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.

Peter McKnight of the Vancouver Sun Weighs in on the Marcus Ross Incident

 
Peter McKnight wrote a column in the Vancouver Sun ['Young Earth' creationist stirs a scholarly storm]. He makes a number of points but I'll confine my comments to those that have a direct bearing on the awarding of a geology Ph.D. to someone who believes the Earth is only 10,000 years old. Read more about my position on this issues at [What Is Science].

Ross's advisers described his work as "impeccable" and they therefore had no reason to deny him his doctorate. But many other scientists, including physical anthropologist and U.S. National Center for Science Education executive director Eugenie Scott, have expressed concern that Ross would use his doctorate from a secular school "to miseducate the public."

I don’t know what motivates Eugenie Scott but I want to make it clear that this is not something I’m the least bit concerned about. Once a student is awarded a Ph.D. they are perfectly free to do and say whatever they want. I will not deny a student a Ph.D. simply because of what I think they might say once they graduate. What I'm concerned about is awarding the degree in the first place.

Furthermore, the fact that his former advisers saw nothing wrong with what they did is part of the problem. You can't use the fact that they gave him the degree as proof that there was nothing wrong with the process. That's a circular argument.

Scott claims that refusing to admit a doctoral candidate like Ross, whose views "are so at variance with what we consider standard science," would be acceptable because it would amount to discrimination "on the basis of science" rather than because of his personal beliefs.

While Scott's concerns are understandable given that Ross has already appeared in a video promoting the anti-evolution theory of intelligent design, there's no evidence that there is anything wrong with his science.

It's apparent, then, that Ross's personal beliefs really are the issue here.

I disagree with Peter McKnight. There is plenty of evidence that something is seriously wrong with the science of someone who believes that the Earth is only 10,000 years old. McKnight, like many others, seems to think that the only thing that counts in a Ph.D. program is what’s written down in a thesis. Not true. Students are also questioned about their understanding of basic concepts and ideas in their chosen field of study. We don’t award Ph.D.’s to students who can’t think on their feet and defend their ideas in an intellectual environment.

We know that Marcus Ross has a flawed understanding of the science of geology and for this reason he does not deserve a Ph.D. in geosciences. We also know that Ross’s flawed understanding is derived from his Christian fundamentalist beliefs. It may seem silly to deny that Ross is not being discriminated against because of his religion but that’s the truth. He should have been discriminated against because of his stupidity and not directly because of his religion.

Does this mean that Ross’s “personal beliefs” are really the issue as Peter McKnight suggests. Well, yes, if by personal beliefs you mean what someone is thinking. When I flunk an undergraduate for not understanding the material in my biochemistry course then I’m definitely making their “personal belief” the issue. What else could it be? Let’s not confuse the examination of a student’s personal understanding of the material with the “personal belief” canard that raises the specter of religious discrimination.

That said, Ross's views present an even greater challenge to religion than to academic institutions. After all, there are only two ways to explain how Ross can simultaneously subscribe to two incompatible belief systems, and neither way is particularly palatable: Either Ross is dishonest, with little interest in witnessing what he believes to be the truth, or he is a relativist, with no belief in truth at all.

As for being dishonest: If, as he claims, Ross really believes in the Biblical account of creation, then he must also believe that many of the statements in his dissertation are patently false. If the world really is less than 10,000 years old, then mosasaurs couldn't have disappeared 65 million years ago, which means Ross doesn't believe what he wrote.

Ross is cagey on this issue, as he essentially dodged the issue by telling the Times, "I did not imply or deny any endorsement of the dates." This suggests a kind of agnosticism, and leads to the second way of explaining his incompatible beliefs.

I disagree. To me the evidence is strongly in favor of outright deception and not “no belief in the truth at all.” Ross fully intended to misrepresent his beliefs in his thesis, and perhaps during the oral exam as well. I’m pretty certain that Ross has created a rationalization in his own mind that justifies this form of cognitive dissonance. In other words, Ross probably doesn’t think that he’s being deceitful—but that’s only because he has taken the time to deceive himself first.

And now it seems that young Earth creationists want a piece of the action. Ross's insistence that there is no conflict between his paleontological and Scriptural beliefs, because he is capable of "separating the different paradigms," reveals that he is a true believer in the Kuhnian revolution.

But he must then necessarily cease to be a true believer in another very important sense. In accepting that Scripture merely presents one paradigm among many, and that the claims in the Bible are therefore no more or less true than the claims made in any other paradigm, Ross must abandon the belief that the Bible speaks the Truth -- not just the truth relative to a specific conceptual framework, but the truth that exists always and everywhere.

I realize that the logic here seems impeccable, but only if you make the assumption that Ross is speaking the truth when he talks of different paradigms. We all know that the assumption is overly gratuitous. In Ross’s mind there’s only one truth and everything else is false.

[Hat Tip: John Pieret]

Phillip E. Johnson on Intelligent Design Creationism

 
... my personal view is that I identify the designer of life with the God of the Bible, although intelligent design theory as such does not entail that. Phillip JohnsonPhillip Johnson has just posted a long essay on Intelligent Design Creationism [Intelligent Design in Biology: the Current Situation and Future Prospects].

Like most IDiot arguments, this one relies on two main points: (1) evolution is wrong, (2) the bad guys are picking on us. There isn't one single scientific argument in favor of intelligent design.

This isn't really news but it's still worth pointing out. The Intelligent Design Creationists often claim that their case does not rely on disproving evolution but instead relies on positive evidence for intelligent design. Well, here was their big chance to prove it in an essay by the founding father. They blew it. I hate hypocrisy.

What Is Science?

The recent controversy over Marcus Ross has raised serious questions about science. In case you've forgotten about Ross, let me refresh your memory.

Ross received his Ph.D. in geosciences from Rhode Island University His thesis topic was on a class of marine lizards called mosasaurs. These animals lived more than one hundred million years ago and they went extinct at the end of the Cretaceous, 65 million years ago. Ross is a Young Earth Creationist (YEC). He believes in the literal truth of the Bible. This includes a belief that all species were created in a 6 day week only 10,000 years ago. Ross is currently a Professor of Biology at Liberty University, run by Rev. Jerry Falwell, where he teaches a Christian version of Earth Science and a required course (CRST 290) on the History of Life.

CRST 290
An interdisciplinary study of the origin and history of life in the universe. Faculty of the Center for Creation Studies will draw from science, religion, history, and philosophy in presenting the evidence and arguments for creation and evolution. This course is required for all Liberty students. The video taped course is 3 semester hours credit.According to an article in the New York Times (Believing Scripture but Playing by Science’s Rules) Ross did not discuss his YEC beliefs in his thesis, Instead, he wrote his thesis as though he believed in an Earth that was billions of years old and as though species evolved and went extinct over periods of millions of years. In other words, Ross did not tell the truth about his true "scientific" beliefs when he wrote his thesis. I assume that he also didn't discuss his true beliefs during the Ph.D. oral exam when his examining committee questioned him on his thesis work, including his interpretation and its implications.

What does the creationist community think of all this? Well, first of all they don't think that Ross was "deceptive" but they have a very peculiar definition of deceptive. The creationists admire Ross for not hiding his belief in a 10,000 year old Earth while getting a Ph.D. in geology. They see nothing wrong with "pretending" to be a scientist while attending a "secular" university. Here's how Sal Cordova puts in on Uncommon Descent.

For the pro-ID and creationist students out there, Ross shows how to make it through a Darwinist controlled secular institution. Ross was never deceptive about his beliefs, yet demonstrated he could accept Old Earth Darwinism as a working but falsifiable hypothesis. One has a better chance of overturning prevailing paradigms when one is well-versed in it. Accepting a wrong theory as a working hypothesis is no more a profession of faith than accepting the wrong idea that the square root of two is rational in order to prove it is irrational.

Let's hear from Evelyn, a graduate student in geology who just happens to be working on dating technology for her thesis (Young Earth Creationists Are NOT Geologists).

Why else am I so worked up about “Dr.” Ross and his Young Earth Creationist “geologist” friends? Currently, I date rocks for a living. In my free time, I try to date men, but mostly I’m dating rocks these days. More formally, I am a graduate student in training to become an argon-argon isotope geochronologist. Basically, I am learning how to use argon isotopes to determine dates for rocks.

I am learning that dating rocks and minerals is no easy task. For instance, this spring I am working on obtaining ten dates from a group of volcanic rocks from the Ninetyeast Ridge, a 5000 km long hotspot track in the Indian Ocean. I anticipate that my samples will range in age from about 40 million to 80 million years old. These ten age dates are going to require a solid three months of my time. Not just three months of ordinary, 9 to 5 labwork either. I am working 60+ hour weeks, and I’m also trying to do some homework now and then between samples. The past week has been particularly grueling as we (two of us– I’m working with the lab supervisor) are trying to prepare a group of samples to send off to the nuclear reactor we use to turn potassium into argon, an important step in the argon-argon dating process. For the past week, I’ve been working 14-15 hour days during the week. On the weekend, I took it easy… I worked for six hours on Saturday and for eleven hours on Sunday. Monday morning I was back at lab at 9 am, and I just returned home now (Tuesday) at 2 in the morning. Once we ship the samples off to the reactor next week, my schedule will relax again, and I’ll only work 8 to 10 hour days.

I work very hard as a geochronologist. There are many people like me who work extremely hard to produce these dates of rocks and minerals. Theoretically, someone with a Ph.D in geology appreciates how difficult these dates are to obtain and understands the science behind the isotopic dating systems. I just don’t understand how a well-educated geologist could be a Young Earth Creationist. I am angry because here is someone who is clearly NOT a very good geologist but who has GOOD geological credentials… and he’s essentially trying to discredit what is swiftly becoming my life’s work. I feel insulted, personally, by people like “Dr.” Ross. I work hard, every day, to better understand the Earth. I work hard, very hard, to obtain concrete dates for my rocks. Having a Ph.D geologist tell me that Earth is only 6,000 years old is absurd and makes me very angry and also very, very sad.

There are two issues here and it's best to separate them. First and foremost, should we give Ph.D. degrees in paleontology to students who say the Earth is less than 10,000 years old and life didn't evolve? In order to simplify the discussion, let's just consider a hypothetical honest Marcus Ross who tries to defend Young Earth Creationism in a thesis. We can imagine that the thesis will be largely devoted to refuting all of the evidence for an old Earth and for evolution.

Asked whether it was intellectually honest to write a dissertation so at odds with his religious views, he said: “I was working within a particular paradigm of earth history. I accepted that philosophy of science for the purpose of working with the people” at Rhode Island.

And though his dissertation repeatedly described events as occurring tens of millions of years ago, Dr. Ross added, “I did not imply or deny any endorsement of the dates.”Ross is a Young Earth Creationist. Of that there's no doubt. He rejects all evidence that the Earth is 4.5 billion years old. He rejects evolution in favor of a six day spree of poofing species into existence. But an old Earth and evolution are scientific facts that form the core principles of biology and geology. All scientific concepts, ideas, and theories are based on those scientific facts. You can't make sense of biology for example, unless you understand and accept evolution. ("Nothing in biology makes sense except in the light of evolution.")

If Ross rejects evolution and an old Earth then there's something seriously wrong with his science. He doesn't deserve to get the highest degree that a university has to offer. Why is that so hard for people to understand? If science isn't about scientific truth then what is science?

Part of the problem is that people make the common mistake of assuming that science is little more than doing a bunch of experiments and publishing the results in a thesis or a scientific paper. They seem to think that science is all about collecting data and little else. But science is much more than that. You also have to be able to interpret your results and put them into context. You have to formulate reasonable hypotheses, not just test them. In order to interpret your results you need to demonstrate that you understand and accept the basic concepts that have been worked out over many decades by the giants upon whose shoulders you wish to stand.

Of course there's no rule in science that says you must accept the current consensus. Quite the contrary. One of the requirements of good science is that you always question authority and try to keep an open mind. Skepticism goes hand-in-hand with curiosity. But, as the saying goes, your mind mustn't be so open that your brains fall out.

The defenders of kooks will always point to the men and women who led us in new directions and overthrew the reigning consensus. As scientists, we also revere these men and women. The trick is to distinguish the true revolutionaries from the true kooks. We all know the, mostly apocryphal, stories about how they laughed at Darwin. Wegener, and Einstein. We forget that they also laughed at Bozo the clown.

We encourage students, especially graduate students, to come up with new explanations of natural phenomena. Personally, I have a soft spot for students whose intelligence and curiosity leads then to question authority—I'm not as fond of students who simply memorize and regurgitate what's in the textbooks. Questioning is evidence of a working mind.

So, how do we resolve differences of opinion in an academic environment? How do we distinguish between a revolutionary and Bozo? The answer is we fight it out in the meeting rooms and the journals. The weapons are facts and rational thinking. If someone wants to question a scientific consensus then all they have to do is marshal the facts and evidence and present it to the scientific community in a rational and logical manner. If you are successful, then science advances another step and the scientist who came up with the idea gets lots of praise and kudos (and maybe a Nobel Prize).

Of course there's a downside. If you fail in your attempt then you may be branded as a kook unless you recognize that you fought the good fight and abandon your untenable idea. It is honorable to give up when your ideas are shot down. This sort of thing happens all the time. I've had many wonderful ideas that didn't pan out.

Dr. Fastovsky and other members of the Rhode Island faculty said they knew about these disagreements, but admitted him anyway. Dr. Boothroyd, who was among those who considered the application, said they judged Dr. Ross on his academic record, his test scores and his master’s thesis, “and we said, ‘O.K., we can do this.’ ”

... Dr. Fastovsky said he had talked to Dr. Ross “lots of times” about his religious beliefs, but that depriving him of his doctorate because of them would be nothing more than religious discrimination. “We are not here to certify his religious beliefs,” he said. “All I can tell you is he came here and did science that was completely defensible.”If a student writes a thesis that fails to convince the examining committee then the student fails or re-writes the thesis. This is a normal part of the process. You have to understand that by "failing to convince" I don't mean that the members of the Ph.D. oral committee are instantly converted to the student's way of thinking. What usually happens is that they are convinced that the thesis is a valid scientific idea even though they may not agree.

I don't think people understand this. The thesis and its defense are as much—perhaps more—about concepts and ideas than about data. If you use the world "belief" in this context then, yes, students can be failed for their "beliefs." (I prefer not to use "belief" since it's such a loaded word.) We don't flunk students because of their religious beliefs; we flunk them because their understanding of basic scientific concepts is flawed. If their science is motivated by their religion then that's just unfortunate coincidence. Students who believe in a 10,000 year old Earth should flunk a Ph.D. oral no matter how they came to believe such nonsense. They could be atheists.

What about the second issue that's mentioned above? The Ross case gets complicated because he did not do what any honest scientist should do and defend his "scientific" opinion in public. There's nothing in his thesis about Young Earth Creationism. However, his real views were well known because he had been consorting with Young Earth Creationists for some time. Ross even made a DVD attacking the fossil record. You can see part of it at The Cambrian Explosion, Lecture by Stephen Meyer and Marcus Ross. Incidentally, Marcus Ross comes across as a very well-spoken and knowledgeable young man in this video.

In this situation we have an example of someone who carefully hid his true belief from the thesis committee, or at least went out of his way to give them an excuse to avoid facing up to the main problem. This is deceptive and antithetical to how science is supposed to operate (see Some People Defend Lying for Jesus). It opens a whole other can of worms. While most of us would agree that openly advocating a young Earth in your thesis would be grounds for failure, we couldn't fail someone who effectively lied about his "scientific" opinion. We put our faith in honesty and scientific integrity whenever possible. It's the default assumption.

But here's the rub. Although there wasn't anything in his thesis about a 10,000 year old Earth it wasn't the case that his examining committee was completely ignorant of Ross' true views on paleontology. In fact, they were aware of the history. They knew Ross was a Young Earth Creationist when they admitted him to graduate school and they had no reason to suspect that he had changed his mind.

The bottom line is that faculty of Rhode Island University gave a Ph.D. degree in geology to someone they knew to be a "scientist" who believed that the Earth is only 10,000 years old. Furthermore, they gave a Ph.D. to someone who they knew was deliberately misrepresenting his "scientific" views in his thesis. They had every reason to suspect that this misrepresentation was for the sole purpose of getting the Ph.D. since Ross knew that by being honest about his rejection of a old Earth, he would not graduate. This is a double whammy since not only was Ross ignorant of the basic principles in his field but also ignorant of the principles of scientific integrity.

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