American Justice in Italy

 
Steve Watson was kind enough to supply me with two links that I otherwise would have missed. The first is to a column by Neil Macdonald on the CBC News website [Exceptions are U.S.]. Macdonald makes a point that Candians and Europeans are very familiar with; namely, the fact that America has little respect for the laws of other nations.

Here's the outline of the case. You'll have to read the rest of the column to see the outrage.

Nobody in the Italian government thought Osama Moustafa Hassan Nasr was clean. The Italian police had for some time been building a case against the Islamic cleric for spreading extremism.

Prosecutors in Milan believed he was a jihadist who had fought in Afghanistan and Bosnia, and, further, that he was in Italy recruiting fighters for radical Islamic causes. They intended to bring him to trial.

But the Americans were watching, and they had no patience with the pace and procedures of Italian law enforcement.

On Feb. 17, 2003, a squad of agents grabbed Nasr off a Milan street as he walked to a nearby mosque. He was, allegedly, taken to the U.S. air force base in Aviano, Italy, and flown to Germany, from where he was transshipped to his native Egypt. There, prison and the tender mercies of Egyptian interrogators awaited.

Nasr says he was tortured during his four years behind bars. Given the Egyptian government's pitiless attitude toward the radical Muslim Brotherhood and its many affiliates, that is not a claim many people doubt. The Nasr case was, say critics of the Bush administration, yet another case of America quietly subcontracting torture to deal with its enemies.

But two things happened last week to move this case out of the shadows: An Egyptian court freed Nasr, saying his imprisonment was "unfounded." And in Italy, a democratic U.S. ally, a judge indicted 26 Americans, most of them agents of the CIA, for kidnapping the cleric. The spies will almost certainly be tried in absentia. They've all left the country.

Genetics of ABO Blood Types

Now that we understand the biochemistry behind the ABO blood types [ABO Blood Types] it's time to look at the genetics. Recall that the human ABO gene on chromosome 9 has three common variants of the gene. Different variants are called alleles. The A allele encodes N-acetylaminogalactosyltransferase and this enzyme makes the A antigen that confers blood type A. The B allele encodes a variant enzyme that makes B antigen and gives rise to blood type B. The O allele encodes a defective enzyme that doesn't make either antigen. In the absence of both A antigen and B antigen your blood type will be O.

Vestigial Structures Are Evidence of Evolution

 
Bill Dembski writes in Vestigial Structures by Design ....

Vestigial structures in biology are commonly cited as evidence for evolution, and it may well be that they did evolve. But if it is evidence of evolution, it is evolution in the wrong direction — it’s not the sort of function enhancing/innovating evolution that is supposed to give evolutionary theory its bite. Vestigial structures, after all, are structures that have lost their function. If all of evolution proceeded in this fashion, we’d quickly descend to a world of nonfunctionality.

Dear IDiot,

You can't have your cake and eat it too.

Either vestigial structures are evidence of evolution or they aren't. You don't get to pick and choose whatever fairy tale version of evolution you like whenever it takes your fancy. The fact that some whales have tiny pelvis bones and tiny legs buried deep under their skin tells us something about evolution. It tells us that whales are descended from ancestors that had hind limbs. The fossil record confirms this.

How does the wonderful scientific theory of Intelligent Design Creationism explain this?

Australia: Dick Loves You, He Really Loves you!

 
Cheney praises Howard's loyalty.

The alliance between Australia and America was strong because both nations worked at it and respected each other as equals, United States Vice-President Dick Cheney said today.

In a major speech to the Australian-American leadership dialogue in Sydney, Mr Cheney said the deep affinity between the countries had grown into a great alliance over time.

"Australia and America share an affinity that reaches to our souls," he said.

"Over time, that deep affinity has grown into a great alliance.

You must be so proud. He never says that about Canada.

Human ABO Gene

The human ABO gene encodes N-acetylgalactosaminyltransferase. This is the enzyme that determines the ABO blood types (see ABO Blood Types). This gene is found in all mammals, which makes it unfortunate that HUGO choose such a human-centered name [ABO Gene]. The gene will have a very different name in other species.

The GenBank website for this gene is GeneID=28. The ABO gene islocated at 9q34.1-q34.2 on chromosome 9. This is in approximately the same region as the HSPA5 gene but don't let that fool you. The genes are very far apart. [map]

There are many variants of this gene [OMIM 110300]. The DNA used in the human genome project came from people with different blood types so all three major variants (A, B, O) are present. Many of the other known variants have also been sequenced. You can look at the sequences in the Evidence Viewer on the Entrez Gene website [Evidence Viewer ABO Gene. Here's a bit of the sequence from the O allele and the A allele.

The nucleotide sequence of the O allele is shown at the top with the amino acid sequence. (It's hard to see at this scale. Go to the evidence viewer for a better view.) Note the presence of a single nucleotide deletion. This shifts the reading frame of the coding region so that it ends shortly after the deletion in a stop codon (*). The O allele produces a truncated defective protein.

The nucleotide sequence of the active gene (A allele) has a "G" (small red blob) at that position. The reading frame continues uninterrupted beyond the region shown and a functional enzyme is produced from this allele.

The ABO gene has seven exons, some of them are quite short. There are six introns and one of them is large so the total length of the gene is over twice as long as the length of the coding region.

Less Torture in "24"

 
We used to watch "24" every week but a couple of years ago we stopped because of the torture scenes. I just don't enjoy watching programs where people are tortured. Once or twice might be okay but it was getting to the point where every show had a scene where someone was tortured.

We weren't alone. Quite a few of our friends also stopped watching. It's not that we're opposed to violence on television—far from it. I think there's lot of shows where violence is quite appropriate and good entertainment. (I feel the same way about sex, by the way.) But I don't have to watch if I don't like it and I choose not to watch "24".

Gail Shister now reports in the Philadelphia Inquirer ['24' tamps down the torture] that the show is cutting back on the violence.

Fox's 24 will become less torturous, but not because the U.S. military, human rights groups and children's advocates want it to....

The decision to cut back on torture is driven by creativity, not criticism, according to Gordon. In its sixth season, 24 has become so torture-heavy that it borders on cliche, he says.

"What was once an extraordinary or exceptional moment is starting to feel a little trite. The idea of physical coercion or torture is no longer a novelty or surprise.

"It's not something that we, as writers, want to use as a crutch. We'd like to find other ways for Jack to get information out of suspects," says Gordon. "Our appetite has decreased. Personally, I think the audience may be tiring of it as well. My wife says it's too much."

"Cliché?" That's a strange word to use. The audience that I know hasn't gotten "tired" of torture. We've gotten disgusted by it.

I hope they stick to their promise. If they really are going to cut back on the torture (but not necessarily other violence) then I'll start watching again.

Jury Duty: Day #3

 
Dismissed at 9:50 AM. Services no longer required. "See you in three years!"

Wikipedia Bad - Conservapedia Good

 
Did you know that Wikipedia was anti-Christian and (gasp!) anti-American? Next thing they'll be telling us that it favors gays, drugs, and premarital sex. Not to worry. Help is at hand.

Conservapedia is a much-needed alternative to Wikipedia, which is increasingly anti-Christian and anti-American. On Wikipedia, many of the dates are provided in the anti-Christian "C.E." instead of "A.D.", which Conservapedia uses. Christianity receives no credit for the great advances and discoveries it inspired, such as those of the Renaissance. Read a list of many Examples of Bias in Wikipedia.

Conservapedia is an online resource and meeting place where we favor Christianity and America. Conservapedia has easy-to-use indexes to facilitate review of topics. You will much prefer using Conservapedia compared to Wikipedia if you want concise answers free of "political correctness".

We can all sleep better now, especially us furriners. Now we know where to go to learn about the real America.

Google Co-founder Shows His Ignorance

 
According to Reuters, Google co-founder Larry Page made a fool of himself in front of a bunch of scientists [ Google co-founder: Science needs entrepreneurs]. Here's what Reuters says,

Scientists need more entrepreneurial drive and could benefit by doing more to promote solutions to big human problems, Google Inc. co-founder Larry Page told a meeting of academic researchers.

I hope readers of this blog will recognize that Page isn't talking about science. He's talking about technology. It's sad that he doesn't know the difference.

[Hat Tip: Shelley Batts]

ABO Blood Types

I described glycoproteins in a previous posting (Glycoproteins). Recall that these are proteins with long oligosaccharide chains attached to them. The oligosaccharides are normally put on as the proteins are being processed for export to the exterior of the cell. The process involves attaching a “core” oligosaccharide then modifying it once it is bound to the glycoprotein. The modifications include removing some sugar residues and adding others.

The cell surface of blood cells is covered with glycoproteins and the carbohydrate chains project out into the blood stream where they can easily be recognized by antibodies. We make antibodies to all sorts of things but the ones that attack our own cells are removed before they can do any harm. This anti-self screening of antibodies is one of the things that goes wrong in auto-immune diseases.

The proteins on the erythrocyte cell surface contain a wide variety of different oligosaccharides that are attached in various ways to the protein. However, it spite of this variation, there are a few structures that are very common. One of the most common “core” structures is something called H-antigen. It is composed of many different sugars but the outside end of the H-antigen structure always consists of a fucose (Fuc) residue, a galactose residue (Gal), and an N-acetylglucosamine (GlcNAc) residue.

In most primates, including humans, this core oligosaccharide is subsequently modified by adding an N-acetylgalactosamine (Monday’s Molecule #14) residue to form a branched structure at the end of the oligosaccharide (see diagram below). The enzyme that catalyzes this reaction is called N-acetylaminogalactosyltransferase or A enzyme. The gene for this enzyme is located on chromosome 9. The OMIN (Online Mendelian Inheritance in Man) entry for the ABO blood group is 110300. It contains a wealth of information on the topic.

If your red blood cells have oligosaccharides with a terminal GalNAc then you have blood type A. If you have a completely defective gene for A enzyme then your cells will have the unmodified H antigen structure and your blood type will be O. People with blood type A will not have antibodies to H antigen since this is the normal precursor to A antigen and there will always be some on the cell surface. In other words, the H antigen will be recognized as self.

Normal red blood cells are recognized as “self” so we don’t have antibodies against our own cells. However, we will have antibodies against the red blood cells of other people’s blood if their cell surface carbohydrates are different from ours. This is the basis of ABO blood group and it’s why we have to match blood types in a blood transfusion.

The ABO blood group was discovered over one hundred years ago by Karl Landsteiner (Nobel Laureate: Karl Landsteiner). The biochemical basis was only elucidated in the 1970’s when the technology for examining the carbohydrate structure of glycoproteins was worked out.

There’s an allele of the A enzyme gene that involves only a very small number of mutations but the result is to switch the enzyme from one that transfers GalNAc to one that transfers galactose (Gal). The variant enzyme is called B enzyme (galactosyltransferase) and the B antigen structure has a terminal galactose (Gal) instead of a terminal GalNAc.

If you are homozygous for the B allele on chromosome 9 then all of your red blood cells will have the B antigen oligosaccharide on their surface. You will not make antibodies against this structure because it’s “self.” You also won’t have antibodies against H-antigen for the reasons explained earlier. But you won’t recognize A antigen as self so your antibodies will attack any foreign cells that come from people with the normal wild-type allele (A).

People with blood type A will have antibodies against B antigen. They can receive blood from people with O blood type but they will reject blood from people with B blood type. You now have all the information you need to figure out who can give and receive blood from every possible combination of alleles: AA, AO, AB, BO, and OO.

There are no known natural effects of these differing blood types. People with A, B, AB and O phenotypes do not differ in fitness in any major way that we have been able to detect. This suggests that the complete absence of the enzyme (null mutation) is neutral in the current human population and so is the switch from one form of the enzyme to another. (Suggestions that blood type determines susceptibility to some infections are common in the scientific literature. Most of them have not held up. The best correlation is a possible association between blood type O and susceptibility to cholera. This looks pretty good but the cause-and-effect relationship is still up in the air.)

The ABO alleles seem to be segregating in the human population by random genetic drift. The O allele (non-functional enzyme) is the most common allele. The B allele is the least common—probably because it arose more recently. Some Native American populations are homogeneous for the O allele; in those populations everyone has blood type O. (For maps of the frequencies A and B alleles see Distribution of Blood Types.)

Jury Duty: Day 2

 
There were a lot fewer potential jurors in the assembly room this morning. That’s because Panel #13 was told not to come in today so only my panel (#14) was there. There are about 100 people on each panel.

Yesterday we watched the video on the monitors hanging from the ceiling. We might be selected for either a Civil trial or a Criminal trial. There are six jurors in a civil case and twelve in a criminal case. A typical case lasts two or three days. Potential jurors wait in the assembly room until a trial that’s already in progress needs a jury. A subgroup of us will be selected and shuffled off to the courtroom where jury selection takes place.

At 9:20 the Sheriff’s Official began taking attendance in the assembly room. She read out everyone’s name and we had to shout out “here” if we really were here. It was just like grade two, including the few who shouted out “present” just to be different. Since we have to pass by the Sheriff’s desk as we enter the room, it’s not clear to me why we couldn’t just have signed in when we arrived instead of wasting 12 minutes in a roll call. A sign-in would have spared us having to listen to someone mispronounce our names. You have to wonder why someone who does this every single day wouldn’t have learned how to pronounce “Nguyen” by now.

At 10:30 another Sheriff’s Official showed up. She had just received word from the judge that jury selection in her trial was going to be delayed due to legal issues. Since that was the only trial that might have required a jury we were dismissed for today. (There are 50 courtrooms and 40,000 cases per year. This gives you some idea of how few of them require a jury.)

Come back tomorrow at 9AM.

Nobel Laureate: Karl Landsteiner

The Nobel Prize in Physiology or Medicine 1930.

"for his discovery of human blood groups"


Karl Landsteiner won the Nobel Prize in 1930 for his discovery of the ABO blood groups. He showed that individuals could be A,B, AB, or O blood group and identified each type by their agglutinating properties. (He didn't actually discover type O - that came a few years after Landsteiner's original work on the AB types.)

His work is described in the presentation speech.

In order to avoid, in the publication of research on this subject, detailed descriptions which would otherwise be necessary - of the four blood groups and their appropriate cell structures, certain short designations for the blood groups and corresponding specific cell structures have been introduced. Thus, one of the two specific cell structures, characterizing the agglutinating properties of human blood is designated by the letter A and another by B, and accordingly we speak of «blood group A» and «blood group B». These two cell structures can also occur simultaneously in the same individual, and this structure as well as the corresponding blood group is described as AB. The fourth blood-cell structure and the corresponding blood group is known as O, which is intended to indicate that people belonging to this group lack the specific blood characteristics typical of each of the other blood groups. Landsteiner had shown that under normal physiological conditions the blood serum will not agglutinate the erythrocytes of the same individual or those of other individuals with the same structure. Thus, the blood serum of people whose erythrocytes have group structure A will not agglutinate erythrocytes of this structure but it will agglutinate those of group structure B, and where the erythrocytes have group structure B the corresponding serum does not agglutinate these erythrocytes but it does agglutinate those with group structure A. Blood serum of persons whose erythrocytes have structures A as well as B, i.e. who have structure AB, does not agglutinate erythrocytes having structures A, B, or AB. Blood serum of persons belonging to blood group O agglutinates erythrocytes of persons belonging to any of the groups A, B, or AB, but erythrocytes of persons belonging to blood group O are not agglutinated by normal human blood serum. These facts constitute the actual basic principles of Landsteiner's discovery of the blood groups of mankind.

By the time the Nobel Prize was awarded it was known that the ABO human blood types were genetic traits that segregated according to "Mendel's Laws."

The group characteristics are handed down in accordance with Mendel's laws. The characteristics of blood groups A, B, and AB are dominant, and opposing these dominant characteristics are the recessive ones which characterize blood group O. An individual cannot belong to blood group A, B, or AB, unless the specific characteristics of these groups are present in the parents, whereas the recessive characteristics of blood group O can occur if the parents belong to any one of the four groups. If both parents belong to group O, then the children never have the characteristics of A, B, or AB. The children must then likewise belong to blood group O. If one of the parents belongs to group A and the other to group B, then the child may belong to group A or B or it may possess both characteristics and therefore belong to group AB. If one of the parents belongs to group AB and the other to group O, then in accordance with Mendel's law of segregation the AB characteristic can be segregated and the components can occur as separate characteristics in the children. If a child has the A-group structure (either A or AB), then the A-group characteristic must be present in at least one of the parents, i.e. one of them must belong to group A or AB. If the child belongs to group AB, then one of the parents must belong to group A and the other to group B, or one of the parents must belong to group AB and the other to group A or B, or else both parents must belong to group AB. Application of the discovery of blood groups in questions relating to the establishing of paternity is based on these principles governing the hereditary transmission of blood groups.

See [ABO Blood Groups] for a modern description of the biochemistry.

Responsible Journalism? Responsible Science?

 
The headlines in both Toronto papers were exciting. Anyone glancing at the papers would think that a major breakthrough in fighting autism was just on the horizon. The truth is that one small step has been taken toward identifying a possible genetic component to autism.

This is not responsible journalism. More importantly, it is not responsible science. The press releases should be much more cautious about the actual result and its significance. It the scientists themselves hype the result then we can't fault the journalists.

Jury Duty: Day 1

 
The summons from the Ministry of the Attorney General said to show up at 9AM or else I would be liable to the penalties provided by the juries act of Canada.

It warned me that parking might be a problem so I arrived early. The security was just like airport security except that this time there really were criminals in line with me. We were ushered into a large room that looked like the kind of waiting room you see in a bus terminal. I had to swear that there was nothing I knew of that would prevent me from serving on a jury. I am juror #13522 on Panel #14.

Thanks to the warning about parking, I was in time to get the last carrel on the side of the room and set up my laptop. The time was exactly 8:50AM. At 10AM a Sheriff's Officer showed up looking all official-like. She announced that they had nothing for us today. Come back tomorrow at 9AM.

Oh yes, don't forget that you may have trouble finding a parking place.

Glycoproteins

 
Glycoproteins are proteins that have covalently attached sugar residues. One of the common linkages between the sugar(s) and the protein is an N-glycosidic likage between the -OH group of the sugar at C1 and the side chain of a an asparagine residue in the protein. The linkage is called an N-glycosidic linkage and the asparagine residue is part of a specific sequence within the protein where sugars will be attached.

The sugar residue shown here is a modified form of glucose called N-acetyl glucosamine or GlcNAc. Other kinds of sugars can be attached to proteins. Most of them are modified versions of the standard carbohydrates. Another example is N-acetylgalactosamine or GalNac (see Monday's Molecule #14).

As a general rule, a bunch of these sugars are strung together to form an oligosaccharide chain (see below) and it's this long chain that's attached to the protein to form a glycoprotein.


Glycoproteins are usually secreted proteins that normally function outside the cell. One of the roles of the attached sugars is to stabilize the folded protein in an exterior environment and another role is to protect the protein against degradation by shielding it from enzymes that degrade proteins.

Most secreted glycoproteins have a specific kind of polysaccharide decoration that's added by specific enzymes in the lumen of the endoplasmic reticulum. (Recall that secreted proteins are imported into the ER were they are then targeted for secretion though small vesicles that carry them to the cell membrane.) An example of a typical oligosaccharide chain is shown below. The common part, called the "core", is shown in red. Note that there are many different kinds of sugars and the oligosaccharide can have branches. The strange looking code (e.g., β-(1→4)) describes the specific type of linkage between sugar residues.


Many secreted glycoproteins are inserted into the outer membrane of the cell. This results in a cell surface that bristles with a protective covering of complex carbohydrates.