the RNA at various points to release the mature 18S, 5.8S, and 28S RNAs. The processing steps are well understood. In bacteria, some of the cleavages occur before transcription is terminated but eukaryotic nuclei usually accumulate long precursors that are only processed when transcription terminates. In those species that have nucleoli the nucleolus represents the location of ribosomal RNA genes that are being transcribed.

The electron micrograph shows clusters of ribosomal RNA transcription units being transcribed a high rates in nucleoli. The RNA molecules are splayed out from the DNA like the branches of a Christmas tree. RNAs near the beginning of the gene are short and as transcription proceeds the RNAs get longer and longer until the complete precursor is released at the termination site.

In some species the 28S ribosomal RNA gene contains an intron near the 3′ end. In this case the intron sequence is removed and the two ends of the 28S RNA are joined together to produce the mature ribosomal RNA. The remarkable thing about this splicing event is that it is often autocatalytic. In other words, the precursor RNA folds up all by itself, cuts itself in two places, and rejoins its own ends. No proteins or other molecules are needed for this reaction to occur.



The classic example is the ribosomal RNA transcription unit from the protozoan Tetrahymena thermophilus shown above [Monday's Molecule #59]. The self splicing reaction was characterized by Tom Cech who received the Nobel Prize in 1989 along with Sydney Altman for discovering catalytic RNAs. This particular type of intron is called a group I intron and the mechanism of self-splicing requires a guanosine cofactor. Remarkably, the excised fragment of RNA also has catalytic activity; it can act as an endonuclease cleaving other RNAs.

RNA genes in most species do not have introns.

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Ribosomal RNA Genes in Bacteria

 
Ribosomal RNA is the major component of ribosomes [The Compositon of Ribosomes]. This RNA, by itself, is capable of catalyzing the amino acid joining reaction (peptidyl transferase) during translation but inside the cell the RNA is closely associated with many proteins to form the complete ribosome.



In bacteria (prokaryotes) there are three different ribosomal RNAs called 5S, 16S, and 23S. Eukaryotes have homologous RNAs called 5S, 28S, and 18S ribosomal RNAs. In addition, they have a 5.8S RNA that is homologous to one end of the prokaryotic 23S RNA. (The sizes of eukaryotic RNAs vary considerably and different species might have slightly different names.)

The 5S, 16S and 23S ribosomal RNAs are produced from a single operon in bacteria. An operon is a group of genes that are cotranscribed; that is, they form part of a single transcriptional unit. In this case the parts of the genome that specify each of the ribosomal RNAs are contiguous and the "genes" are transcribed into a single precursor RNA beginning at the promoter (P) and ending at the terminator (t). This large precursor RNA is then cleaved to make the smaller mature ribosomal RNAs. This is one of the problem cases when one is attempting to define a gene [What Is a Gene?].



Bacterial cells need a lot of ribosomal RNA so they usually have multiple copies of the ribosomal RNA operon (rrn). In E. coli for example, there are usually seven different rrn operons called rrnA, rrnB, etc.

In bacterial genomes the operons are located in different parts of the genome—they are unlinked. (By contrast, in eukaryotic genomes they cluster in large tandem arrays.) The example shown above is the rrnC operon in E. coli. The rectangular boxes represent regions that are transcribed into the large RNA precursor. Open boxes are pieces at the ends that are removed by direct cleavage. The purple boxes are internal regions that removed by making two cuts, one on either side.

In this operon there are four transfer RNA genes (tRNA) embedded in the transcriptional unit. These are processed as described in Transfer RNA: Synthesis. The parts of the transcription unit located between the "genes" (i.e., the purple regions) are called "transcribed spacers." When processing is complete the mature 5S, 16S and 23S RNAs are ready to be incorporated into ribosome and the four tRNAs are ready to act in translation.

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Skeptical About Adaptationism

 
Over on Evolution News & Views (a creationist blog) Robert Crowther writes.

Every so often the Darwinists get all riled up about the Scientific Dissent From Darwin list, which lists over 700 PhD scientists who publicly affirm: “We are skeptical of the claims for the ability of random mutations and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian Theory should be encouraged.” As statements go, it’s simple and straightforward. And that perhaps is what concerns Darwinists. People instantly understand what it is saying, what the scientists are courageously endorsing, and why it matters. [Doubts About Darwin Stem from Science Not Religion]

Hmmm ... let's test that claim. I agree with the two statements that are quoted. Does everyone understand why?

I do not agree with the title of the list Scientific Dissent from Darwinism because I don't dissent from Darwinism. In fact, I think that natural selection is a proven mechanisms of evolution and it is immensely important in the evolution of life on Earth. What I don't agree with is the idea that random mutation and natural selection alone can account for the complexity of life.

I suppose that's what Robert Crowther means when he says, "People instantly understand what it [the statements] is saying, what the scientists are courageously endorsing, and why it matters." Right?

Of course not. All intelligent people understand that the purpose of the list is to reveal the ignorance of Intelligent Design Creationists who think that questioning one aspect of evolution is equivalent to belief in God. Some of those 700 people may have been tricked into signing the "Dissent" because they did not instantly understand what it meant to a creationist.

I'm glad we've cleared that up.

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100% Un-deluded

 
One of my readers has designed a T-shirt for atheists. You can buy one at Zazzle.

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