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.

Message from the Chair

 
Get yours here.

An open letter to Oprah Winfrey

 
Rebecca Watson of Skepchick publishes An open letter to Oprah Winfrey. Here's part of it ....

And then there’s Dean Radin and The Secret. Oprah, you promoted a “documentary” that claims to show proof that you can literally alter reality by wishing. We’re not talking about the power of positive thinking; we’re talking about the ability to create a pony that farts rainbows by merely thinking about it. Anything is possible, they say. They use a poor muddling of quantum physics to try to confuse people into believing their nonsense. That’s like me claiming that I have a scientific theory to back up my ability to read the future in caramel fudge sundaes: it’s called stratigraphic succession. This proven scientific theory, first developed in the early 19th century, deals with the careful study of layers, and how we can use layers to obtain a deeper understanding of time. Following in the footsteps of the revolutionary researchers who discovered this amazing theory, I simply take it to the next logical level and apply stratigraphic succession principles to the world around me, allowing me to “see” ahead into time.

Did you understand any of that? No? That’s okay, I’ll publish a whole book of that complete and utter nonsense and then come on your show and explain it to you and your audience of millions, going very slowly using the exact same words. Then you can cut me a big check and I’ll buy myself a god damned swimming pool full of caramel fudge sundae. Every year or so I’ll put out another book with the same words rearranged in a different order, and as the money rolls in I’ll laugh at all the suckers who keep me swimming in ice cream for the rest of my diabetes-ridden days.

Monday's Molecule #14

 
Name this molecule. You must be specific. We need the correct scientific name.

As usual, there's a connection between Monday's molecule and this Wednesday's Nobel Laureate. Bonus points for guessing Wednesday's Nobel Laureate(s).

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

The Central Failure of Evolutionary Psychology

 
We wish to question a deeply engrained habit of thinking among students of evolution. We call it the adaptationist programme, or the Panglossian paradigm.
S.J. Gould & R.C. Lewontin (1979) p. 584There are lots of things wrong with evolutionary psychology. One of the most important is the tendency to construct just-so stories about the evolution of human behavior. Most of these stories don't make any sense to people who really understand evolutionary theory. A recent editorial in ScienceWeek makes this very point [History Denied: The Central Failure of Evolutionary Psychology].

On close examination, it becomes apparent that the central failure of evolutionary psychology as an effort to understand human behavior is that it essentially ignores two important corollaries of this major premise concerning universality of behavior across present-day cultures. The first corollary is that any behavior pattern that is NOT universal across cultures is NOT derived from Darwinian evolution, but probably derived from cultural evolution plus individual learned experience. The second and more important corollary is that any behavior pattern within a culture that is not universal across decades, or generations, or centuries, or even millennia is also NOT derived from Darwinian evolution, and more likely derived from cultural evolution plus individual learned experience. On these small time scales, Darwinian evolution just doesn't have enough time to work and cannot be responsible for any behavior changes within a culture.

Thus the central failure of evolutionary psychology is the failure to recognize that universality across both time AND geography are necessary to identify a behavior pattern derivable from Darwinian evolution.

Does Darwinism (sic) Predict Anything

 
The collection of IDiots at Cornell University have put together a webpage called The Design Paradigm. It consists mostly of the usual whining by commentators who are afraid to use their real names on a blog. (In fairness, I would also be embarrassed to use my real name on some of those postings.) One anonymous IDiot asks Does Darwinism predict anything?

We’ve heard over and over again from the Darwinist side of this debate that ID offers no novel predictions. Intelligent design actually offers many intriguing and novel predictions (you can head over to ResearchID.org to see some of them), but what about Darwinism?

I would love it if some of our commentators or readers would offer what they think are predictions of Darwinism. The definiton of Darwinism that we’ll use is the following proposition:

"The origin and diversity of life has occured solely by undirected processes such as natural selection."

For a prediction to count, of course it will have to be one that only Darwinism makes.

These are supposed to be university students. The fact that they can't tell the difference between evolutionary biology and "Darwinism" speaks volumes about their intelligence. It's not as though the difference hasn't been explained over and over and over and over ...

The "definition" they use is not a definition of evolution and it's not a description of evolutionary theory. However, it is a reasonable conclusion (or "prediction") based on everything we know about science. Purists will argue that ruling out God in evolution is philosophical naturalism and this goes beyond the methodological naturalism that's required in science.

Whether this is strictly true or not is debatable but that's not the point. The IDiot students have carefully phrased the question in a way that requires scientists to prove a negative. The kind of "predictions" they're looking for are those that "prove" unguided and undirected processes.

Don't believe me? Just watch how they respond to my evolutionary theory-based prediction that whenever we start using a new drug to treat bacterial infections we will soon discover bacteria that are resistant to the drug.

This is standard freshman biology stuff. Either the IDiot club at Cornell is full of people who don't understand first year biology or they intend to use rhetorical trickery to reject all predictions that they don't like.

Meanwhile, I'm going to hop on over to ResearchID.org to see what kind of predictions the IDiots have come up with.

IDiot Predictions

 
ResearchID is a Wiki devoted to Intelligent Design Creationism. One of the pages conatins Predictions of intelligent design. Let's see what kind of "predictions" you can generate by postulating a supernatural creator who's in charge of designing life.

It's really hard to sort though the gobbledygook to find solid predictions but I think I've found four that count as partially scientific. For each of them I'll quote the ReseardID.org prediction in yellow. My prediction follows.

Much so-called “junk DNA” will turn out to perform valuable functions.

The classic Darwinist prediction about junk DNA would be that none of it is really junk. That's because classic Darwinism attributes selectable function to almost everything and there's no place for things that have evolved by accident. My prediction is that most junk DNA will always be junk. That is, it has no function in the cell and is free to evolve randomly by accumulating mutations that become fixed by random genetic drift.

Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).

Based on my understanding of evolutionary biology I also predict that we will continue to discover natural structures that look like molecular machines. Such structures will be complex and they will catalyze highly specific reactions. This is exactly what we expect of an evolved structure.

In general, vestigial organs (sic) will yield some function for the organism.

Many vestigial structures such as rudimentary eyes in cave-dwelling fish, tiny wings on flightless beetles, small useless hind limbs within the body of whales, wisdom teeth that fail to erupt, and pseudogenes, will continue to provide evidence for evolution and evidence against an "intelligent" designer.

The correlation between habitability and discovery will strengthen.

IDiots will continue to say the stupidest things in an effort to sound scientific.

Oprah Has a Secret

 
UPDATE: Mike beat me to it. Read his posting [Here's The Secret: Blame the Victim]. He has videos!

Oprah Winfrey is a sucker for new-age psycho-babble. The latest people to dupe her are some kooks who've discovered "THE SECRET." The secret, as it turns out, is to think positively and radiate good thoughts. If you do that then good things will come back to you.

Apparently this latest version of self-help nonsense was triggered by a movie called The Secret produced by an Australian named Rhonda Byrne. (Why is it always Australians who cause trouble?) She discovered that the The Secret has been around since 3500 B.C., although it seems to have been forgotten from time to time. (Like you're going to forget the secret that makes your life wonderful?)

It wasn't long before others recognized a good thing. In this case people like Rev. Dr. Michael Beckwith and James Arthur Ray. These are two of the charlatans who conned Oprah into advertising their ignorance on national television.

If you want to profit from the secret it helps if you accept Jesus as your Saviour. (Apparently atheists aren't very good at radiating good thoughts. Who knew?)

Michael says The Secret involves the laws of the universe and they, in turn, describe the nature of how God works. "[Jesus] said, 'Pray believing that ye have that ye may receive.' That's The Secret in a nutshell," he says. "Pray believing and feeling and sensing that you already have it, and then you're available to receive it."

Millions of American and Canadian women (and a few hundred men) have been transformed by discovering The Secret. In less than a week their lives have changed dramatically. Oprah broadcast the first show about ten days ago and she had to follow up with a repeat performance yesterday. She was just as gullible the second time, and so was the audience.

Maureen Dowd watched the Oprah show and wrote a column aboout it in today's New York Times [A Giant Doom Magnet]. Here's part of what she says ..

So I was sitting around watching “Oprah” yesterday afternoon when I realized how I could stop W. and Crazy Dick from blowing up any more stuff.

All I needed to do was Unleash my Unfathomable Magnetic Power into the Universe!

Energy flows where intention goes. Or maybe it’s the other way around.

Anyhow, Oprah taught me how to stop abusing myself and learn The Secret. I finally get it: because the Law of Attraction dictates that like attracts like, my negativity toward the president and vice president is attracting their negativity and multiplying the negative vibrations in the cosmos, creating some sort of giant doom magnet.

In spite of Maureen's sarcasm, this is actually very serious. If people like Oprah Winfrey can't tell the difference between truth and nonsense then we're in big trouble. It's bad enough that she fell for John Edward. Now she falls for this?

People should speak out. We need to get out the message that this stuff is unacceptable in a rational society. It's weird. It's like believing in witchcraft.

Gene Genie: The First Issue

 
Gene Genie is a blog carnival that discuses human genes.The first installment of Gene Genie has been posted on ScienceRoll.

Gene Genie is a new carnival and judging by the first issue it's going to be a great one. You can learn about all kinds of things. Check it out.

Here are the human genes covered today: GDF5, DARPP-32, HSPA5, GAA (acid α-1,4-glucosidase, SHH (sonic hedgehog). Only 23,995 to go!

The coffee plant genes, SUS1 and SUS2. are also described.

Shermer v Dembski

 
Michael Shermer and Bill Dembski debated evolution and intelligent design last night. You can read two very different versions of the debate. Jason Rosenhouse posted a summary on The Panda's Thumb. He thought Shermer was good and Dembski wasn't. Salvador Cordova over at Uncommon Descent says Dembski won the debate.

Basing my conclusion entirely on the credibility of the two reporters, I'd say Shermer had a good night.

A Prelude to War

 

WASHINGTON (Reuters) - Stepping up the Bush administration's financial pressure on Iran over its nuclear program, the U.S. Treasury Department labeled three Iranian companies on Friday as proliferators of weapons of mass destruction, banning U.S. transactions with them.

The Treasury, invoking an executive order recently used against Iranian state-owned banks, said it would also seek to freeze any U.S. assets of Kalaye Electric Co., Kavoshyar Co. and Pioneer Energy Industries Co.

It said the companies are either owned by, controlled by or acting for the Atomic Energy Organization of Iran, the government agency that manages Iran's overall nuclear program.

"Treasury is taking this action to deny Iran access to the materials and services that support its nuclear ambitions," Stuart Levey, the Treasury's under secretary for terrorism and financial intelligence, said in a statement. He added that the action was consistent with the U.N. Security Council's recent resolution aimed curbing Iran's nuclear program.

Some People Defend Lying for Jesus

 
Judging by the number of different opinions on the Marcus Ross case, there appear to be a variety of standards for the Ph.D. degree at different universities. Several bloggers think that it's okay to lie in your thesis about which scientific facts you accept and which ones you reject.

The University of Toronto has a Code of Behaviour on Academic Matters that specifies how students and teachers are supposed to behave in an academic environment. Here's part of the preamble,

What distinguishes the University from other centres of research is the central place which the relationship between teaching and learning holds. It is by virtue of this relationship that the University fulfils an essential part of its traditional mandate from society, and, indeed, from history: to be an expression of, and by so doing to encourage, a habit of mind which is discriminating at the same time as it remains curious, which is at once equitable and audacious, valuing openness, honesty and courtesy before any private interest.

This mandate is more than a mere pious hope. It represents a condition necessary for free enquiry, which is the University's life blood. Its fulfilment depends upon the well being of that relationship whose parties define one another's roles as teacher and student, based upon differences in expertise, knowledge and experience, though bonded by respect, by a common passion for truth and by mutual responsibility to those principles and ideals that continue to characterize the University.

This Code is concerned, then, with the responsibilities of faculty members and students, not as they belong to administrative or professional or social groups, but as they cooperate in all phases of the teaching and learning relationship.

Such cooperation is threatened when teacher or student forsakes respect for the other—and for others involved in learning—in favour of self-interest, when truth becomes a hostage of expediency. On behalf of teacher and student and in fulfilment of its own principles and ideals, the University has a responsibility to ensure that academic achievement is not obscured or undermined by cheating or misrepresentation, that the evaluative process meets the highest standards of fairness and honesty, and that malevolent or even mischievous disruption is not allowed to threaten the educational process.

Call me old-fashioned, but I believe in those values. I believe that truth and honesty are essential requirements in a university environment. I believe that freedom of enquiry is threatened when a student misrepresents the truth and makes it hostage to expediency. I believe that students who violate the fundamentals of a university should not graduate, especially with the highest degree that the university can offer (Ph.D.).

Jason Rosenhouse put up a message on EVOLUION BLOG [Why is This in the New York Times?]. Jason says,

This is a complete non-story. By all accounts Ross produced competent scientific work. That he was effectively an actor playing a character reflects very badly on him, but does not reflect badly on URI. If he chooses to use his degree to lend credibility to asinine religious ideas that's his business. The rest of us will have to settle for bashing him for the things he now does. It's not the job of URI, or any other university, to pass judgment on the religious views of others.

It's not the job of a university to discriminate on the basis of religious beliefs. However, it is the job of a university to uphold minimal standards of honesty and accuracy. Ross misrepresents his position when he writes about 65 million year old fossils in his thesis. He doesn't believe that any of those fossils are more than a few thousand years old. He can't honestly discuss explanations for the extinction of marine reptiles at the end of the Cretaceous without revealing that he rejects any explanation that dates this event to the ancient past.

But apparently that's exactly what he didn't do. He misrepresented his true scientific opinion in his thesis. He did this deliberately because he knew that telling the truth in his thesis would probably mean it would be rejected.

John Pieret says,

Some people have questioned whether such a person is engaging either in a mammoth mental disconnect or deliberate deception and, in turn, whether he should be awarded the Ph.D. I think that that is a dangerously slippery slope to climb onto, given the relative risk posed.

The difference between "mammoth mental disconnect" and "deliberate deception" isn't as great as you might imagine. It only requires that before deceiving others you take the time to deceive yourself. In either case the candidate is guilty of stupidity for not accepting the scientific evidence and deception for hiding it. Universities should not award Ph.D.'s to students who are either stupid or intellectually dishonest; and they should definitely not award advanced degrees to students who are both.

This is a slippery slope. It's only asking for trouble when we excuse stupidity and dishonesty because it's part of a religious belief. You don't deserve a free pass through a university just because you get your ignorance from the Bible. Religious students should be subjected to the same rigorous standards as all other students.

No atheist student would get a Ph.D. in paleontology if he rejected all the evidence for an ancient Earth and claimed that our planet was built by aliens 10,000 years ago, and all species were created in just a few days. Such a student would be laughed out of the Ph.D. oral exam—if he ever got to it.

Another Boring Just-so Story

 
From ScientificAmercian.com.

Child molestation and rape top the social taboo list, according to a survey of 186 people between the ages of 18 and 47, and smoking marijuana ranks lowest among the 19 choices of forbidden behavior. In the middle—worse than robbing a bank but better than spousal murder—lies incest between brothers and sisters. Given the deleterious genetic impacts of offspring from such mating, some researchers have suggested that there may be an evolved mechanism designed to prevent that from occurring. And now evolutionary psychologist Debra Lieberman of the University of Hawaii–Honolulu believes she may have elicited some of its functions from this simple questionnaire....

The evolutionary psychologists hypothesize that some form of mental mechanism assesses various cues to come up with an estimate of how related two people are. "The real question is: What are these cues?" Lieberman says. "A potent cue is seeing your mom caring for a newborn. That would have served as a great cue that the infant is a sibling, at least a half sibling." But for younger siblings, who would have no opportunity to make this observation, another cue might be the amount of time spent living with another child/potential sibling. Dubbed the "Westermarck hypothesis"—after the Finnish sociologist who first noted it in a book published in 1889—it posits that children reared together do not often end up being sexually attracted to each other.

How to Save Yourself in a Falling Elevator

 
Friday's Urban Legend: FALSE

Imagine the cable on your elevator breaks and you're in free fall for ten stories. What do you do? Maybe you should wait until the elevator is just about to hit the ground then jump up as high as you can?

Bible Skeptics Conference

 
Come with us to the Bible Skeptics Conference in Whitby (East of Toronto) on Friday Feb. 23 and Saturday Feb. 24.

What the heck is a Bible Skeptics Conference? It's not what you think ...

At this conference named after you, the skeptic, we hope to challenge your views on evolution and ultimately the meaning of life. We promise no singing (not that there's anything wrong with that), no offering plate and no pressure to join a denomination or church - just reasonable arguments for the existence of a creator - and that His book is the Bible.

It should be a barrel of fun! (The Institute for Creation Research will supply the barrels and the fish.)

Another Canuck Atheist

 

I had lunch at the Faculty Club today with a fellow atheist who lives in the Toronto area. Mike McCarron and I have a lot of things in common so we'll undoubtedly be seeing more of each other in the future. Meanwhile, check out his blog Mike's Weekly Skeptic Rant.

Gene HSPA5 Encodes BiP-a Molecular Chaperone

 
Molecular chaperones are proteins that help other proteins to fold properly (see Heat Shock and Molecular Chaperones). The most important chaperones were indentified as heat shock proteins because they were produced following exposure of cells to excess heat. Their role in heat shock is to repair misfolded proteins and their role in normal cells is to assist in the proper folding of newly synthesized proteins.

The most important chaperone is HSP70 (Heat Shock Protein, M_r=70,000). It is present in all normal cells where it binds to polypeptide chains as they are being synthesized. Most cells contain multpile versions of HSP70. The different members of the gene family occupy different cell compartments. For example, there are distinct HSP70 chaperones in mitochondria, chloroplasts and cytoplasm.

The endoplasmic reticulum (ER) is a network of membranes within eukaryotic cells. Proteins that cross the ER membrane end up inside the ER in a special compartment that's isolated from the cytpolasm. Most of these proteins are destined to be exported from the cells in vesicles that bud off of the ER.

Proteins that need to be imported into the lumen of the ER are synthesized on the membrane surface. As they exit the ribosome tunnel they pass directly through a pore in the membane. When they reach the interior of the ER they are helped to fold by a member of the HSP70 gene family called BiP (Binding Protein) or GRP78 (Glucose Regulated Protein). BiP binds to the newly synthesized peptide while it is being made and while it is passing through the ER pore complex.

The HSP70 chaperones are interesting because of the role they play in protein synthesis but they are also interesting because they are the most highly conserved proteins in all of biology. This makes them ideal candidates for studies of molecular evolution. Several thousand sequences are available (HSP70 Sequence Database). The BiP gene in mammals is called HSPA5—a name choice made by the HUGO (Human Gene Organization) Naming Committee [HSPA5]. (HUGO tends to ignore names given to homologues in other species and choose human specific names. The gene is called BiP in most other species.)

HSPA5 is located near the end of the long arm of chromosome 9 at 9q33-q34.1 (chromosome map NCBI, chromosome map UCSC Genome Browser). The Entrez Gene Locus is GeneID=3309 and it lists 7 different independently-cloned genomic sequences and 8 full-length cDNAs. My favorite site is the SwissProt database (P11021) because it combines all the sequence information from each clone into one annotated sequence.

The HSPA5 gene has 8 exons in a relatively compact gene spread out over 6.5kb (6,500 bp). See the sequence [here]. There's nothing particularly unusial about this gene other than the fact that the introns are smaller than normal. All of the mamalian genes have the same intron/exon organization but other eukaryotic BiP genes may have fewer introns or none ar all.


The gene encodes a proein of 654 amino acid residues with a relative molecular mass of 72,300 (close to 70kDa, which is typical for HSP70's). The protein contains an N-terminal leader sequence that controls its import into the ER and a C-terminal ER retention signal that keeps it in the ER lumen. The rest of the sequence closely resemble all of the other members of the HSP70 gene family.

Bush Flubs the Message

 
The Washington Post reports considerable skepticism about the upcoming war against Iran. Apparently there are people who are suspicious about the latest propaganda effort [Skepticism Over Iraq Haunts U.S. Iran Policy].

They have every reason to be suspicious, especially since President Bush can't seem to stay on message.

In yesterday's White House news conference, Bush grappled with the issue head-on. "What makes you so certain," a reporter asked Bush, of the military's charge that "the highest levels of Tehran's government" are responsible for shipments of lethal weapons to Iraq for use against U.S. troops?

Bush contradicted the military's account, saying, "We don't know . . . whether the head leaders of Iran ordered" it.

"But here's my point," he added. "Either they knew or didn't know, and what matters is, is that [the weapons] they're there."

Oops. That's not the right answer, Dubya. Once you're coerced the military leaders into sticking their necks out you've got to back up the big lie. You were supposed to say that you have secret information linking Iran's leaders to the killing of brave American soldiers.

Dick will not be happy. Now he'll have to go on the Sunday talk shows and drop hints about what he learned when he visited CIA headquarters.

The IDiots Confess to Deliberate Quote Mining

 
You won't believe this. Scordova has a posting on Uncommon Descent titled [quote mine] “we regard as rather regrettable the conventional concatenation of Darwin’s name with evolution”. Here's what he said,

Here is a quote mine for the day which I found in an article Bill referenced earlier (see: Start the revolution without ID). The quote is by one of the world’s leading scientists, Carl Woese:

we regard as rather regrettable the conventional concatenation of Darwin’s name with evolution

I agree. Let me suggest that if the conventional concatenation is “Darwinian evolution” a better concatenation would be “designed evolution” or even (hehe) “created evolution”.

Here's a copy of the original article with the "quote mine" underscored in red.

The IDiots have been told time and time again that there's more to evolution than just Darwinian natural selection. They've been told that use of the word "Darwinism" as a synonym for evolution is wrong. Now, they read an article where some prominent evolutionary biologists make the same point and even give one of the other mechanisms.

So, what do the IDiots do? They quote mine and then the announce to the world that they have deliberately taken a quote out of context. (That's what quote mining is.) Are they really as stupid as this suggests, or are they evil as Dawkins once feared?

I'm Spartacus

 
We are all Spartacus.

Can You Hear the Drums Beating?

 
The International Herald Tribune reports on how Bush defends buildup of pressure on Iran.

Under pressure to explain the buildup of American military and economic pressure on Iran, President George W. Bush said Wednesday that highly lethal explosives smuggled into Iraq had certainly come from an arm of the Iranian government, and that it did not much matter whether top Iranian government officials had sanctioned the smuggling.

Iran has WMD—weapons of minor destruction—and they're sneaking them into Iraq. Does this sound familiar? Who is providing this information about Iran? Is it the same people who told us about WMD's in Iraq and how Saddam Hussein was in cahoots with Al-Qaeda?

Where is Dick Cheney?

There's an old saying in Tennessee — I know it's in Texas, probably in Tennessee — that says, fool me once, shame on — shame on you. Fool me — you can't get fooled again.
                                                   George W. Bush 2002

The Anfinsen Experiment in Protein Folding

Disulfide bridges can be disrupted by treating a protein with 2-mercaptoethanol (HS-CH₂-CHOH). The bond between the two sulfurs in the protein is broken and a new bond is created between two sulfurs at the end of two molecules of 2-mercaptoethanol. (2-mercaptoethanol used to be called β-mercaptoethanol or βME.) Treatment with 2-mercaptoethanol is now standard procedure for denaturing proteins. For example, 2ME is always included when proteins are prepared for SDS polyacrylamide gel electrophoresis.

Anfinsen wanted to show that the information for protein folding resided entirely within the amino acid sequence of the protein. He choose ribonuclease A as his model for folding but he couldn't completely denature the protein unless he treated it with the denaturant urea plus 2ME to break the disulfide bridges.

Under those conditions, the protein unfolded. It would refold spontaneously once he removed urea and 2ME from the folding solution. Ribonuclease A regained biological activity under those conditions. This demonstrated that refolding could take place in vitro.

Anfinsen discovered that removing 2ME but not urea led to recovery of 1% of the activity. This is attributed to the formation of random disulfide bridges between the 8 cysteines present in the protein. There are 105 different possibilities (7x5x3x1) so the 1% recovery makes sense. It also shows that the correct three-dimensional conformation must be achieved fairly rapidly when urea is removed since most of the protein under those conditions becomes active.

However, recovery is not 100%. Mistakes are made in vitro and presumably in vivo as well. This led to the discovery of an enzyme called protein disulfide isomerase (PDI)—an enzyme that catalyzes reduction of incorrect disulfide bonds and allows a protein trapped in an incorrect conformation to unfold and try again.

PDI is a ubiquitous enzyme as expected from its important role in proper folding. The active site of the enzyme contains a disulfide (shown as two yellow sulfur atoms in the figure). Thus, the enzyme acts very much like 2-mercaptoethanol, catalyzing a disulfide exchange reaction where the incorrect disulfide bridge in the misfolded protein is reduced and PDI is oxidized. (The correct name of the protein is "thiol-disulfide oxidoreductase. Oxidoreductases form a large class of very important enzymes.)

The enzyme preferentially recognizes incorrect disulfide bridges since these tend to be exposed on the surface of the misfolded protein, whereas correct disulfide bridges are usually buried in the hydrophobic interior of the correctly folded protein.

Nobel Laureate: Christian B. Anfinsen

 
The Nobel Prize in Chemistry 1972.

"for his work on ribonuclease, especially concerning the connection between the amino acid sequence and the biologically active conformation"

Christian B. Afinson won the Nobel Prize in 1972 for his studies on the folding of ribonuclease A and the role of disulfide bonds. (See Disulfide Bridges Stabilize Folded Proteins and The Anfinsen Experiment in Protein Folding.) Anfinsen made some of the key observations demonstrating that protein folding is spontaneous. Here's part of the presentation speech by Bo Malmström,

Every living organism has its own characteristic pattern of enzymes. It can also produce a copy of itself, and this progeny has the same enzymes. An important question concerns the source of the information which has to be passed on from generation to generation for the enzyme pattern to be preserved. We know, thanks to contributions which have led to earlier Nobel Prize awards, that a specific molecule, called DNA, serves as the carrier of the traits of inheritance. These traits are expressed by DNA controlling the synthesis of enzymes. DNA accomplishes this by determining the sequence of the amino acids making up a particular protein molecule. An active enzyme does not, however, consist just of a long chain of amino acids linked together, but the chain is folded in space in a way which gives the molecule a globular form. What is the source of the information responsible for this specific folding of the peptide chain? It is this question in particular which has been the concern of Anfinsen's investigations. In a series of elegant experiments he showed that the necessary information is inherent in the linear sequence of amino acids in the peptide chain, so that no further genetic information than that found in DNA is necessary.

Snow Day

 
Today's a snow day in my town. Here's what the kids are doing in the park at the end of our street.

Now the IDiots Don't Get Evolution

 
Bill Dembski says Start the Revolution without ID. He's got his knickers in a knot over a paper that was originally published in the Jan. 25, 2007 issue of Nature. An updated version is available [here]. The original reference is,

Goldenfeld, N. and Woese, C. (2007) Biology’s Next Revolution. Nature 445:369-371.

The paper discusses Carl Woese's ideas on early evolution. The same ideas that I covered in The Three Domain Hypothesis (part 6). This isn't new, lots of people have written about it over the past dozen years or so. The idea is that rampant horizontal gene transfer obscures early phylogeny and makes it difficult to distinguish the relationship between eukaryotes and primitive prokaryotes. (It means the Three Domain Hypothesis is dead.)

Dembski probably doesn't know any of this because he's scientifically illiterate, like most IDiots. However, he can read an abstract ...

ABSTRACT: The interpretation of recent environmental genomics data exposes the far-reaching influence of horizontal gene transfer, and is changing our basic concepts of organism, species and evolution itself.

That's enough to trigger the following knee-jerk reaction from an IDiot.

So here’s the deal: When trying to derail ID in the court of public opinion, say that there is NO controversy over evolution. Say that scientists have achieved a consensus and that evolution is as well established as the earth going around the sun. But when out of the public eye, feel free to publish on how the entire field of evolutionary biology is in disarray and in need of a “next revolution.”

No, Bill, you just don't get it. Nobody is questioning the fact of evolution. We're just trying to figure out exactly how it works. You know, science and all that? I though that's what you want us to do?

What Woese and others are doing is sorting out what happened at the beginning of life on this planet, approximately 3.8 billion years ago. That's pretty amazing when you think about. A few decades ago, nobody would have thought that science could address this problem. But that's not good enough for the likes of Bill Dembski. Dembski thinks we should have all the answers before we can say with confidence that life has evolved over the past 3 billion years.

The irony here is that Dembski and his fellow IDiots refuse to tell us anything about their explanation. Dembski is even being coy about whether the Earth is that old. According to Dembski's logic, Intelligent Design Creationism must be bankrupt because they can't even give us a simple description of how humans appeared, and when.

Oh, and concerning that little quip about "out of the public eye." This was published in Nature for God's sake. If even Dembski can find it, then it's hardly out of the public eye, is it?

A Must-read From Sean Carroll

 
Sean Carroll has just posted an article on Cosmic Variance that everyone just has to read—especially the appeasers who think that Richard Dawkins is harming the "cause." Read Thank You, Richard Dawkins right now and enjoy your St. Valentine's Day.

Best and Worst of the Year Awards

 
New Mexicans for Science and Reason have just announced their Best and Worst of the Year Awards for 2006. Two of the awards in the "worst" category were no-brainers.

The "New Word: Pignorant" Award goes to Jonathan Wells, whose new book "The Politically Incorrect Guide to Darwinism and Intelligent Design" contained so many egregious falsehoods that the scientific critics decided to shorten the phrase "Pig Ignorant" to simply "PIGNORANT" in order to cope (Sept.).

The "Last Nail in The Coffin of ID" Award goes to William Dembski, who absolutely destroyed any remaining credibility Intelligent Design may have had, when he responded to Judge John E. Jones' powerful ruling of December 2005, not by defending ID in science journals, nor in courts of law, but by parodying the judge's decision with an Internet video that featured animated farting sounds. The Awards Committee had the most trouble with this award, as several members wanted to name it the "Not So Noble Gas" Award. However, all members were agreed that Dembski edged out Wells and Coulter, and did the most damage to ID this year. (Dec.)

[Hat Tip: John Pieret of Thoughts in a Haystack]

Happy Valentine's Day

Tangled Bank #73

 
Tangled Bank #73 is up at Lab Cat.