Gene Genie #7

 
The 7th version of Gene Genie has been posted at Gene Sherpas.

Christianity Today Poll

 
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[Hat Tip: Friendly Atheist]

Methodological Naturalism

UPDATE: This post no longer reflects my opinion on this subject. I now believe that science is not bound by methodological naturalism. Science as a way of knowing is free to investigate claims of the supernatural. [Is Science Restricted to Methodologial Naturalism?] [Accommodationism in Dover] [Methodological Naturalism].

In a comment on The Neville Chamberlain Atheists thread "slc" repeats a claim that he/she has been making for several months. I started to reply on that thread but the comment grew too long so I'm making it into a separate posting.
"slc" says,

As I have commented on this and other blogs, Prof. Morans' position, along with Myers and Dawkins is that philosophical naturalism is science and therefore science == atheism.

Indeed, I've seen you make that claim several dozen times. I'm glad it makes you happy.
For the record, I am an atheist so naturally I'm a philosophical naturalist. (Duh!) But I do not claim that good science requires philosophical naturalism. I claim that methodological naturalism is a requirement.
Most of my arguments [e.g. Theistic Evolution: The Fallacy of the Middle Ground] are based on the idea that methodological naturalism is the foundation of science and that, therefore, science is effectively atheistic in practice. I've been trying to show that methodological naturalism all by itself is capable of highlighting all of the important conflicts between science and religion. In my opinion, it's simply not true that the only conflicts that arise are when you make the leap to philosophical naturalism.
In this sense—and this sense only—I'm defending the concept of non-overlapping magisteria (NOMA) promoted by Stephen Jay Gould. As long as religion sticks to it's proper domain (magisterium) and stays out of science then it's okay (e.g., I have no problem with Deism and most versions of Buddhism). The problem is that most believers want to violate the rules of methodological naturalism and still be praised for being good scientists. One of the ways they rationalize this obvious conflict is to try and equate methodological naturalism with philosophical naturalism. They claim that it's okay to allow a little bit of religion into science because science is not the same as atheism. We see an example of that in "slc"'s attempt to dismiss what many of us are saying about the conflict between science and religion.

The Neville Chamberlain Atheists

There seem to be a lot of people who don't understand the origin of the term "Neville Chamberlain School of Evolutionists." I've seen it attributed to PZ Myers and even to me.

For the record, it comes from The God Delusion and I'm going to quote from the Dawkins' book below. But before doing that I want to acknowledge that I don't like the term very much even though I used it several times last Fall. I think it does an injustice to Neville Chamberlain. Lately I've been referring to this group as just appeasers but now I prefer to use "accommodationist" to describe them.

If you recognize yourself in the description below and want to offer up a term that fits with your position then please make a comment and we'll see if we can reach an agreement about what to call you.

Another prominent luminary of what we might call the Neville Chamberlain school of evolutionists is the philosopher Michael Ruse. Ruse has been an effective fighter against creationism, both on paper and in court. He claims to be an atheist, but his article in Playboy takes the view that

we who love science must realize that the enemy of our enemies is our friend. Too often evolutionists spend time insulting would-be allies. This is especially true of secular evolutionists. Atheists spend more time running down sympathetic Christians than they do countering creationists. When John Paul II wrote a letter endorsing Darwinism, Richard Dawkins's response was simply that the pope was a hypocrite, that he could not be genuine about science and that Dawkins himself simply preferred an honest fundamentalist.

From a purely tactical viewpoint, I can see the superficial appeal of Ruse's comparison with the fight against Hitler: "Winston Churchill and Franklin Roosevelt did not like Stalin and communism. But in fighting Hitler they realized that they had to work with the Soviet Union. Evolutionists of all kinds must likewise work together to fight creationism." But I finally come down on the side of my colleague the Chicago geneticist Jerry Coyne, who wrote that Ruse

fails to grasp the real nature of the conflict. It's not just about evolution versus creationism. To scientists like Dawkins and Wilson [E.O. Wilson, the celebrated Harvard biologist], the real war is between rationalism and superstition. Science is but one form of rationalism, while religion is the most common form of superstition. Creationism is just a symptom of what they see as the greatest enemy:religion. While religion can exist without creationism, creationism cannot exist without religion.

Dawkins agrees with Coyne, and so do PZ Myers, me, and many others. The real battle is between rationalism and superstition and that's why we have to point out the superstitious beliefs of Theistic Evolutionists just like we point out the superstitious beliefs of Intelligent Design Creationists.

Some of you are only interested in the American struggle to keep Intelligent Design out of the schools—a serious tactical error, as far as I'm concerned. In that battle you may see the Pope as an ally. That's fine. You can be accommodationists if it suits you in order to win that fight. But don't assume that your fight is my fight. That's where you make a mistake in criticizing my position and that of Dawkins etc.

Glycogen Storage Diseases

Type 0: Hypoglycemia due to lack of glycogen synthase [OMIM 240600, OMIM 138571]

Glycogen synthase is the enzyme required for glycogen synthesis [Glycogen Synthesis]. There are two forms of the enzyme; liver and muscle. The muscle form is found in many different tissues but the liver version of the enzyme is only found in liver cells. Mutations in the gene for the liver enzyme (GTS2) cause glycogen storage disease type 0.

The disease is usually recognized in infants who have very low blood sugar (hypoglycemia) after a short fast. The low sugar is due to the fact that there's no store of glycogen in the liver. In normal cases, the liver stores glucose as glycogen right after a meal then breaks it down as blood glucose is depleted. In the absence of liver glycogen synthase the maintenance of blood sugar levels is impaired.

Here's what OMIM has to say about typical cases.

Gitzelmann et al. (1996) described 3 children with liver glycogen synthase deficiency from 2 German families and compared the observations with the previously published 3 families comprising 8 patients. The 2 index cases presented with morning fatigue, had ketotic hypoglycemia when fasting which rapidly disappeared after eating, and hepatic glycogen deficiency with absent or very low hepatic glycogen synthase activity. Metabolic profiles comprising glucose, lactate, alanine, and ketones in blood were typical for hepatic glycogen synthase deficiency. Symptoms were rapidly relieved and chemical signs corrected by introducing frequent protein-rich meals and nighttime feedings of suspensions of uncooked corn starch. The discovery of oligosymptomatic and asymptomatic sibs suggested that there are persons with undiagnosed hepatic glycogen synthase deficiency. Gitzelmann et al. (1996) stated that the disorder should be sought in children who, before the first meal of the day, present with drowsiness, lack of attention, pallor, uncoordinated eye movements, disorientation, or convulsions, and who have hypoglycemia and acetone in the urine.

Type I: Von Gierke's Disease: Deficiency in glucose 6-phosphatase [Ia OMIM 232200, Ib OMIM 602671, Ib OMIM 232220, Ic OMIM #232240]

The synthesis of glucose (gluconeogenesis) in the liver ends with glucose 6-phosphate. It can be stored as glycogen in the liver for use later on or it can be converted to glucose. Glucose is then secreted into the blood stream where it can be taken up by muscle cells. The cycling of glucose between muscle and liver is called the Cori Cycle.

One of the key enzymes is glucose 6-phosphatase. This is the enzyme that removes the phosphate group from glucose 6-phosphate to make free glucose. In mammals, this enzyme is located in the membranes of the endoplasmic reticulum. The enzyme is part of a complex that includes a glucose 6-phosphate transporter (G6PT) and a phosphate transporter. G6PT moves glucose 6-phosphate from the cytosol to the interior of the ER where it is hydrolyzed to glucose and inorganic phosphate. Phosphate is returned to the cytosol and glucose is transported to the cell surface (and the bloodstream) via the secretory pathway.

The other enzymes required for gluconeogenesis are found, at least in small amounts, in many mammalian tissues. By contrast, glucose 6-phosphatase is found only in cells from the liver, kidneys, and small intestine, so only these tissues can synthesize free glucose. Cells of tissues that lack glucose 6-phosphatase retain glucose 6-phosphate for internal carbohydrate metabolism.

Defects in glucose 6-phosphatase affect mostly liver and kidneys where stored glycogen can accumulate to high levels due to the fact that it can't be broken down to free glucose for secretion into the blood stream. Glycogen storage disease Ia results from mutations in the catalytic subunit of glucose 6-phosphatase (G6PC gene) while Ib and Ic are caused by mutations in the transporter subunits.

The major problem is hypoglycemia (low glucose) and lactic acidemia due to inefficient conversion of lactic acid to free glucose. These can be fatal but nowadays the symptoms are treated by feeding carbohydrates at regular intervals throughout the day and though a gut tube at night. This is an autosomal recessive disease.

Type II (Pompe Disease): Deficiency of α-glucosidase [OMIM #232300, OMIM 606800]

Glycogen granules are taken up by lysosomes where they are broken down by a pathway that's different from the normal glycogen degradation pathway. One of the key lysosomal enzymes is α1,4-glucosidase. Mutations in the gene for this enzyme cause glycogen storage disease type II.

This is a very severe form of the disease. Although glycogen breakdown in lysosomes is relatively minor in terms of overall glycogen metabolism, the inability to process glycogen granules leads to their accumulation in lysosomes and consequent disruption of many important lysosomal functions. This disruption takes place in all cells and all tissues.

In the classic cases, infants are inactive and hypertonic with enlarged hearts. Death usually occurs before the first year, usually from heart failure. An adult onset version is known. It usually begins with respiratory difficulties and often ends in death from ruptures of the arteries or respiratory failure.

Type III: (Cori Disease): Defects in glycogen debranching enzyme [OMIM 232400, OMIM 610860]

The glycogen debranching enzyme is required for the complete mobilization of glucose from glycogen. The standard glycogen phosphorylase enzyme will lop off glucose residues until it come to within for residues of a branch point in the glycogen chain. This produces a truncated glycogen molecule known as limit dextrin.

Further degradation of glycogen requires the activity of the debranching enzyme which actually has two separate activities: a glucanotransferase activity that transfers glucose residues from the end of one branch to the end of another, and a glucosidase activity that chops off the last glucose residue on a branch. The gene is the AGL gene (amylo-1,6-glucosidase, 4-α -glucanotransferase) in humans and the GDE gene (glycogen debranching enzyme) in many other species.

There are several subtypes of type III glycogen storage disease. They all result from mutations in the AGL gene. The most common type is IIIa where debranching activity is missing in both liver and muscle cells [see The Cori Cycle]. Patients have muscle weakness and liver problems similar to those in von Gierke's Disease (type I) but the symptoms are milder and not usually life threatening.

In type IIIb the deficiency in debranching enzyme is only detectable in liver. This is probably due to lower production of functional enzyme that only affects liver cells where more debranching enzyme is needed than in muscle cells.

Types IIIc and IIId are quite rare. They only affect the glucanotransferase activity (IIIc) or the glucosidase activity (IIId).

Type IV (Anderson Disease): Deficiency in glycogen branching enzyme [OMIM #232500, OMIM 607839]

Glycogen storage disease IV is caused by a deficiency of glycogen branching enzyme (amylo-(1,4 → 1,6)-transglycosylase). This is the enzyme that adds new branches for glycogen during synthesis. A deficiency in this enzyme results in reduced ability to store glucose residues in glycogen.(This is the enzyme responsible for the wrinkled pea phenotype that Gregor Mendel studied. [ Biochemist Gregor Mendel Studied Starch Synthesis.)

The disease is severe according to OMIM.

Glycogen storage disease type IV is a clinically heterogeneous disorder. The typical 'classic' hepatic presentation is liver disease of childhood, progressing to lethal cirrhosis. The neuromuscular presentation of GSD IV is distinguished by age at onset into 4 groups: perinatal, presenting as fetal akinesia deformation sequence (FADS) and perinatal death; congenital, with hypotonia, neuronal involvement, and death in early infancy; childhood, with myopathy or cardiomyopathy; and adult, with isolated myopathy or adult polyglucosan body disease (Bruno et al., 2004). The enzyme deficiency results in tissue accumulation of abnormal glycogen with fewer branching points and longer outer branches, resembling an amylopectin-like structure, also known as polyglucosan (Tay et al., 2004).

Type V (McArdle Disease): Deficiency of muscle glycogen phosphorylase [OMIM 23600, OMIM 608455]

Glycogen phosphorylase is the enzyme that degrades glycogen [Glycogen Degadation]. Deficiencies in the muscle form of the enzyme lead to severe muscle cramps. Patients are not able to perfom strenuous exercise. The lack of muscle glycogen phosphorylase prevents breakdown of glycogen in muscle and consequent lack of glucose to fuel ATP production via glycolysis. One of the characteristic symptoms is an absence of blood lactate since muscle cells are unable to convert glycogen to glucose and then to lactate.

Muscle tissue breaks down due to lack of ATP leading to general weakness, especially in adults. The disease is not fatal; in fact, it is relatively harmless as long as patients avoid exercise.

Type VI (Hers Disease): Deficiency in liver phosphorylase [OMIM 23700]

Deficiencies of the liver form of glycogen phosphorylase are not as harmful as deficiencies of the muscle version (type V). The disease is inherited as an autosomal recessive and it's due to mutations in the gene for the liver form of glycogen phosphorylase.

The symptoms are mild compared to other forms of glycogen storage disease, giving rise to enlarged liver with mild hypoglycemia, mild ketosis, and retarded growth.

Type VII (Tarui Disease): Muscle phosphofructokinase deficiency [OMIM #232800, OMIM 610681]

According to OMIM,

Glycogen storage disease VII is an autosomal recessive metabolic disorder characterized clinically by exercise intolerance, muscle cramping, exertional myopathy, and compensated hemolysis. Myoglobinuria may also occur. The deficiency of the muscle isoform of PFK results in a total and partial loss of muscle and red cell PFK activity, respectively. Raben and Sherman (1995) noted that not all patients with GSD VII seek medical care because in some cases it is a relatively mild disorder.

Muscle phosphofructokinase (PFKM) is an enzyme required for glycolysis. When glycolysis is blocked in muscle cells glycogen cannot be broken down and there is no abundant supply of ATP available for muscle activity.

Type IXa (X-linked liver glycogenosis): Deficiency of liver phosphorylase kinase [OMIM 306000

Phosphorylase kinase is the enzyme that phosphorylates glycogen phosphorylase in order to regulate its activity [Regulating Glycogen Metabolism]. Defects in the phosphorylase kinase gene (PHK) cause glycogenstorage disease type IXa&mdash a very mild form of the disease according to OMIM.

Deficiency of liver phosphorylase kinase (PHK; ATP:phosphotransferase; EC 2.7.1.38) produces one of the mildest of the glycogenoses of man. The clinical symptoms include hepatomegaly, growth retardation, elevation of glutamate-pyruvate transaminase and glutamate-oxaloacetate transaminase, hypercholesterolemia, hypertriglyceridemia, and fasting hyperketosis (Schimke et al., 1973; Willems et al., 1990). With age, these clinical and biochemical abnormalities gradually disappear and most adult patients are asymptomatic.

Phosphorylase kinase consists of α, β, γ, and δ sunbuits each of which is encoded by specific genes. Defects in the α subunit gene (PHKA) are what causes glycogen storage disease type IXa. There are two different genes for α subunits on the X chromosome: one for the liver specific version of the enzyme (PHA2) and one for the muscle specific version of the enzyme (PHA1). Mutations in either one cause the disease, which is why it is called an X-linked glycogen storage disease.

99 Years and Counting

At this time next year, the Department of Biochemistry at the University of Toronto will be celebrating its 100th anniversary with a symposium and a party. Everyone is invited!

Our department was the first biochemistry department in Canada and one of the first in the world [Biochemistry at the University of Toronto - A Short History]. Readers are invited to submit examples of older biochemistry departments if you can find them

The first chair of the department, Archibald Byron Macallum, was appointed in 1907 for the 1907-08 academic year. We've decided to celebrate at the end of the 2007-2008 academic year.

Former students, staff, faculty, post-docs and anyone else who has ever been associated with the department will meet here for several days in May 2008. We expect to play host to guests from every biochemistry department in Canada and from many other places throughout the rest of the world.

Nobel Laureate: Eduard Buchner

 
The Nobel Prize in Chemistry 1907.

"for his biochemical researches and his discovery of cell-free fermentation"



Eduard Buchner (1860-1917) won the Nobel Prize in 1907 for discovering that cell free extracts of yeast could convert sugar to ethanol. This was one of the greatest discoveries in biology [Fermentation: Synthesis of Ethanol]. The presentation speech outlines the importance of the discovery so I'll quote a large part of it below. This speech was never actually delivered because the award ceremony had to be cancelled due to the death of King Oscar II just two days earlier.

... it has been found possible to lift the veil which hitherto covered the phenomena of organic life. Thus a very large number of substances, which at the time in question it was assumed could only be formed by living organisms, can now be prepared synthetically. When, however, it is a matter of the inner course during the formation and conversion of these substances in living beings, we have to admit that our knowledge is still very far from complete. To be sure, it is no longer said that the living being is governed by a special "life force", but very often we have to make do even today with another expression which, in its actual meaning, does not differ very much from the first. It is frequently said now that this or that process should be regarded as a "life phenomenon" or "life expression" in certain cells. Regrettably we have to recognize that in this we are to a great extent merely providing a word instead of a deeper insight. It is certainly true that the frontier territories in which chemical research is now struggling to penetrate the complicated, mystic phenomena of life have in many respects advanced far beyond where it stood in 1813. Meanwhile, it still remains a fact that we owe considerable unconditional recognition to a work which in this field has taken experimental chemical research a sure step farther.

This is applicable to the work which is now the subject of the Prize award.

In a few words I shall try to explain to you what it is about.

For a long time chemists have been paying great attention to the phenomena which we now call fermentation. Under this name we include a number of chemical processes which occur in living beings and for which they are of the greatest importance. Usually these are decomposition processes in which compound substances are split under the influence of agents which we call ferments. These ferments act, so to speak, by their mere presence. Without being themselves transformed, they cause certain definite changes in other substances, the effect of each ferment being limited to a certain substance or a certain group of substances. It is an important property of ferments that, precisely under such circumstances as obtain in living beings, they exert a powerful action, whilst under others they frequently and easily become ineffective. Since, on the other hand, by means of other chemical aids, chemical processes can be brought about which appear similar to the actions of the ferments-several examples of which are available-it often happens that for this purpose agents are necessary whose nature makes them quite foreign to, and often incompatible with, conditions in living beings.

In very recent times, particularly, the advancement of our knowledge has made it probable that there are processes which are fermentative to a particularly high degree, which bring about the conversion of substances in living beings and which thus control this condition of life. Just as chemical science has during the past century acquired an extensive knowledge of the composition and structure of organic substances, so a thorough knowledge of the nature and action of ferments is now essential, in order that this science may be in a position to master the laws of the formation and dissociation of substances within the organism.

Meanwhile, we know these ferments up to now only by the effects they produce. Their inner nature and the constitution of their substance are still unknown to us. It is to be hoped, however, that a solution to this puzzle may be the subject of a future Nobel Prize.

A number of fermentations have been readily observable. This relates, for example, to the ferments which occur in dissolved state in the secretions which are discharged into the digestive system and exert such a great influence there. It has thus been possible to gain very considerable experimental experience concerning these fermentations.

Another group of fermentations, however, had been seen to occur only in the presence of living cells. To this group belonged, among others, the decomposition of sugar into alcohol and carbon dioxide, under the action of ordinary yeast. The connection between this fermentation and the presence of live yeast cells appeared so irresolvable that this fermentation process was regarded as an "expression of life" by the cells. This process thus appeared to be inaccessible to more detailed research.

Through Pasteur this view was accepted and generally adopted in scientific circles.

The unforgettable service done by Pasteur is that he showed that there are living organisms which are the originators of putrefaction and fermentation and of a number of processes which are of very great significance. Pasteur, who was distinguished not only by the genius of his ideas but also by an eminent talent as an experimenter, also tried - particularly as regards ordinary alcohol fermentation - to investigate the intrinsic interrelationship in this process. In particular he tried to answer the question whether the fermentation of alcohol was due primarily to a ferment produced by the yeast cells, in which case this ferment must be separated from them and be able to work independently of the presence of live yeast cells. His experiments, however, like those of others, concerning the occurrence of such a soluble ferment gave a negative result. Pasteur's view was thus considered to be confirmed, namely that the chemical process in alcoholic fermentation was a life expression by the yeast cells, and was thus inextricably linked with their life. This view prevailed for several decades.

At the same time as Pasteur earned for himself undying fame by his brilliant exposition of the significance of living beings as the ultimate cause of such processes, he put a brake on the progress of science in this field by the vitalistic concept of the actual course of fermentation. So long as fermentation was regarded as an "expression of life", and hence a phenomenon inseparable from life, there was little hope of being able to penetrate more deeply into the question of its course. It should be noted that this was of all the greater importance as it concerned not only alcoholic fermentation but a large group of important processes.

Under these circumstances it can easily be understood that a great sensation was created when E. Buchner, after many years' work, succeeded in showing that alcoholic fermentation could be produced from the juices expressed from yeast cells, free from live cells. He demonstrated incontrovertibly that this fermentation was due to a ferment produced by the yeast cells, from which it can be separated. Fermentation is not a direct expression of life by yeast cells; the cells can be killed and destroyed, while the ferment remains.

By Buchner's work, the fermentation mentioned and various other processes analogous to it have been freed from the shackles which previously held them and which prevented any progress in research. Now, no special difficulty is encountered in obtaining from yeast cells and various other cells an ample amount of powerfully active cell substance which is free from live cells. Numerous clarifying investigations into its properties have also been made, partly by Buchner himself and partly by others. Hitherto inaccessible territories have now been brought into the field of chemical research, and vast new prospects have now been opened up to chemical science.

Fermentation: Synthesis of Ethanol

 
Monday's Molecule #26 was actually three molecules: pyruvate, acetaldehyde, and ethanol. They're part of the pathway from sugar to ethanol.

In the first part of the pathway glucose is converted to pyruvate by the standard reactions of glycolysis. In the presence of oxygen the end product, pyruvate, will be oxidized to acetyl-CoA and CO₂ by pyruvate dehydrogenase. Acetyl-CoA will enter the citric acid cycle to complete the oxidation of glucose. There are several other fates of pyruvate including the conversion to lactate or ethanol. Both of these pathways take place in the absence of oxygen. They are called fermentation pathways.

The ability of yeast to ferment grapes and other fruits has been known for several millenia. Yeast cells can take the sugar from fruit (or grain) and convert it to pyruvate. If you mix yeast and fruit in a container that doesn't have much oxygen then the yeast cells will obligingly produce ethanol, a compound that has proven to be useful in the human diet. Yeast also produces CO₂ under these conditions and shown in the pathway above.

Today we know all about the enzymes that carry out these reactions but one hundred years ago things were less clear. It wasn't certain that fermentation could occur outside of living cells.

In one of the major conceptual advances in biology, Eduard Buchner (in 1897) was able to ferment sugar using a cell free extract of yeast. The reason why this was such an important discovery is that it removed all doubt about vitalism and the possibility that life was some special property outside of chemistry. Buchner showed that the production of ethanol from sugar was just a series of chemical reactions that did not need a living cell. This led directly to the discovery of enzymes and the elucidation of their properties. In a very real sense Buchner is the father of biochemistry [Nobel Laureate: Eduard Buchner].

Marks Are Posted!

 
The grades for my biochemsitry course have just been released to the students. I've already got several email messages from students who are complaining about their marks. One student got "only" 84% and wants to know how to petition for more marks. One student failed the final exam and ended up with a C- for a final grade. She thinks this is unfair.

Sigh. Why do we have to go through this every year? Is it just my students or does eveyone have this problem?

Alister McGrath

Last night I went to hear Alister McGrath speak on the topic Deluded about God? Responding to Richard Dawkins' God Delusion. He was in town as part of a conference organized by Wycliffe College, an evangelical Anglican graduate school of theology at the University of Toronto [Refresh!].

The people who attended the conference are not fans of Richard Dawkins and neither is Alister McGrath. McGrath is a Professor of Theology at Oxford University (UK). The lecture consisted almost entirely of quotations from Dawkins followed by statements that Dawkins has not proven his case; or the issue is still being debated; or Dawkins has misrepresented true religion (i.e. Anglicanism). There were very few actual attempts to rebut the Dawkins arguments. For this audience it seemed to be sufficient to simply state that Dawkins is wrong. If you want to see what kinds of points McGrath raised, then read this review of McGrath's upcoming book called The Dawkins Delusion! [Deluding Who About What?].

PZ Myers does not seem to be a fan of McGrath either as he pointed out in a posting this morning [Somebody needs to write a book called "The McGrath Delusion" now].

McGrath's main points were,

1. Atheism is a religion just like Christianity. Both require faith.
2. Science cannot prove that God doesn't exist.
3. Religion isn't all bad.
4. The Dawkins version of religion isn't the one most people believe in.

These are all boring points, and, to be fair, the audience of 150 people was not receiving them with enthusiasm except for the "amen" crowd in the first few rows.

McGrath made one additional point that I'm hearing more and more frequently. He claims that the plethora of recent books on atheism is evidence that the atheists are frightened. They think they're losing the battle and that's why they have to get out books to rally the troops.

According to McGrath, Christianity is on the rise and that's why the atheists are scared. The atheists can't understand why religion hasn't disappeared yet. At the end of the lecture we were allowed to submit written questions. One that got through the screening asked about the clear increase in the number of non-believers in polls over the past thirty years. (In Canada the number of non-believers has gone from about 2% to almost 20% in some recent polls.) McGrath responded that these polls were very deceptive because they weren't really recording atheists but people who were abandoning organized religion in favor of a more personal spiritual religion. That's why the polls don't reveal the real truth; namely, that Christianity is winning and atheists are scared.

The real reason for the recent books is the exact opposite of what McGrath wants to believe. Atheism is more and more popular and it's time for all non-believers to come out of the closet. As Dawkins points out, ten years ago he never would have been able to sell copies of a book called The God Delusion but today it's on the best seller list and Dawkins, Hitchins, Harris, Dennett and other atheists are on television every single day. It's the Christians who should be worried and in spite of the bravado last night, I think they are.

I'm sure McGrath would object to my characterization of his talk but to me it seemed very defensive. He was reacting to the Dawkins book and making rather banal attempts to defend Christianity against the assault of rationalism (his term). This is not something I've seen before at a conference of believers. The Christians in the audience were told in no uncertain terms that they have to get their act together and learn how to mount a sophisticated, rational defense of their beliefs. (Strange that they would need this call to arms if they're winning the war, isn't it?)

BTW, McGrath is another one of those former "atheists" who have converted to Christianity. This seems to be the new badge of "honor" among theologians. He makes this point several times and compares himself to Antony Flew. The fact that Flew has not converted to Christianity is only one of several dozen errors in the lecture. See [Deluding Who About What?] for a list. McGrath is still making the same errors.

Theistic Evolution According to Francis Collins

 
Another kerfuffle over Theistic Evolution has broken out in response to PZ Myers' complaint about Mitt Romney [Mitt Romney, theistic evolutionist…and this is supposed to be a good thing?]. I've been reading the comments over at Good Math, Bad Math [Religion != ID]. There are others such as the discussion on Primordial Blog [Theistic Evolution].

Update: PZ asks someone to explain to him the difference between Theistic Evolution and Intelligent Design Cretionism [Romney redux]. So far nobody's been able to do it. Stay tuned, read the comments over on Pharyngula.

Part of the problem is that we don't have a universally agreed upon definition of Theistic Evolution. The Wikipedia site does a pretty good job of covering all the possibilities [Theistic Evolution] based mostly on the original statement by Eugenie Scott [The Creation/Evolution Continuum] who says ....

Theistic Evolution is the theological view that God creates through evolution. Astronomical, geological and biological evolution are acceptable to TEs They vary in whether and how much God is allowed to intervene -- some come pretty close to Deists. Other TEs see God as intervening at critical intervals during the history of life (especially in the origin of humans), and they in turn come closer to PCs. In one form or another, TE is the view of creation taught at mainline Protestant seminaries, and it is the official position of the Catholic church. In 1996, Pope John Paul II reiterated the Catholic TE position, in which God created, evolution happened, humans may indeed be descended from more primitive forms, but the hand of God was needed for the creation of the human soul. (John Paul II, 1996).

As I stated in my essay [Theistic Evolution: The Fallacy of the Middle Ground], the true deist end of the continuum does not conflict with science but most other versions do.

Let's look at the version promoted by Francis Collins in his book The Language of God. This version seems to be closer to the popular versions than the benign deist versions. Collins lists six premises of Theistic Evolution (page 200).

1. The universe came into being out of nothingness, approximately 14 billion years ago.
2. Despite massive improbabilities, the properties of the universe appear to have been precisely tuned for life.
3. While the precise mechanism of the origin of life on earth remains unknown, once life arose, the process of evolution and natural selection permitted the development of biological diversity and complexity over very long periods of time.
4. Once evolution got under way, no special supernatural intervention was required.
5. Humans are part of this process, sharing a common ancestor with the great apes.
6. But humans are also unique in ways that defy evolutionary explanation and point to our spiritual nature. This includes the existence of the Moral Law (the knowledge of right and wrong) and the search for God that characterizes all human cultures throughout our history.

I'd also add one further point to this list since it's an important part of the conflict between science and religion that characterizes the Collins' version of Theistic Evolution.

Miracles do not pose an irreconcilable conflict for the believer who trusts in science as a means to investigate the natural world, and who sees that the natural world is ruled by laws. If, like me, you admit that there might exist something or someone outside of nature, then there's no logical reason why that force could not on rare occasions stage an invasion. On the other hand, in order for the world to avoid descending into chaos, miracles must be very uncommon.

I think points #2 and #6 and the issue of miracles, all impinge on science. This is why Theistic Evolution conflicts with science although we all admit that the conflict is less obvious that the conflict between science and Young Earth Creationism.

What's at stake here is the separation of science and religion discussed by Stephen Jay Gould in Rock of Ages. He proposed that science and religion could be Non-overlapping Magisteria (NOMA). What this means is that religion is okay as long as it sticks to things that do not conflict with science. I'm not a big fan of NOMA but the basic concept is worth adopting as a point of discussion. Does the Collins version of Theistic Evolution respect the NOMA Principle?

Here's how Gould describes it (pages 93-94).

The fallacies of such fundamentalist extremism can be easily identified, but what about a more subtle violation of NOMA commonly encountered among people whose concept of God demands a loving deity, personally concerned with the lives of all his creatures—and not just an invisible and imperious clockwinder? Such people often take a further step by insisting that their God mark his existence (and his care) by particular factual imprints upon nature. Now science has no quarrel whatsoever with anyone's need or belief in such a personalized concept of divine power, bu NOMA does preclude the additional claim that such a God must arrange the facts of nature in a certain set and predetermined way. For example, if you believe that an adequately loving God must show his hand by peppering nature with palpable miracles, or that such a God could only allow evolution to work in a manner contrary to to facts of the fossil record (as a story of slow and steady liner progress toward Homo sapiens for example), then a particular and partisan (and minority) view of religion has transgressed into the magisterium of science by dictating conclusions that must remain open to empirical test and potential rejection.

So, what do you think, dear readers? Does the idea that the universe is "precisely tuned for life" involve a transgression of religion into the proper domain of science? Does the idea that "humans are also unique in ways that defy evolutionary explanation" violate NOMA? Are miracles compatible with science?

I think the Collins version of Theistic Evolution is not compatible with science and therefore Collins has not resolved the conflict between science and religion. I think that most versions of Theistic Evolution conflict with science. The only version that's compatible is one that should be called Deistic Evolution.

Monday's Molecule #26

 


Today's molecule is actually three molecules. Name all three. The trivial names will do since they're very well known but if you can supply the correct chemical names that would be good.

As usual, there's a connection between Monday's molecules and this Wednesday's Nobel Laureate(s). This one is even easier than last week's. The reward (free lunch) goes to the person who correctly identifies both the molecule and the Nobel Laureate(s). (Previous free lunch winners are ineligible for one month from the time they first collected the prize. There are no ineligible candidates for this Wednesday's reward since Dunbar bought me lunch on Thursday. Therefore, technically, he did not collect a prize.)

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The Bigs

 

My favorite son¹ works on computer games with a whole team of people in Vancouver. The trailer for their latest game is just out. It's professional baseball and it looks amazing. See it at The Bigs. (Gord does stadia, you can see what else he does at Gordon Moran.)

1. Also my only son.

My Ideal US Presidential Candidate

 
I don't get a vote but I decided to take the quiz anyway [2008 SelectSmart.com Presidential Candidate Selector]. I'm pretty happy with the result, it corresponds to my impression of the candidates. Initially I was impressed with John Edwards but that was a mistake. If I had a vote today it would probably go to Al Gore (if he were running) or Dennis Kucinich.

The ABC Nightline "Debate"

 
Just in case you haven't seen the "debate" here are the YouTube videos for your enjoyment. I'm sure the "intellectual" believers will disown Kirk Cameron and Ray Comfort but I wonder if they really could do a better job?

The "Coke Can" proof of the existence of God is a classic. Watch it in the second clip. It's hard to believe that Ray Comfort's intended audience can be stupid enough to fall for that argument but I have to assume that Comfort knows who he's talking to. After all, he convinced Kirk Cameron and he has years of experience preaching to average Christians.