What Scientific Instrument Enhances the Quality of Life for People Around the World?

 
Eva, one of our own graduate students, asks this question on her blog easternblot [Quality of Life]. It's a multiple choice question. How hard can it be?

I mean, there can't be all that many scientific instruments that enhance the quality of life for people all around the world, right? Before checking her list, see if you can think of a few possibilities.

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What Could Possibly Go Wrong if Everybody Has a Gun?

 
The title of this article is a rip-off of Canadian Cynic [ I mean, what could possibly go wrong?]. That article, in turn, is a response to a provocative article on Halls of Macadamia titled "In Canada, you have to run and hide...".

The story is about certain laws in the USA covered in "Stand Your Ground" bills. Here's a description of the issue from Feb. 2006 in The Christian Science Monitor [Is self-defense law vigilante justice?].

Instead of embracing a citizen's "duty to retreat" in the face of a physical attack, states may be taking cues from the days of lawless frontier towns, where non-deputized Americans were within their rights to hold the bad guys at bay with the threat of deadly force.

First enacted in Florida last year, "Stand Your Ground" bills are now being considered in 21 states including Georgia, according to the National Rifle Association and the Brady Campaign to Prevent Gun Violence. The South Dakota senate approved one just last week.

These new measures would push the boundaries beyond the self-defense measures already on the books. Twelve states already allow citizens to shoot intruders in their homes, and 38 states permit concealed weapons in public places. The "Stand Your Ground" laws would allow people to defend themselves with deadly force even in public places when they perceive a life-threatening situation for themselves or others, and they would not be held accountable in criminal or civil court even if bystanders are injured.

Laws putting more judgment in an individual's hands stem from people's increased concern about crime in their communities. Proponents say it helps shift the debate from gun control to crime control, and that these laws are part of the rugged individualism of Americans.

Yes, folks. This is not a joke. There really are people out there who think that Dodge City was crime free because everyone was armed to the teeth before restrictions on carrying guns were imposed [Only in America] [Should Christians Be Armed?]. After all, what could possible go wrong when you give everyone a hand gun and expect them to serve up vigilante justice?

"These laws send a more general message to society that public spaces belong to the public - and the public will protect [public places] rather than trying to run into the bathroom of the nearest Starbucks and hope the police show up," says David Kopel, director of the Independence Institute in Golden, Colo.

Some critics say such "Wild West" laws are vigilante justice, and commonplace confrontations and more likely turn to violence.

Well, one thing that could go wrong is that innocent people could possibly get hurt. Canadian Cynic points us to this example from the New York Times in 1994 [Judge Awards Damages In Japanese Youth's Death].

A judge today awarded more than $650,000 in damages and funeral costs to the parents of a Japanese exchange student, saying there was "no justification whatsoever" for the killing of the 16-year-old boy who approached a suburban homeowner's door in a Halloween costume almost two years ago....

Mr. Peairs was at home with his family in October of 1992 when the student, Yoshihiro Hattori, and an American companion mistakenly rang his doorbell in search of a Halloween party. Mr. Peairs's wife, Bonnie, answered and, frightened, yelled to her husband to get his gun. Mr. Peairs shot Mr. Hattori dead after warning him to "freeze," a phrase the young man apparently did not understand.

This isn't the only case of this type. The problem with encouraging people to take the law into their own hands is that they tend to act aggressively instead of just running away (or slamming the door). We shouldn't encourage people to use guns to act out their paranoia.

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Diversity and the Major Histocompatibility Complex

 
A number of authors have applied this test [for homozygosity] to protein polymorphism data. In most cases, either no selection or purifying selection was indicated. In the case of human HLA (MHC) loci, however, Hedrick and Thomson (1983) found a significant reduction in homozygosity. It is, therefore, likely that the high polymorphism at these loci is maintained by some sort of balancing selection.

Masatoshi Nei (1987)The adaptationist/pluralist debate really began in earnest with the discovery that there was much more genetic diversity in a population than expected if natural selection was the major mechanism of evolution [The Cause of Variation in a Population]. This lead to Neutral Theory and the recognition—by all but a few stubborn holdouts—that random genetic drift was responsible for most of evolution at the molecular level [Silent Mutations and Neutral Theory].

However, there are adaptationist explanations for diversity. They usually involve some form of balancing selection as is the case with sickle cell alleles in those parts of the world where malaria is a problem. Other versions of balancing selection are more complicated, especially those where the goal is to maintain multiple alleles that benefit the population as a whole.

The classic example is the major histocompatibility (MHC) locus that contains multiple alleles at the same genetic locus as well as multiple alleles segregating in the population. The case for selecting diversity seems strong.

In spite of the fact that this is an important concept I'm not going to touch this particular example since it's much too complicated. Fortunately for us, we have an immunologist blogger at Mystery Rays from Outer Space who works on antigen presentation. He bravely goes where Sandwalk fears to tread.

Read "Heavyweight championship: Overdominance vs. frequency-dependent selection" to see what the controversy is all about. If you need a refresher course on MHC class I molecules then "iayork" has that base covered as well [ It was twenty years ago today] [ MHC molecules: The sitcom].

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DriPs and the Inefficiency of Translation

 
There's been a lot of talk recently about junk DNA and the possibility that large parts of it may, after all, have a function. Some of this speculation revolves around reports that most of the junk DNA is transcribed [Junk RNA] [Transcription of the 7SL Gene].

I believe that a great deal of this transcription is accidental and artifact. It's consistent with the idea that DNA replication, transcription, and translation are complex processes that are error-prone. Not every transcript, for example, has to be functional.

Iayork over on Mystery Rays from Outer Space has picked up on this theme in order to discuss mistakes in translation and the Drips hypothesis [RNA, protein, and information]. Check it out. There's more coming.

Students need to be aware of the fact that biology is messy. Some things just happen by mistake and we shouldn't fall into the trap of assuming that every peptide and every bit of RNA is made for a purpose. Life isn't as well-designed as some people think.

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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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