Teach the Controversy

 
The latest issue of the McGill Journal of Education is devoted to the Evolution/Creationism debate. There are several interesting articles but one that caught Greg Laden's eye was by Eugenie Scott on teaching the controversy [WHAT’S WRONG WITH THE “TEACH THE CONTROVERSY” SLOGAN?]. Greg agrees with her that we should not address the evoluton/creationism controversy in shools [How To Get Away With Teaching The Controversy].

I'm on the opposite side on this one. In Canadian schools I think we should teach the controversy—even in biology class. Here's my reasoning. You'd have to be some kind of idiot not to recognize that there's a conflict between evolution and many religious beliefs. Pretending that it's not there is no way to educate students.

If we really want to educate then we should address this issue head on and explain why the religious point of view contradicts science. One clear example is the age of the Earth. Students need to hear about the scientific evidence and why it isn't compatible with a 6000 year old Earth as described in the Bible. Another obvious example is the evidence for evolution and how it conflicts with most religious myths.

My children heard about this in their public high school and the biology teacher even organized debates between the two sides (creationists vs. evolutionists). He made an effort to keep everyone honest and avoid insults but there was no attempt to disguise the fact that a controversy existed.

Other Ontario schools did this too. On three occasions I was invited to other high schools to explain the evolution/creationism controversy. One one of these occasions I debated a Christian fundamentalist creationist in a Roman Catholic school. What's wrong with that?

There's nothing wrong with that. Teaching the controversy is a good idea. It's good when teachers explain what's wrong with astrology and it's good when they explain what's wrong with Young Earth Creationism.

The reason this won't work in the USA has nothing to do with whether we should address public controversies that involve science. I assume that students will be allowed to debate the pros and cons of global warming and they might even get lessons on what's wrong with holocaust deniers. The reason the evolution/creation controversy is banned is because religion is involved and that's a taboo subject in American schools.

How does Eugenie Scott deal with the position I advocate?

An argument that has been persuasive in both the United States and Canada is the claim that having students decide between ID and evolution, or to have students “critically analyze” evolution, is pedagogically sound critical thinking instruction from which students would benefit. Of course, all teachers want students to be critical thinkers! It might be a useful critical thinking exercise for students to debate actual scientific disputes about patterns and processes of evolution, as long as they have a solid grounding in the basic science required. (For further discussion, see Alters & Alters, 2001; Scott & Branch, 2003; Dawkins & Coyne, 2005.) It would, however, not be a good critical thinking exercise to teach students that scientists are debating whether evolution takes place: on the contrary, it would be gross mis-education to instruct students that the validity of one of the strongest scientific theories is being questioned. It would, therefore, be gross mis-education to teach students the inaccurate science presented in Icons of Evolution, and other Intelligent Design literature.

I think she's making an incorrect assumption here. We can "teach the controversy" by dealing directly with the conflict between religion and science and by explaining that scientists do not question evolution. The whole idea behind teaching, as far as I'm concerned, is to teach the truth and not some made-up stories that the Intelligent Design Creationists are pushing. Scott is assuming that in order to teach the controversy we have to present the IDC side as if it were true. That's nonsense. It makes about as much sense as assuming that you have to pretend that astrology is true in order to demonstrate that it isn't. (Everyone agrees that there's a controversy over the validity of horoscopes, right? Should we teach about it in school?)

I just finished teaching a section on the evolution/creation controversy to second year students. We used Icons of Evolution as our textbook and the students each picked a single chapter and wrote an essay explaining why Wells is wrong. You could easily do the same thing in high school and that would be a real contribution to education. As it is, by ignoring those arguments you allow them to stand unchallenged.

Now, we all know that there's an additional problem that isn't being mentioned. It's the quality of teachers. I think many people want to avoid teaching the controversy in American schools because it would give teachers the opportunity to promote creationism. That's the point that Greg Laden mentions on his blog. If that's the problem then we should fix it. If teachers don't understand the material they're supposed to be teaching then educate them, or fire them. (I know, it's not that easy.)

We want our students to be critical thinkers and this issue is a perfect one for them to put that critical thinking into practice. If you dare not go there because; (a) you don't want religion in the school, or (b) you don't trust the teachers, then, please, state those reasons up front and don't pussy foot around the issue by pretending that there's something else involved.

Here's the essay that should have been written.

We can't educate our students about the conflicts between science and religion because that would require teachers to bring up religion in school. It is forbidden to discuss religion in public schools in America and that's why we can't allow teaching the controversy. This is too bad because otherwise it might be a good vehicle for teaching critical thinking. It's better to allow the local churches to undermine everything we teach in school because the alternative violates the constitution. (Of course, this argument might become moot with one more appointment to the supreme court.)

Furthermore, even if we could mention religion in school, it wouldn't be a good idea to debate evolution vs. creationism because there are too many "science" teachers who reject evolution in favor of Biblical creationism. We prefer the status quo where neither evolution nor creationism is being taught. Teaching the controversy under these circumstances just opens the door to teaching creationism instead of evolution.

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Another Dr. Moran!!!

 
From UNC PHYSICS AND ASTRONOMY WEEKLY CALENDAR:

Monday, October 29
12:20 p.,m. Room 258, Phillips Hall (UNC-CH)

Ph.D. Defense

Jane Moran (Physics and Astronomy, UNC-CH)


Investigating the Circumstellar Environments of Young Stars with the PROMPT Polarimeter

Abstract: We have designed and built a prototype imaging polarimeter for use on the PROMPT robotic telescopes located at Cerro Tololo International Observatory. The polarimeter uses a Fresnel rhomb and wollaston prism to image two orthogonal polarization states onto a single CCD chip, with an image field of view of 10 x 4.5 arcmin. Using the polarimeter, we have investigated the circumstellar regions of 11 Herbig Ae/Be stars, and done extensive follow-up observations on 3 stars of interest: KK Oph, a well-studied star with previously limited polarimetric data; NX Pup, a star known to vary photometrically but with previously unknown polarimetric variability; and SS73 44, a star with very limited previous photometric data and no prior polarimetric data. We have found polarimetric and photometric variations in KK Oph and NX Pup that are consistent with models of dust obscuration. Both KK Oph and NX Pup show an increase in polarization accompanied by a decrease in visual magnitude and a reddening. However, neither star shows the "blueing" at deep photometric minima and maximum polarization characteristic of the UXor classification of stars. We have demonstrated that SS73 44 has an intrinsic polarization component, but does not display the photometric and polarimetric variations expected from a young star with an evolving circumstellar environment, indicating that this object either has a disk seen in an orientation that has little inclination, or one with no appreciable puffed-up inner rim.

My daughter just called. She's now Dr. Moran!

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[Photo Credit: (top) PROMPT telescopes in Chile today. (bottom) Jane at the beginning of construction.]

Why Do Leaves Turn Red in the Fall?

 
In the Northern Hemisphere this is the time of year when the leaves of deciduous plants turn color and fall off. Why do they change color and why are some leaves so red?

There are two different answers to the question. The first one deals with the trigger for leaf senescence. It's the shortening of daylight hours that starts the process and from the time it is triggered by photoperiod the process proceeds in a manner that is not influenced very much by the environment, including whether the weather is cold or hot (Keskitalo et al. 2005). What this means is that the leaves all fall off at about the same time each year. The intensity of leaf color, on the other hand, is affected by the weather. Warm weather tends to produce a less spectacular display of fall colors.

The second answer addresses the reason for leaf color. It has to do with senescence. In the autumn the leaves of deciduous trees fall off the tree to prepare for winter. As the leaves die, the tree attempts to salvage as much nitrogen and carbohydrate as it can. While the photosynthetic apparatus is winding down it is more likely to produce free radicals and oxidative damage [Superoxide Dismutase Is a Really Fast Enzyme]. To prevent excess damage the leaves produce pigment molecules that block some of the light and reduce levels of photosynthesis. Red pigments, such as anthocyanins are especially effective (Feild et al. 2002).

Anthocyanins are only produced in the autumn. They are not found in leaves during the summer and their main role is to block sunlight from the photosynthesis machinery during leaf senescence. Other leaf colors are due to the unmasking of accessory pigments as chlorophyll breaks down. The regular pigments such as carotenoids (orange) [Vitamin A (retinol)] and xanthophylls (yellow) become more prominent because their breakdown is delayed [Why Leaves Change Color].

The intensity of the color is influenced by the composition of the soil. When the soil is deficient in nitrogen the tree needs to recover more nitrogen from the leaves before they fall off. This leads to increased production of anthocyanins in order to prolong the period when the leaf cells can remain metabolically active to export nitrogen and carbohydrates [Why do autumn leaves bother to turn red?].

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Feild, T.S., Lee, D.W. and Holbrook, N.M. (2002) Why leaves turn red in autumn. The role of anthocyanins in senescing leaves of red-osier dogwood. Plant Physiol. 127:566-574. [PubMed]

Keskitalo, J., Bergquist, G., Gardeström, P. and Jansson, S. (2005) A cellular timetable of autumn senescence. Plant Physiol. 139:1635-48. [PubMed]

Monday's Molecule #49

 
Today's molecule is very simple. You don't get any credit for just naming the molecule.

There's an indirect connection between this molecule and Wednesday's Nobel Laureate(s). Let's see who knows and loves biochemistry!

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. The prize is a free lunch at the Faculty Club.

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(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. This way I may select multiple winners if several people get it right. This one is easy. Get your response in quickly.

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

UPDATE: The molecule is polyphosphate. We have a winner!

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Where Was I?

 

Today I was not too far from this place. Unfortunately I didn't have time to stop and see the drawings. Where was I?

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Where Was I?

 
Today I was near this place. Where was I?

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Help Build The Beagle

 
A replica of HMS Beagle is being built as part of the 2009 celebrations surrounding the 150th anniversary of the publishing of On Origins of Species, and the 200th anniversary of Darwin's birth. The ship will sail around the world stopping at all the places Darwin stopped at on his famous voyage.

You can help build the Beagle. Check out The Beagle Project Blog.

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Biochemist Arthur Kornberg (1918 - 2007)

 
Arthur Kornberg died yesterday of respiratory failure. He was 89 [Arthur Kornberg, Biochemist, Dies at 89.

Kornberg won the Nobel Prize in 1959 for his discovery of DNA polymerase (now known as DNA polymerase I). His son, Roger Kornberg was awarded the Nobel Prize last year for working out the structure of RNA polymerase [Nobel Laureate: Roger Kornberg]. Another son, Tom, was co-discoverer of the DNA replication enzymes DNA polymnerase II, and DNA polymerase III. Tom and I were graduate students together in the early 1970's and the lab I was in (B. Alberts) worked on the same problems as Arthur Kornberg's lab at Stanford. Bruce Alberts and Arthur Kornberg received the Gairdner Award here in Toronto in 1995.

Kornberg was proud to be known as a biochemist and he always defended the principles of biochemistry. His autobiography For the Love of Enzymes extolled the virtues of purifying and characterizing enzymes as a way to understanding how life works at the molecular level.

One of his most famous defenses of biochemistry is Kornberg (2004).

Fashions prevail in science as in all human affairs. In recent years, biochemistry has become less fashionable, but there is no doubt that the discipline is important for the full understanding of biology.

Biochemists also know him for creating the Ten Commandments of Enzymology. Unlike the author of the original ten commandments, Kornberg was able to modify and amend his commandments as new developments came along (Kornberg, 2003).

Thou shalt…

• I. Rely on enzymology to resolve and reconstitute biologic events
• II. Trust the universality of biochemistry and the power of microbiology
• III. Not believe something just because you can explain it
• IV. Not waste clean thinking on dirty enzymes
• V. Not waste clean enzymes on dirty substrates
• VI. Use genetics and genomics
• VII. Be aware that cells are molecularly crowded
• VIII. Depend on viruses to open windows
• IX. Remain mindful of the power of radioactive tracers
• X. Employ enzymes as unique reagents

My condolences to the family.

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[Photo Credit: University of Rochester Medical Center]

Kornberg, A. (2004) Biochemistry matters. Nature Structural & Molecular Biology 11:493. [PubMed]

Kornberg, A. (2003) Ten commandments of enzymology, amended. Trends Biochem Sci. 28:515-7. [PubMed]

Reconstituting a Virus

 
This week's citation classic from John Dennehy is
Fraenkel-Conrat and Williams (1955) [This Week's Citation Classic].

This week's citation classic is probably the coolest experiment you've never heard of.

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This Is so Sad!

 
Over the past several days Sandwalk has been spammed with hundreds of comments linking to sites like those listed below. Because I can't keep up with deleting them all, I've had to introduce word verification into the comments posting section of the blog. I'm really, really sad about this.

Why do people behave this way? What ever happened to common decency?

Is there anything I can do to get even?

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Where Am I?

 

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Nobel Laureate: James Batcheller Sumner

 

The Nobel Prize in Chemistry 1946.

"for his discovery that enzymes can be crystallized"



In 1946, James Batcheller Sumner (1887-1955) won the Nobel Prize in Chemistry for crystallizing the enzyme urease from jack bean [see: Dealing with Uric Acid and Monday's Molecule #48]. This was definitive proof that enzymes were proteins, something that was still controversial back when the work was done in the early 1920's.

The Presentation Speech was given by previous Nobel Prize winner Professor A. Tiselius, member of the Nobel Committee for Chemistry of the Royal Swedish Academy of Sciences.

Your Majesty, Royal Highnesses, Ladies and Gentlemen.

In 1897 Eduard Buchner, the German research worker, discovered that sugar can be made to ferment, not only with ordinary yeast, but also with the help of the expressed juices of yeast which contain none of the cells of the Saccharomyces. The discovery was considered so important that in 1907 Buchner was awarded the Nobel Prize for Chemistry.

Why was this apparently somewhat trivial experiment considered to be of such significance? The answer to this question is self-evident, if the development within the research work directed on the elucidation of the chemical nature of the vital processes is followed. Here, as in other fields of research, progress has taken place step by step, and the conquest of new fields has often been very laborious. But there, more than in most fields, a tendency has showed itself to consider the unexplained as inexplicable - which is actually not strange where problems of life and the vital processes are concerned. Thus ordinary yeast consists of living cells, and fermentation was considered by the majority of research workers - among them Pasteur - to be a manifestation of life, i.e. to be inextricably associated with the vital processes in these cells. Buchner's discovery showed that this was not the case. It may be said that thereby, at a blow, an important class of vital processes was removed from the cells into the chemists' laboratories, to be studied there by the chemists' methods. It proved, too, that, apart from fermentation, combustion and respiration, the splitting up of protein substances, fats and carbohydrates, and many other similar reactions which characterise the living cell, could be imitated in the test tube without any cooperation at all from the cells, and that on the whole the same laws held for these reactions as for ordinary chemical processes. But - and this is a very important reservation - this was only possible if extracts or expressed juices of such cells were added to the solution in the test tube. It was then natural to assume that these cell juices or cell extracts contained some substance which had the capacity of initiating and maintaining the reactions and guiding them into the paths they follow in the cell. These unknown active substances were called enzymes or ferments, and the investigation of their effects became one of the principal problems of chemistry during the first decades of this century, which for the rest it still is.

The important question of the nature of the enzymes remained unsolved, however, in spite of the energetic efforts of the research workers. It is manifestly a question of substances of complicated structures, which are present in such extremely small amounts that they, so to speak, slip through the fingers when one tries to grasp them. It is really remarkable to see how far it was possible to get in the study of the effects of the enzymes and the course of the enzymatic reactions, without knowing anything definite about the nature of these very active substances, nay, even without even being quite clear that they were substances which could be isolated in the pure form at all.

In 1926, however, in connection with his studies of a special enzyme "urease", James B. Sumner of Cornell University, Ithaca, U.S.A. succeeded in producing crystals which exhibited strikingly great activity. The basic material was the bean of a South American plant, Canavalia ensiformis, in America called the "jack bean", and the crystals had an activity that was about 700 times as great as that of bean flour. What was still more important was that it was possible to dissolve the substance and re-crystallize it several times without its activity being affected. The crystals proved to consist of a protein substance. Sumner expressed the opinion that in reality this protein substance was the pure enzyme.

As is so often the case with important discoveries, this result will probably to a certain degree have "been in the air", in that at the time it had been assumed in many quarters that the enzymes were protein substances of quite a special nature. On the other hand, Willstätter, the German chemist and Nobel Prize winner, had carried out far-reaching purifying experiments with enzymes and had arrived at results which caused him to doubt whether it was a question of protein substances or carbohydrates at all. We know now that this was due to the fact that Willstätter's purifying methods yielded solutions which were all too weak for it to be possible for chemical reactions to give a definite result.

For the chemist crystallization is the final goal in the preparation of a substance in pure form. Even though crystallizability is not such a reliable criterion of purity in the case of protein substances as in that of simpler substances, nevertheless Sumner's results have now been accepted as verified and thus also accepted as the pioneer work which first convinced research workers that the enzymes are substances which can be purified and isolated in tangible quantities. Thereby the foundation was laid for a more detailed penetration of the chemical nature of these substances, on which an understanding of the reactions taking place in living cells must finally depend.

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[Photo Credit: The photograph of urease crystals is from Sumner (1926) (urease crystals)]

Sumner, J.B. (1926) The Isolation and Crystallization of the Enzyme Urease. J. Biol. Chem. 69:435-441.

I Rank Number One on Google

 
David Ng at The World's Fair has invented a new blogging meme [The World's Fair exceptional "I rank number one on google" meme!!]. The rules are:

I'd like to suggest a meme, where the premise is that you will attempt to find 5 statements, which if you were to type into google (preferably google.com, but we'll take the other country specific ones if need be), you'll find that you are returned with your blog as the number one hit.

Here are my 5 statements ....

• Larry Moran
• Sandwalk
• Three Domain Hypothesis
• adaptationist-pluralist
• is there a genetic component to intelligence

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[Hat Tip: PZ Myers at Pharyngula (#1 on Google!)]

Tangled Bank #91

 
The latest version of the Tangled Bank has been posted on The Radula [Tangled Bank #91].

This one is remarkable because I finally figured out how to submit an article. The people who run this carnival don't make it easy.

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Dealing with Uric Acid

Most animals have to deal with excess nitrogen, which they get from food. One of the common sources is the nitrogen in purines such as adenosine, guanosine, deoxyadenosine, and deoxyguanosine. These nucleosides are broken down into the bases adenine and guanine plus the sugars, ribose and deoxyribose.

Adenine and guanine are converted to uric acid, via xanthine. Uric acid cannot be further metabolized in birds, some reptiles, and primates. These species excrete uric acid in their urine. They also excrete urea but this is derived from the breakdown of amino acids.

All other species convert uric acid to allantoin. This is the end product for most mammals, turtles, some insects, and gastropods. The remaining species can break down allantoin to allantoate and this product is excreted in some bony fishes.

The next step in the degradation pathway is the splitting of allantoate to two molecules of urea. Urea derived from purines is excreted by most fishes, amphibians, and freshwater mollusks. The remaining animal species degrade urea to ammonia and carbon dioxide using the enzyme urease.

In some cases the free bases adenine and guanine are salvaged to be used in synthesizing ATP, RNA, and DNA. The salvage pathways require special enzymes to recover the bases. Adenosine phosphoribosyltransferease converts adenine back to AMP and hypoxanthine-guanine phosphoribosyltransferase (HGPRT) salvages hypoxantinine and guanine.

Lesch-Nyhan Syndrome and Gout

As with other pathways, defects in purine metabolism can have devastating effects. In 1964 Michael Lesch and William Nyhan described a severe metabolic disease characterized by mental retardation, palsylike spasticity, and a bizarre tendency toward self-mutilation. Individuals afflicted with this disease, called Lesch–Nyhan syndrome, rarely survive past childhood. Prominent biochemical features of the disease are the excretion of up to six times the normal amount of uric acid and a greatly increased rate of purine biosynthesis. The disease is caused by a hereditary deficiency of the activity of the enzyme hypoxanthine–guanine phosphoribosyltransferase ((HGPRT) [OMIM 300322]. The disease is usually restricted to males because the mutation is recessive and the gene for this enzyme is on the X chromosome (Xq26-27.2). Lesch–Nyhan patients usually have less than 1% of the normal activity of the enzyme and most show a complete absence of activity. In the absence of hypoxanthine–guanine phosphoribosyltransferase, hypoxanthine and guanine are degraded to uric acid instead of being converted to IMP and GMP, respectively. The PRPP normally used for the salvage of hypoxanthine and guanine contributes to the synthesis of excessive amounts of IMP, and the surplus IMP is degraded to uric acid. It is not known how this single enzyme defect causes the various behavioral symptoms. The catastrophic effects of the deficiency indicate that in some cells the purine salvage pathway in humans is not just an energy-saving addendum to the central pathways of purine nucleotide metabolism.

Gout is a disease caused by the overproduction or inadequate excretion of uric acid. Sodium urate is relatively insoluble, and when its concentration in blood is elevated, it can crystallize (sometimes along with uric acid) in soft tissues, especially the kidney, and in toes and joints. Gout has several causes, including a deficiency of hypoxanthine–guanine phosphoribosyltransferase activity, which results in less salvage of purines and more catabolic production of uric acid. The difference between gout and Lesch–Nyhan syndrome is due to the fact that gout patients retain up to 10% enzyme activity. Gout can also be caused by defective regulation of purine biosynthesis.

Gout can be treated by giving patients allopurinol, a synthetic C-7, N-8 positional isomer of hypoxanthine. Allopurinol is converted in cells to oxypurinol, a powerful inhibitor of xanthine dehydrogenase. (Xanthine dehydrogenase is the enzyme responsible for synthesis of uric acid.) Administration of allopurinol prevents the formation of abnormally high levels of uric acid. Hypoxanthine and xanthine are more soluble than sodium urate and uric acid, and when they are not reused by salvage reactions, they are excreted.

Allopurinol and oxypurinol. Xanthine dehydrogenase catalyzes the oxidation of allopurinol, an isomer of hypoxanthine. The product, oxypurinol, binds tightly to xanthine dehydrogenase, inhibiting the enzyme.

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[The text and figures in the box are from Horton et al. (2006) Principles of Biochemistry ©L.A. Moran and Pearson/Prentice Hall]

[The gout cartoon is by James Gillray 1799]