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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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]

No Intelligence Allowed

 
Ben Stein is the star of a new film that's about to be released. It's called Expelled: No Intelligence Allowed and it's supposed to document the behavior of the evil atheist Darwinists who are suppressing the truth about how life began. (It was God that did it, dummy.)

Stein is interviewed by Bill O'Reilly, providing us with an excellent example of the intelligence that's being expelled from scientific debate. Why in the world should we have any respect for the opinion of Ben Stein?



One of the things that constantly amazes me about this issue is how people like Bill O'Reilly can survive on a major TV network. I guess intelligence isn't a requirement.

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[Hat Tip: PZ Myers at Pharyngula (Two people vying to out-stupid each other)]

Why Five Fingers?

Josh Rosenau is settling into his new job at the National Center for Science Education (NCSE). Part of his mission is to educate us in the ways of evolution and so far he's doing a great job. NCSE has always had a correct perspective on evolution, as far as I'm concerned, even though some of the people who used to work there tended to favor adaptationism.

Here's Josh's latest from his blog Traveling from Kansas [The Panglossian Paradigm, or as science moves forward, creationists move back]. Note that the opinions on his blog do not necessarily reflect those of NCSE.

For really confused students, I draw on a point Stephen Jay Gould made in Eight Little Piggies (in the essay by the same name), that the number of fingers we have is entirely contingent on history. While one can try to construct an explanation for the superiority of 5 fingers, paleontological history shows that there were potential ancestors of the tetrapod clade (which we are part of) which had as many as eight rays per fin. If they had succeeded, 8 fingers would be the norm, and the Simpsons would look very odd with only 4. As Gould says of historical contingency: "Other configurations would have worked and might have evolved, but they didn't--and five works well enough."

In the essay, Gould is building on a point he made most forcefully in an essay he wrote with Richard Lewontin, "The Spandrels of San Marcos and the Panglossian Paradigm: A Critique of the Adaptationist Program." The point was that biologists were too quick to insist that every feature was adaptive and a result of natural selection. Spandrels are triangular structures produced when two round arches meet. They are necessary byproducts of joining rounded and flat surfaces. Nonetheless, in many churches they are richly decorated and the entire artistic vision for a space can be shaped by the spandrels. One might, Gould points out, be lead to think that the spandrels are there in order to be used for paintings, and not that they are necessary by-products nicely dressed up. The worldview he criticizes treats anything, whether spandrels or five fingers, as the product of intense selection, a perfect solution to the problems it faces.

There's lot more where that came from so get on over to Travelling from Kansas for more information on the "correct" worldview.

By coincidence, today's Scientific American question is Why do most species have five digits on their hands and feet?. While there's a bit of catering to an adaptationist perspective the answer to the question is ...

Is there really any good evidence that five, rather than, say, four or six, digits was biomechanically preferable for the common ancestor of modern tetrapods? The answer has to be "No," in part because a whole range of tetrapods have reduced their numbers of digits further still. In addition, we lack any six-digit examples to investigate. This leads to the second part of the answer, which is to note that although digit numbers can be reduced, they very rarely increase. In a general sense this trait reflects the developmental-evolutionary rule that it is easier to lose something than it is to regain it. Even so, given the immensity of evolutionary time and the extraordinary variety of vertebrate bodies, the striking absence of truly six-digit limbs in today's fauna highlights some sort of constraint.

Remember the take-home lesson (mostly from Josh's article). Living organisms are not well designed in spite of what the creationists and the adaptationists would have you believe.

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Monday's Molecule #48

 
Today's molecule is several molecules and a reaction. You have to identify all the molecules in the reaction and name the common enzyme that catalyzes the reaction.

There's connection between this reaction and Wednesday's Nobel Laureate(s).

The reward goes to the person who correctly identifies the molecules, the enzyme, and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There are only two ineligible candidates for this Wednesday'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 molecules, the enzyme, 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 not open.

UPDATE: We have a winner!

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Gene Genie #18

 

The 18th edition of Gene Genie has just been published on Eye on DNA [Gene Genie #18 with the PG Tips Chimp].

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Is There a Genetic Component to "Intelligence"?

 
This is not my field and, quite frankly, I don't really care about any differences or similarities in intelligence between different human demes. However, the recent kerfuffle over the intemperate remarks of a Jim Watson have raised a number of interesting issues. One of these is whether there is a genetic component to intelligence.

I have always thought there was. I remember reading Richard Dawkins' take on this subject some years ago. He pointed out that if the average "intelligence" of humans has increased over the past million years by evolution then it follows logically that there were genes (alleles) for differences in intelligence that were selected. It seems unreasonable to imagine that all the alleles have reached fixation so that in today's 7 billion members of the Homo sapiens species there is no genetic variation for "intelligence." (I'm putting "intelligence" in quotation marks because I don't want to get into protracted battles about how to measure it or even how to define it. Let's just agree that there's something called intelligence that exists.)

Up until now I have been under the impression that certain genetic defects resulted in lowered intelligence. For example, Down's Syndrome is strongly correlated with low scores on an IQ test suggesting that the presence of extra chromosome 21 genes affects intelligence. That's a genetic component of intelligence by most reasonable definitions.

In spite of evidence to the contrary, there seem to be a number of people who deny that there's a genetic component to intelligence. One of these is Greg Laden, whose opinion I greatly respect. In a recent posting [Watson’s Lecture Canceled] he even disputes the twin studies that show a strong correlation between intelligence and heritability.

Heritability does not distinguish in and of itself between traits passed on with genes from traits passed on via culture, learning, environment, and so on. For instance, which language a person speaks has a very high heritability value, but this “trait” is entirely, 100% learned with absolutely no genetic component whatsoever. Twin studies have been used to suggest that IQ has a component of heritability that is genetic since it is more correlated in twins than in, say, full sibs. However, non-genetic traits can follow the same pattern. Non-genetic traits can show this pattern because, with respect to environments, full sibs who are not twins do not share the same environment as twins. (And for other reasons.)

It seems to me that Greg is arguing against a genetic component to intelligence. He seems to be going out of his way to discredit any studies that suggest otherwise. I'm not sure where he's coming from on this and that's the reason for posing the question in this posting.

Later on in the comments section of Greg's article he says the following.

We have, on this site anyway, not discussed the fact that neural development in humans does not really allow for much influence from genetics in the way that is asserted by the Rushtonian race argument; we have seen some discussion that the allegations that intelligence = g = IQ = something measurable in a simple way = something that varies across individuals because of allelic differences in some set of genes. But there are a LOT of reasons to not accept this idea, aside from the major disconnect between the genome and the functioning of the brain owing to the actual way real brains actually develop in real life. There has been very little discussion regarding the disconnect between the concept of heritability and the concept of subspecies in animals (race is simply another term for subspecies).

There are so many levels at which this is so wrong that I can’t help but feel … and I’ve said this already … that the Race Concept and the intelligence piece of this are simply not valid scientific arguments, and are almost always either political arguments or arguments being made from ignorance. They are political in their motivation, because the science here is simply operating in a totally different place (a little place I call reality).

Clear as mud. I fully sympathize with the mixture of politics and science that confuses this issue. There are people who want there to be differences in intelligence between races because it fits with their political agenda.

I wonder if there aren't people who believe the opposite because it fits with their political agenda? I wonder if there aren't people who go out of their way to construct pseudo-scientific arguments denying that there can be a genetic component to intelligence. Why would they do this? Because if there's no genetic component to intelligence then there can be no differences between demes and this avoids a messy political debate.

Frankly, I'm not sure if Greg Laden is doing this so I'd like to see some clarification. Is there a genetic component to intelligence? Are there "intelligence" alleles segregating within the human population such that some people are smarter than others because of their parents and not just because of socioeconomic environment? Or, are all differences in intelligence due to environment?

Please, let's not let this thread degenerate into a discussion about racism. Let's talk about the science and stick to the question.

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The It's Its There Their They're Quiz

 

You Scored an A

You got 10/10 questions correct. It's pretty obvious that you don't make basic grammatical errors. If anything, you're annoyed when people make simple mistakes on their blogs. As far as people with bad grammar go, you know they're only human. And it's humanity and its current condition that truly disturb you sometimes.

The It's Its There Their They're Quiz

This is a quiz designed to find out whether you know the difference between its, it's, they're, their, and there. I doubt very much whether any blogger, or any reader, would get less than 10 on this quiz.

We all make mistakes from time to time. The problem isn't that we don't know the right word it's that we sometimes slip up when we're typing quickly and not concentrating on grammar. I am not one of those people who jump all over a fellow blogger when they make a mistake. I assume they're just like me. We're perfect in lots of things but attention to silly details like spelling isn't one of them.

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[Hat Tip: GrrlScientist at Living the Scientific Life (How is Your Punctuation and Grammar?]

I knew There Had to Be a Good Reason!

 
(for avoiding tofu)

Eating soya could slash men's sperm count.

Men who eat just half a serving of soya a day have drastically fewer sperm than those who do not consume such foods, according to a small, preliminary study.

The study's researchers say larger trials are needed to determine whether men hoping to conceive a child should try to avoid soya foods, such as tofu, tempeh and soya milk. However, soya industry representatives caution that the new findings contradict earlier studies that have shown no impact on sperm count from soya-based products.

Soya foods contain high amounts of isoflavones, compounds that mimic the effects of oestrogen in the body. For this reason, women sometimes increase their intake of soya foods to treat hot flushes caused by declining oestrogen levels in menopause.

Oestrogen-like compounds can also have a dramatic impact on the male body. And previous rodent studies have suggested that high intake of soya products can reduce male fertility. This has led scientists to wonder how isoflavones might influence men's reproductive function, which is highly sensitive to hormones.

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I'm skeptical of everything about nutrition and health but one of the important things about this study is that it alerts people to the presence of strange chemicals in natural plant foods. This is something that most people need to know in order to put nutritional studies into perspective. There are a lot of potentially dangerous chemicals in plants but the vast majority have no effect whatsoever.

Maher Arar Appears (Remotely) Before US Congressional Committee

 
In September 2002 Maher Arar was detained at New York's JFK Airport on the grounds that he was a suspected terrorist. At the time Maher, a Canadian citizen, was on his way back to Canada.

American officials sent him to Syria were he was tortured and held in prison for a year. When he eventually returned to Canada (avoiding US air space) he was acquitted of all charges in a special hearing and awarded 10 million dollars in compensation.

However, the US government refuses to clear his name and he remains on the no-fly list. Thus, when asked to appear before a joint committee of the House of Representatives he was denied permission to enter the USA and had to appear via a video link from Ottawa. The episode is reported on the front page of today's Toronto Star [U.S. leaders apologize to Arar].

Republicans joined with Democrats yesterday to offer Maher Arar something he has never received from the Bush administration – an apology for the U.S. role in wrongly detaining him, then sending him to Syria where he was tortured.

More than five years after his nightmare began, Arar received the apologies from congressmen as far apart on the ideological spectrum as possible in Washington, even if they differed widely on the value and legality of the Bush administration's practice of "extraordinary rendition" of terror suspects.

Canadians are outraged at the behavior of the Bush administration. There's no reason to keep persecuting a man who has been found innocent in Canadian courts. Doesn't the Bush administration have any respect for the legal procedures of their closest allies?

The surprise was the reaction of California Republican Dana Rohrabacher, a conservative who defended the rendition program, but also offered heartfelt apologies to Arar and said that he should be compensated.

"I join in offering an apology and I wish our government could join me in doing this officially," he said.

"When we make a mistake, we should own up to it."

He said the fact that the administration blocked Arar's personal appearance was evidence of "an arrogance that I don't like to see in our government.

"It only adds insult to injury," he said. "You should be let off the list, compensated and allowed to come here and tell your story."

But the Bush administration has not backed down from its story that Arar was deported, and it has not explained why he was sent to Syria when he asked to be allowed to return to Canada where his family and livelihood awaited.

Besides continuing to bar Arar from the country, the administration is working to block his lawsuit in a New York court.

The appeal will be heard next month.

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The Watson Affair

 
This Watson dust-up is going to get very interesting. First we have all those people who were quick to condemn Jim Watson as a low-life racist bigot on the basis of a few sentences in a newspaper article. That's before even hearing what he had to say about it.

Then we have the Science Museum canceling his talk on the grounds that they don't tolerate bigots. This is an incredible thing to do. Watson has been a well-known figure in scientific circles for half a century. It's just not credible that all of a sudden he has become such a racist that he's no longer welcome. He may be lots of things that people don't like but being a ugly racist isn't one of them.

On the other hand, we have the Newcastle Centre for Life and the Cambridge Union who are going ahead with plans to hear Watson speak. According to the Telegraph [Nobel Prize scientist 'mortified' at racist slur],

His earlier comments caused outrage among politicians and equality campaigners and led to the Science Museum cancelling a talk he was due to give. However, his planned appearance at Newcastle's Centre for Life on Sunday will go ahead, organisers said yesterday.

Linda Conlon, chief executive of the centre, said: "James Watson has been a regular visitor to Life and has often been outspoken and controversial. His views are not those held by the Centre but many people are keen to hear what he has to say. This discussion is part of a well established and popular lecture series, which gives the public an opportunity to explore and challenge topical life science issues."

The Cambridge Union said it would go ahead with a speech Dr Watson is due to deliver on Tuesday.

Roland Foxcroft, President of the Cambridge Union Society, said: "James Watson was invited to address the Union over two months ago. He was invited to discuss his past scientific achievements and the launch of his new book. We were unaware that he would make the comments that appeared in the Sunday Times Magazine, and we certainly did not invite him to speak to the Union in order to air these views or to support them.

"The Standing Committee of the Union has decided that the event should proceed in the name of the values of free speech and academic freedom with which we were founded. We would like to reiterate that Dr Watson's invite stands on the basis of his discovery of DNA and not on the basis of his social views."

Good for them. I'm glad to see that someone has some gumption. Now let's see how this plays out over the next few days and whether some politically correct people are willing to admit they went too far.

Admittedly, second-guessing Watson is complicated. But what upsets me the most is the totally irrational knee-jerk response of labeling him a racist. That just doesn't make sense. If he were the kind of racist that people are claiming he wouldn't have held the positions he held and he wouldn't have any friends in the scientific community.

Those friends have now commented [Nobelist's Race Comments Spark Outrage].

"Jim has a penchant for making outrageous comments that are basically poking society in the eye," Dr. Francis Collins, director of the National Human Genome Research Institute, said Thursday.

Collins, who has known Watson for a long time, said his latest comments "really ... carried it this time to a much more hurtful level."

In a brief telephone interview, Collins told The AP that Watson's statements are "the wildest form of speculation in a field where such speculation ought not to be engaged in." Genetic factors for intelligence show no difference from one part of the world to another, he said.

Several longtime friends of Watson insisted he's not a racist.

"It's hard for me to buy the label `racist' for him," said Victor McElheny, the author of a 2003 biography of Watson, whom he's known for 45 years. "This is someone who has encouraged so many people from so many backgrounds."

So why does he say things that can sound racist? "I really don't know the answer to that," McElheny said.

Biologist and Nobel laureate Phil Sharp at the Massachusetts Institute of Technology, who's known Watson since 1971, said, "I've never considered Jim a racist. However, Jim likes to use statistics and observations to provoke people, and it is possible that he is provoking people by these comments."

Calling Watson "one of the great historical scientific figures of our time," Sharp said, "I don't understand why he takes it upon himself to make these statements."

Mike Botchan, co-chair of the molecular and cell biology department at the University of California, Berkeley, who's known Watson since 1970, said the Nobelist's personal beliefs are less important than the impact of what he says.

"Is he someone who's going to prejudge a person in front of him on the basis of his skin color? I would have to say, no. Is he someone, though, that has these beliefs? I don't know any more. And the important thing is I don't really care," Botchan said.

"I think Jim Watson is now essentially a disgrace to his own legacy. And it's very sad for me to say this, because he's one of the great figures of 20th century biology."

Watson has a history of "poking society in the eye" that's for sure. For some reason, this time it backfired big time. I guess it depends on whose eye is being poked. The Watson affair is sad because I have a fondness for curmudgeons. I hope it isn't a sign that any dissent from standard dogma will be severely punished.

What is this standard dogma? Francis Collins puts it well when he says, "Genetic factors for intelligence show no difference from one part of the world to another." This is something that nobody can question without being called a racist. See Race and Intelligence for more discussion and a possible exception.

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Email Message Warns about Canadian Health Care

 
Friday's Urban Legend: MOSTLY FALSE

The email message begins with,

This was sent from Canada to a friend in the States.

I saw on the news up here in Canada where Hillary Clinton introduced her new health care plan. Something similar to what we have in Canada. I also heard that Michael Moore was raving about the health care up here in Canada in his latest movie. As your friend and someone who lives with the Canada health care plan I thought I would give you some facts about this great medical plan that we have in Canada.

First of all:

1) The health care plan in Canada is not free. We pay a premium every month of $96 for Shirley and I to be covered. Sounds great eh. What they don't tell you is how much we pay in taxes to keep the health care system afloat. I am personally in the 55% tax bracket. Yes 55% of my earnings go to taxes. A large portion of that and I am not sure of the exact amount goes directly to health care our #1 expense.

Snopes.com has examined all the claims in this email message and found that most of them are without merit [Canadian Health Care]. For example, there is not a single health care plan in Canada. There are thirteen different ones, one for each province and territories. Most of them do not charge premiums but the British Columbia plan does and it would cost $96 per month for a family of two. This part of the message is partially correct.

The part about taxes is not. Here's what Snopes.com says.

The highest federal income tax rate in Canada is 29% (for persons with annual taxable income over $120,887), and the highest provincial income tax rate in British Columbia is 14.7% (for those with annual taxable incomes over over $95,909). The typical upper-income level Canadian taxpayer is not in a 55% tax bracket.

By way of comparison, a typical upper-income level American taxpayer residing in California pays a roughly equivalant share of his income (40%-45%) in combined federal and state taxes, even though the U.S. has no national health insurance program.

There are many issues concerning health care and whether the USA should adopt socialized medicine like most civilized countries. It doesn't help when people are spreading false information.

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More Restricted Access to Journal Articles

 
The press release from the Dept. of Energy Joint Genome Institute (USA) sounds really cool [Massive reanalysis of genome data solves case of the lethal genes].

It is better to be looked over than overlooked, Mae West supposedly said. These are words of wisdom for genome data-miners of today. Data that goes unnoticed, despite its widespread availability, can reveal extraordinary insights to the discerning eye. Such is the case of a systematic analysis by the U.S. Department of Energy Joint Genome Institute (DOE JGI) of the massive backlog of microbial genome sequences from the public databases. The survey identified genes that kill the bacteria employed in the sequencing process and throw a microbial wrench in the works. It also offers a possible strategy for the discovery of new antibiotics. These findings are published in the Oct. 19 edition of the journal Science.

In nature, promiscuous microbes share genetic information so readily that using genes to infer their species position on the evolutionary tree of life was thought to be futile. Now, researchers at DOE JGI have characterized barriers to this gene transfer by identifying genes that kill the recipient bacterium upon transfer, regardless of the type of bacterial donor. These lethal genes also provide better reference points for building phylogenic trees—the means to verify evolutionary relationships between organisms.

But it's not true. This article was not published in the Oct. 19 edition of Science. You can see for yourself [Science Oct. 19, 2007].

Instead it was posted on ScienceXpress, Publication ahead of print. Access to those articles is restricted. I can't see them even though the University of Toronto has an excellent system for getting articles from journals. Can anyone else get this article?

This really pisses annoys me. What's the point of putting out a press release if nobody can see the paper?

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Does the Universe Have a Purpose?

 
There's a two page ad in last week's issue of NewScientist. It's paid for by the Templeton Foundation and the ad consists of quotations from various people on the question "Does the Universe have a Purpose?" The link to the Templeton Website gives you the complete essays of all the writers [Purpose].

The Templeton Foundation is interested in promoting a truce between science and religion. They offer a prize worth more than $1,000,000 to people who advance this cause. In most cases it goes to religious scientists.

Some of the responses to the question of purpose are worth a comment or two. For example, here's what Christian De Duve says. (De Duve won the Nobel Prize in 1974.)

I should mention first that this is a loaded question, with several hidden implications. A "purpose" presupposes a mind that conceived it, as well as the ability to implement it. In the present case, this means that the owner of the mind not only created the universe the way it is, but could have created another universe and decided to create the existing one for a specific reason. So the question really deals with the belief in a Creator who enjoys almost infinite power and freedom but, at the same time, goes through the very human process of pondering decisions and acting accordingly. In a way, this is a very anthropomorphic vision of God....

It will be noted that there is no logical need for a creator in this view. By definition, a creator must himself be uncreated, unless he is part of an endless, Russian-doll succession of creators within creators. But then, why start the succession at all? Why not have the universe itself uncreated, an actual manifestation of Ultimate Reality, rather than the work of an uncreated creator? The question is worth asking.

This is the response of an atheist. De Duve doesn't believe in supernatural beings that could have created the universe so the only logical response to the question is NO. There is no purpose.

Not all atheists respond this way and that's what I find interesting. Here's the way Lawrence Krauss answers.

Perhaps you hoped for a stronger statement, one way or the other. But as a scientist I don't believe I can make one. While nothing in biology, chemistry, physics, geology, astronomy, or cosmology has ever provided direct evidence of purpose in nature, science can never unambiguously prove that there is no such purpose. As Carl Sagan said, in another context: Absence of evidence is not evidence of absence....

Thus, organized religions, which put humanity at the center of some divine plan, seem to assault our dignity and intelligence. A universe without purpose should neither depress us nor suggest that our lives are purposeless. Through an awe-inspiring cosmic history we find ourselves on this remote planet in a remote corner of the universe, endowed with intelligence and self-awareness. We should not despair, but should humbly rejoice in making the most of these gifts, and celebrate our brief moment in the sun.

Clearly Krauss doesn't believe that the universe has a purpose because he's an atheist. Nevertheless, he feels compelled to hedge his bets on the grounds that you can't prove a negative. This is a cop-out.

In the absence of any evidence the proper response is NO, bearing in mind that this response could change if evidence for God was ever discovered. No is the answer you give to all other questions of this type such as "Does the tooth fairy exist?" or "Do you believe in UFO's?" In fact, I strongly suspect that Krauss would give this answer if the question was reworded to be "Do you believe that the universe has a purpose?"

It shouldn't make a difference how the question is worded. Note that there are several religious people who answer "YES" to the question. If they were to follow Krauss' advice the best they could say would be "Likely" but they don't do that. We all know about the absence of evidence excuse but for some reason it only seems to apply in practice to questions about religion. You don't believe me? Then how would you answer this question: "Did Saddam Hussein have a secret hidden stockpile of nuclear weapons?"

Finally, let's look at the response of another atheist. This time it's Neil deGrasse Tyson. Here's what he says,

Anyone who expresses a more definitive response to the question is claiming access to knowledge not based on empirical foundations. This remarkably persistent way of thinking, common to most religions and some branches of philosophy, has failed badly in past efforts to understand, and thereby predict the operations of the universe and our place within it....

So in the absence of human hubris, and after we filter out the delusional assessments it promotes within us, the universe looks more and more random. Whenever events that are purported to occur in our best interest are as numerous as other events that would just as soon kill us, then intent is hard, if not impossible, to assert. So while I cannot claim to know for sure whether or not the universe has a purpose, the case against it is strong, and visible to anyone who sees the universe as it is rather than as they wish it to be.

Neil deGrasse Tyson is an atheist. Does that last paragraph sound like someone who's not sure? Of course it doesn't.

When he says that "Anyone who expresses a more definitive response to the question is claiming access to knowledge not based on empirical foundations" he's just pandering to religion. Does anyone seriously believe that he's NOT SURE about the existence of Santa Claus and NOT SURE about the existence of God?

Yes, it's true that we can't prove the non-existence of God and we can't prove that the universe has no purpose but those aren't really related to the type of question being asked. When someone asks whether the universe has a purpose you have every right to interpret this to mean whether in your best judgment the universe is designed with a purpose in mind. Especially if the question is being asked by the Templeton Foundation. Religious scientists answered YES, YES, and CERTAINLY. The religious humanities Professor answered I HOPE SO.

De Duve got it right. It was a loaded question and the responses from the wimpy atheists play right into the hands of the Templeton Foundation. They now have a full page ad where eight academics responded and only two said NO. (The other one is Peter Atkins.)

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