Words from a Proud Neville Chamberlain Atheist

 
Chris is a cognitive psychologist (Mixing Memory). He claims to be a proud Neville Chamberlain atheist. He writes about Religion and Social Critique.

While I think it's obvious to anyone with eyes (a category that seems to grow smaller by the day) that within the anti-religious bigotry today there is an underlying feeling of superiority, an unliberal belittling of the little guy, a feeling that "Joe Schmoe" is stupid and to some extent worth less than the intellectually righteous secularist, ...

Whoa! I think he's talking 'bout people like me here. First of all, I'm not a bigot. If you want to have an intelligent discussion about rationalism and superstition then it's best to avoid that term unless you can back it up. Second, I do feel strongly that my opinion is better than contrary opinions. Are there any other possibilities? Are there some people who feel that their opinions are unworthy? Thirdly, some of the people who believe in superstitious nonsense really are stupid. And they really are bigots—yes, I can back that up.

(Incidentally, I'm sure that in the interests of fairness, Chris has posted a strong criticism of the bigotry and intolerance of religious leaders in the USA. I look forward to getting the URL to those postings.)

... there is another element to rabid atheist criticisms of religion that I find both disturbing and puzzling. As many of the comments to my recent post and Pharyngula's post on the same topic illustrate, these criticisms of religion are largely based on its perceived social and political effects. That is, the critique of religion by these atheists (let's call them Churchillians) is a social critique.

Oh, that's a relief. It's not me he's referring to. My criticism of religion is based on the idea that its supporters believe in supernatural beings. That's a delusion because there's no evidence of supernatural beings. The fact that some religions are sexist, racist, and homophobic is incidental. I'm well aware of the fact that this doesn't apply to all religions. I'm equally opposed to the more liberal versions of religion because the underlying premise is wrong, in my opinion.

This is the part that Chris and his fellow appeasers don't get. They oppose the extreme versions of religion because of the outward manifestations of social behavior. But they give a free pass to all those superstitions that don't recruit suicide bombers or put women in the back pews. I don't make that distinction. To me the battle is between rationalism and superstition. The social critique is secondary.

What I find disturbing and puzzling about it is its naïveté. As I believe fellow ScienceBlogger and Chaimberlainian atheist Razib has pointed out before (I don't have a link right now, but if he gives me one, I'll add it later), religion is such an effective user of our cognitive and social composition that it falls naturally out of them. So naturally, in fact, that there is no reason to believe that religion is going away, much less that it is possible, through accusation and invective, to facilitate religion's demise. In other words, as social critiques go, the Churchillians' is about as ineffective as you'll find.

Chris, I'll let you in on a little secret. I don't hide my light under a bushel just because I think my chances of changing the world are slim. So, even if it were true that the USA will always be strongly religious that wouldn't be a reason to keep quiet. I don't believe that America is going to accept gays and lesbians anytime soon but that's not a reason to give up the fight. Or, do you think it is? Do you advocate an appeaser position toward homophobic bigots on the grounds that you'll never change their minds?

But, setting the illogic of your argument aside, let's think about the future of religion. European societies became more and more secular in the 20th century. Canada is much, much less religious than the USA. Do you really think that America will resist the change? I don't. Furthermore, I think your statement that the "Churchillians" are being ineffective is patently absurd. Richard Dawkins has done more to stimulate debate about atheism than hundreds of appeasers. Although you misrepresent his position, the fact is that by being blunt he has got people's attention and that's the first step toward getting them to question their beliefs.

Would it not be better to recognize that the content of specific religions has, historically, varied according to the spirit of the times, and therefore the most effective avenue for social critique is to focus on changing that spirit, thereby necessarily effecting change in the content of religion? If you want to make the religious less intolerant, and less hostile towards members of outgroups, wouldn't it be better to work towards a society that is itself less intolerant and hostile towards members of outgrups?

Yes, if your only goal is to make people more tolerant then that's what you should do. Meanwhile, some of us are trying to get people to abandon superstition—that's a different goal.

In other words, it seems to me that the problem with the Churchillian critique is that it mistakes a symptom for the cause; it fails to recognize that religions are, as they have always beens (and as any social institutions are and will alway be), tools of power and domination, and that the object of critique should be the powerful and the dominant.

Wrong. It is you who is making the mistake. The "Churchillians" are opposed to superstition because it's not rational. We don't distinguish between superstitions that are associated with intolerance and those that aren't. Why is this so difficult to understand?

I think, for example, of the ways in which religion and society changed together in 18th century Europe, or the differences between the focus and attitudes of the religious in many European countries as opposed to the United States today. Religions that have survived for millennia have done so because they are incredibly adaptive, and it is the responsibility of anyone with a progressive world-view, recognizing that religion will not go away, to force religion to change by changing its environment and thereby forcing it to adapt. Calling religious people stupid, and treating religion as inherently evil, simply won't accomplish that.

My goal is to achieve a society where there is no religion. I want people to stop believing in supernatural beings for which there is no evidence. I would also like to live in a society with a "more progressive world-view." Both goals are achievable. We don't want an atheistic intolerant society any more than we want a religious intolerant society.

A State of Extreme Cognitive Dissonance

Poor old GilDodgen. He's really suffering over his inability to understand some basic biochemistry [Yet Another Irreducible Complexity No-Brainer — Twisted Ropes]. Naturally, he interprets his ignorance to be proof that Intelligent Design Creationism has the answers.

Watch this video to see why GilDodgen is in a state of extreme cognitive dissonance.



Here's what GilDodgen says after watching the video ...

I find the phenomenon of the DNA supercoiling problem and its biochemical solution even more compelling than examples like protein synthesis and the bacterial flagellum, since twisted ropes are familiar to everyone. This might make for another highly persuasive ID mascot.

You are right to start looking around for another mascot since protein synthesis and the bacterial flagellum aren't working for you. But you better be careful about adopting a new poster girl. Maybe you should learn some basic biochemistry before you end up looking even more stupid than usual. Reading a textbook would help.

How could random variation and natural selection come up with a pair of biochemical scissors and a repair mechanism that cuts and splices the twisted DNA molecule in order to relieve torsional tension? What would be the functional, naturally-selectable intermediate steps in a hypothetical stochastically generated evolutionary process? It is clear that there could not possibly be any.

Here's a picture of E. coli topoisomerase I bound to DNA. The mechanism of action of this enzyme is well known. There are four basic steps.

In step I, the enzyme binds to a single-stranded bubble region of DNA. Such regions are characteristic of supercoiled DNA. The enzyme then cuts the DNA in an endonuclease reaction that's often referred to as a "nickase" activity. There are dozens of endonucleases that can carry out this reaction. They are required for DNA replication, repair, and recombination and they evolved for that purpose. Topoisomerases evolved from such nickases.

In step 2, one end of the cleaved DNA is covalently attached to the enzyme via a phosphotyrosince bond. This is likely to be the single evolutionary invention of topoisomerases, although there are other enzymes that have covalently attached nucleic acids. The covalent attachment means that the enzyme remains firmly bound to the site of the nick where it will catalyze a resealing reaction.

In step 3, the other stand of DNA passes through the site of the nicked strand. This is a simple consequence of the fact that the enzyme is holding on to the ends of the cleaved strand.

In step 4, the enzyme catalyzes rejoining of the two ends. This is a ligase reaction. There are dozens of known ligases. They are required for DNA replication, repair, and recombination and they evolved independently to faciliate those reactions. Topoisomerases combine the activities of an endonuclease and a ligase in a single protein but these activities arose originally as separate enzymes. (This was probably a gene fusion event—there are dozens of examples of gene fusions where seprate enzyme activities are brought together in a single protein.)

So the evolution of topoisomerases goes like this. In the beginning, separate nicking enzymes and ligase enzymes were all that was required to relieve tension in front of a replication fork. Over time these two activities became combined in a single enzyme that could quickly bind to DNA under tension, nick one strand, allow free rotation around the other strand, and reseal the nick.

The advantage of having a single enzyme do what used to require two separate enzymes is that the nicking-resealing steps could be faster and this allowed for faster DNA replication. That's probably why there was selection for an enzyme with both activites that didn't let go of DNA.

The last step in the evolution of topoisomerases was selection for the covalent attachment of DNA to the enzyme. This allowed for the possibility of topoisomerase binding to regions that were not under torsional stress in order to relieve supercoils. This, in turn, paved the way for the evolution of much longer DNA strands and circular forms of DNA that could store supercoils. Since supercoiling is related to packaging DNA, this also contributed to the evolution of larger genomes.

I’m suffering from a state of extreme cognitive dissonance. How can educated, intelligent scientists continue to defend the obviously indefensible, in light of what is now known about the nature of living systems (at all levels, not just the biochemical)?

I don't have much trouble coming up with a defense of the "indefensible." But then I have a huge advantage over GilDodgen because I'm a scientist and, as he says, scientists are intelligent and educated.

Evolution Is a Fact

DaveScot over at Uncommon Descent writes in Theory of Evolution as well tested as…,

We often hear biologists claim the theory of evolution is as well tested as the theory of gravity.

No, you don't, DaveScot. That's not what you hear at all. You aren't listening. (Either that or you're lying but I'd rather give you the benefit of the doubt even though you're an IDiot.)

What biologists say is that Evolution Is a Fact and a Theory. Gravity is a fact just like evolution. That's what you hear biologists saying. The "Theory of Gravity" and "Evolutionary Theory" are something completely different from facts. It may even be the case that evolutionary theory is on more solid grounds than the theory of gravity.

Let me remind all IDiots of what Stephen J. Gould said 26 years ago. Study these words. It will prevent you from looking stupid in the future.

In the American vernacular, "theory" often means "imperfect fact"--part of a hierarchy of confidence running downhill from fact to theory to hypothesis to guess. Thus the power of the creationist argument: evolution is "only" a theory and intense debate now rages about many aspects of the theory. If evolution is worse than a fact, and scientists can't even make up their minds about the theory, then what confidence can we have in it? Indeed, President Reagan echoed this argument before an evangelical group in Dallas when he said (in what I devoutly hope was campaign rhetoric): "Well, it is a theory. It is a scientific theory only, and it has in recent years been challenged in the world of science—that is, not believed in the scientific community to be as infallible as it once was."

Well evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts don't go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's in this century, but apples didn't suspend themselves in midair, pending the outcome. And humans evolved from ape-like ancestors whether they did so by Darwin's proposed mechanism or by some other yet to be discovered.

Moreover, "fact" doesn't mean "absolute certainty"; there ain't no such animal in an exciting and complex world. The final proofs of logic and mathematics flow deductively from stated premises and achieve certainty only because they are not about the empirical world. Evolutionists make no claim for perpetual truth, though creationists often do (and then attack us falsely for a style of argument that they themselves favor). In science "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional consent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.

Evolutionists have been very clear about this distinction of fact and theory from the very beginning, if only because we have always acknowledged how far we are from completely understanding the mechanisms (theory) by which evolution (fact) occurred. Darwin continually emphasized the difference between his two great and separate accomplishments: establishing the fact of evolution, and proposing a theory—natural selection—to explain the mechanism of evolution.

Stephen J. Gould, " Evolution as Fact and Theory"; Discover, May 1981

Human GULOP Pseudogene

Locus GULOP in the human genome is the site of a pseudogene called GULOP. In most mammals this is an active gene encoding the enzyme L-glucono-γ-lactone oxidase. This is the enzyme that catalyzes the last step in the synthesis of ascorbic acid (vitamin C). The gene is defective in humans and other primates so we can't make ascorbic acid and that causes scurvy if we don't get enough ascorbic acid in our food (Scurvy and Vitamin C).

The GenBank entry for this pseudogene is GeneID=2989. GULOP is located on chromosome 8 at p21.1 in a region that is rich in genes (map).

The human pseudogene was first identified by Nishikimi and Yagi (1991) using the intact rat gene (GeneID=60671) as a probe. They cloned and sequenced four exons that contained several deletions and several in-frame stop codons. This allowed them to conclude that the human pseudogene could not make a functional product. Several of these same mutations are found in chimpanzees, orangutans and macaques indicating that the inactive GULOP gene in all primates descends from a common ancestor that also had an inactive gene (Ohta and Nishkimi 1999).

Subsequent analysis on the GULOP locus in the human genome reveals that the pseudogene is missing most of the 5' exons that are present in the intact rat gene. In particular, exons I to VI are completely absent in the human genome. It is not known whether this deletion is responsible for the original inactivation of the GULOP gene in the primitive ancestral primate (Nishikimi et al. 1994; Ohta and Nishikimi 2003).


UPDATE: see: Creationists questioning pseudogenes: the GULO pseudogene

The human locus is also missing exon XI. In this case the deletion is probably due to recombination between Alu sequences that flank the site of the deletion. This deletion probably took place after the original inactivation event.

Inai, Y., Ohta. Y., and Nishikimi, M. (2003) The whole structure of the human nonfunctional L-gulono-gamma-lactone oxidase gene--the gene responsible for scurvy--and the evolution of repetitive sequences thereon. J Nutr Sci Vitaminol (Tokyo) 49:315-319.

Nishikimi, M. and Yagi, K. (1991) Molecular basis for the deficiency in humans of gulonolactone oxidase, a key enzyme for ascorbic acid biosynthesis. Am. J. Clin. Nutr. 54(6 Suppl):1203S-1208S.

Nishikimi, M., Fukuyama, R., Minoshima, S., Shimizu, N. and Yagi. K. (1994) Cloning and chromosomal mapping of the human nonfunctional gene for L-gulono-gamma-lactone oxidase, the enzyme for L-ascorbic acid biosynthesis missing in man. J. Biol. Chem. 269:13685-13688.

Ohta, Y. and Nishikimi, M. (1999) Random nucleotide substitutions in primate nonfunctional gene for L-gulono-gamma-lactone oxidase, the missing enzyme in L-ascorbic acid biosynthesis. Biochim. Biophys. Acta. 1472:408-411.

Nobel Laureate: Walter Norman Haworth

The Nobel Prize inChemistry 1937.

"for his investigations on carbohydrates and vitamin C"


Sir Norman Haworth won the Nobel Prize in 1937 for his work on the three-dimensional structure of carbohydrates in general and the structure of vitamin C in particular. The presentation speech summarizes his contribution to carbohydrate chemistry.

What has Haworth then accomplished within this domain? The answer may be thus formulated that he has, above all, made clear the chemical structure of vitamin C.

The chemical structure of substances is expressed by the so-called chemical formulas. By chemical analysis the percentage of the different elements - in this case of carbon, hydrogen, and oxygen - which enter into a compound may be ascertained. Further, the weight of the atoms of the different elements, expressed for instance in relation to the atom of hydrogen, has long been known, the hydrogen atom being the lightest of all the elements. It is likewise possible to determine the weight of a particle, or molecule, of a compound, expressed in the same measure. It is hence possible to indicate how many atoms of the different elements are entering into one molecule of the compound. Thus, the gross formula of the compound is obtained. This formula, in the case of vitamin C, is quite simple, considering that it represents a vitamin, viz.: C6H8O6. This formula tells us that one molecule of vitamin C consists of 6 atoms of carbon, 8 of hydrogen, and 6 of oxygen. It also indicates that vitamin C may be conceived as having originated through the elimination of 4 atoms of hydrogen from one molecule of grape-sugar.

But it is possible to advance still further. By ingenious adjustment or speculation, reminding us somewhat of the play of a puzzle, only perhaps a little more intricate, a firm conception has been formed about the order in which the atoms combine. If we conceive an ultra-enlarged model of a molecule, taken at a certain moment - because the atoms are not at a standstill within the molecule - and place a white screen on the one side of the model, while the other is exposed to light, a shadow-figure, also called a projection, of the molecule is obtained on the screen, showing the position of the atoms in their relation to each other. A formula which is intended to reproduce this situation, under the assumption that the atoms were placed on the same plane, is called a structural formula. Such formulas have proved capable of explaining with a high degree of clarity the properties of the compound, and the puzzle thus may be considered as having been solved.

In reality it is, however, hardly correct to suppose that all the atoms within a molecule should be placed on the same plane; if that were the case, even the largest molecules would have the shape of a leaf of paper, which is less than probable. There remains then their dispersion in space, the so-called configuration, which also may be expressed by a formula.

Such a formula for vitamin C has been proposed by Haworth and Hirst, as well as by von Euler and has been subsequently proved to be correct by Haworth.

Haworth's acceptance speech from 1937 contains a number of structures that will be very familiar to biochemistry students. For example, he shows the strucures of α-D-glucopyranose and β-D-glucopyranose.

We recognize these structures today because of the way Haworth drew them to show the three-dimensional configuration. In fact, we now call these figures "Haworth projections" after the man who deciphered the configurations and conformations and developed a way of projecting them on a two-dimensional page.

The final strucure of ascorbic acid (vitamin C) is also presented in Haworth's Nobel Lecture. In this case he choose to show it as a "Fischer projection" rather than the Haworth projection that he is famous for. (See Monday's Molecule #15 for the Haworth projection of vitamin C.)

The relationship between a properly drawn Fischer projection and a Haworth projection is the bane of biochemistry students since it comes up on countless exams. It's probably safe to say that the failure to appreciate Haworth's 1937 Nobel Prize is responsible for lowering the average grade of biochemistry students all over the world by 3-5%.

Canadian Parliament Scraps Anti-terror Laws

 
Given a choice between trusting the "soft-on-terror" Liberals and the "crack-down-on-crime" Conservatives, I go with the softies every time.

OTTAWA, Feb 27 (Reuters) - Canada's Parliament scrapped two contentious anti-terror measures on Tuesday, angering the minority Conservative government, which accuses opposition legislators of being soft on terror.

The House of Commons voted 159-124 not to renew the provisions -- which expire on March 1 -- on the grounds that they had never been used.

One provision allows police to arrest people suspected of planning an imminent terrorist attack and hold them for three days without charge. The other provides for investigative hearings in which a judge can compel witnesses to testify about alleged terrorist activities.

The measures were introduced by the then-Liberal government after the Sept. 11, 2001, suicide attacks on the United States. In a bid to allay fears over human rights, Ottawa agreed the provisions would expire after five years.

The Conservative government controls just 125 of the 308 seats in the House and did not have the votes to extend the measures.

Prime Minister Stephen Harper, whose Conservatives won power in January 2006 on a platform that promised to crack down on crime, says the Liberals of Stephane Dion are soft on terror and cannot be trusted to keep Canadians safe.

Canada Parliament scraps two anti-terror measures

Short on Gas

 
There's a gasoline shortage in Ontario. The main cause was a fire last week at an Esso refinery near Hamilton. The ancillary cause is a CN Rail strike that prevented oil companies from bringing in gasoline from other provinces. Everyone filled up their tanks and this caused shortages everywhere. About 100 Esso gas stations are closed down for lack of fuel. Other stations have also run out of gas.

Ontario is by far the best province in Canada but for some reason the other provinces don't like us very much. This has given rise to a number of nasty comments about us. Nobody seems to be sympathetic to our plight.

Here's one of those mean things that people are saying. This one was sent to us by my wife's aunt who was also my grade 5 teacher. I'm sure you'll agree that this is really below the belt.

A lot of folks can't understand how we came to have an oil shortage here in Canada

Well, there's a very simple answer.

Nobody bothered to check the oil.

We just didn't know we were getting low.

The reason for that is purely geographical.

Our OIL is located in Alberta, Newfoundland, Saskatchewan and B.C.

Our DIPSTICKS are located in Ontario

Peter McKnight on the Marcus Ross Issue

 
One week ago I commented on an opinion piece in the Vancouver Sun. Peter McKnight wrote in support of giving Marcus Ross a Ph.D. in geosciences. I disagreed (Peter McKnight of the Vancouver Sun Weighs in on the Marcus Ross Incident).

I sent Peter a link to my blog and he replied. We've exchanged emails. I then asked permission to post his original message to see what kind of feedback it gets here. Peter has just given permission so here is his letter.

Hi Larry,

Thanks for notifying me of this. It is a worthwhile discussion you're having, but I still don't agree with you.

You say there's plenty of evidence there is something wrong with Ross's science, but you fail to say what that evidence is. Indeed, what you're really saying is that there's something wrong with him - that is, with his belief.

This might be, but it doesn't mean there's anything wrong with his science or his understanding of science. You say doctoral students must understand basic concepts and ideas and think on their feet and defend their ideas etc. Where is the evidence that Ross failed to do so? I assume he did exactly that in his oral exam.

It seems that you want nothing less than Ross's assent to an old Earth theory, which is, of course, a matter of belief, not understanding. And rather than launching into a discussion of epistemic conditions for belief, let me just say that I, for example, understand intelligent design theory quite well I think, and yet I don't believe a word of it.

And one need not be a postmodern relativist or a fundamentalist Christian (which, I've argued for a long time, amount to the same thing) to refuse to accept that that scientific theories are literally true - if by true we mean correspondent with reality. There are, after all, pragmatist philosophies of science that suggest scientific theories are "true" in so far as they work, but that they aren't true in the sense most people give to that term. I assume you reject these philosophies of science, but surely you wouldn't deny a student a doctorate because he doesn't subscribe to the correspondence theory of truth.

Look, I think Ross is dishonest, but I don't know that for a fact. For all I know, maybe he really is a radical relativist, who believes science and religion present two incommensurable paradigms. But either way, he's doing enormous damage to his religion, and it was the point of my column to make that case.

Best,

Peter

Scurvy and Vitamin C

 
Scurvy is a disease characterized by general lethargy and malaise. As the disease progresses the patient develops pain in the extremities, gingivitis, and ulcerations on the skin. Eventually the skin becomes fragile and starts bleeding, teeth fall out, and arteries and veins burst. Death follows. [OMIM 240400 HYPOASCORBEMIA]

Scurvy is caused by lack of vitamin C (Monday's Molecule #15). Vitamin C (ascorbic acid) can be easily oxidized to dehydroascorbic acid and it is this electron donor property that makes it an important biochemical molecule.

In humans there are about a dozen enzymes whose activity depends on ascorbic acid. The most important ones are the enzymes involved in hydroxylation of proline and lysine during the synthesis of collagen fibers (Collagen). In the absence of proper hydroxylation of these amino acids, the collagen molecules cannot be cross-linked and this leads to weaker skin and weaker lining of blood vessels.


In spite of the fact that ascorbic acid is essential in humans, we cannot synthesize it de novo. We need to get an adequate supply from our food—mostly fruits and vegetables. It was the lack of fresh fruit and vegetables that made scurvy so common in the past. Today the disease is rarely seen, except in alcoholics.

All primates have lost the ability to make ascorbic acid. Some other mammals have independently lost this function; guinea pigs and some fruit-eating bats are the best known examples.

Collagen

Collagen is the major protein component of the connective tissue of vertebrates; it constitutes about 25% to 35% of the total protein in mammals. Collagen molecules have remarkably diverse forms and functions. For example, collagen in tendons forms stiff, ropelike fibers of tremendous tensile strength; in skin, collagen takes the form of loosely woven fibers, permitting expansion in all directions.

The structure of collagen was worked out by G. N. Ramachandran (famous for his Ramachandran plots). The molecule consists of three left-handed helical chains coiled around each other to form a right-handed supercoil. Each lefthanded helix in collagen has 3.0 amino acid residues per turn and a pitch of 0.94 nm, giving a rise of 0.31 nm per residue.

The collagen triple helix is stabilized by interchain hydrogen bonds. The sequence of the protein in the helical region consists of multiple repeats of the form –Gly–X–Y–, where X is often proline and Y is often a modified proline called 4-hydroxyproline. The glycine residues are located along the central axis of the triple helix, where tight packing of the protein strands can accommodate no other residue. For each –Gly–X–Y– triplet, one hydrogen bond forms between the amide hydrogen atom of glycine in one chain and the carbonyl oxygen atom of residue X in an adjacent chain. Hydrogen bonds involving the hydroxyl group of hydroxyproline may also stabilize the collagen triple helix. Unlike the more common α helix, the collagen helix has no intrachain hydrogen bonds.

In addition to hydroxyproline, collagen contains an additional modified amino acid residue called 5-hydroxylysine. Some hydroxylysine residues are covalently bonded to carbohydrate residues, making collagen a glycoprotein. The role of this glycosylation is not known.

Hydroxyproline and hydroxylysine residues are formed when specific proline and lysine residues are hydroxylated after incorporation into the polypeptide chains of collagen. The hydroxylation reactions are catalyzed by enzymes and require ascorbic acid (vitamin C).

Collagen triple helices aggregate in a staggered fashion to form strong, insoluble fibers. The strength and rigidity of collagen fibers result in part from covalent cross-links. The groups of the side chains of some lysine and hydroxylysine residues are converted enzymatically to aldehyde groups producing allysine and hydroxyallysine residues. Allysine residues (and their hydroxy derivatives) react with the side chains of lysine and hydroxylysine residues to form Schiff bases, complexes formed between carbonyl groups and amines. These Schiff bases usually form between collagen molecules.

Collagen molecules associate to form long thick fibres with a characteristic banded appearance. These thick fibres confer strength and flexibility to many tissues.

(Collagen molecular image originally produced by J.W. Schmidt for Wikepedia. GNU Free Documentation License)

(Text from Horton et al. Principles of Biochemistry 4th ed.© Pearson Prentice Hall, Inc.)

Joke of the Day: Jonathan Wells

 
Your dose of humor for today comes from an article by Jonathan Wells on the Discovery Institute website [Alchemy, Marxism, and the future of Darwinism]. With a title like that you can expect a good laugh. Normally these jokes begin with "a priest, a rabbi, and a preacher walked into a bar." But if you're an IDiot you start with "I was talking to a physics student and a biochemistry student ...." Here's the set-up ...

I recently found myself in a conversation with two college undergraduates, both of them seniors in the natural sciences (physics and biochemistry, respectively). At one point we were discussing alchemy, which they knew as a pre-modern attempt to transmute lead into gold. I asked them whether they could name any famous alchemists. They could not, though one of them dimly recalled hearing of “someone whose name began with A.”

I then predicted that Darwinian evolution would eventually fade into the same obscurity that now shrouds alchemy. Although I knew from previous conversations that my young friends were skeptical of Darwinian theory, they expressed considerable surprise at my prediction, if only because Darwinism is presently held in such high esteem by their professors.

So I proceeded to explain the basis for my prediction.

An American Rhodes Scholar in Biochemistry

 
Nick Anthis at The Scientific Activist writes about the Rhodes Scholar experience in Oxford [It's OK to Nibble, but Don't Bite Off the Hand that Feeds You]. He discusses an important point, namely the push to finish a Ph.D. in only three years. Is this in the best interests of biochemistry graduate students in general and Rhodes Scholars in particular? I think not, and so does Nick Anthis.

Shift Happens

 
This is interesting. I don't agree with everything—especially the idea that things are going to change that much in the next 15 years but it's worth a look. We can discuss the content.

Just-So Stories

Fanciful evolutionary explanations that have little connection to facts are called "just-so" stories after the collection of stories by Rudyard Kipling. I just found a website with all of the the just so stories [Just So Stories]. It's worth reading a few to get some idea of what we're talking about when we say that the "explanations" of evolutionary psychology, for example, are no better than just-so stories.

The illustration is from The Elephant's Child, a story about how the elephant got its trunk.

'Come hither, Little One,' said the Crocodile, 'for I am the Crocodile,' and he wept crocodile-tears to show it was quite true.

Then the Elephant's Child grew all breathless, and panted, and kneeled down on the bank and said, 'You are the very person I have been looking for all these long days. Will you please tell me what you have for dinner?'

'Come hither, Little One,' said the Crocodile, 'and I'll whisper.'

Then the Elephant's Child put his head down close to the Crocodile's musky, tusky mouth, and the Crocodile caught him by his little nose, which up to that very week, day, hour, and minute, had been no bigger than a boot, though much more useful.

'I think,' said the Crocodile--and he said it between his teeth, like this--'I think to-day I will begin with Elephant's Child!'

At this, O Best Beloved, the Elephant's Child was much annoyed, and he said, speaking through his nose, like this, 'Led go! You are hurtig be!'

The Genetics of Eye Color

The genetics of blood type is a relatively simple case of one locus Mendelian genetics—albeit with three alleles segregating instead of the usual two (Genetics of ABO Blood Types).

Eye color is more complicated because there's more than one locus that contributes to the color of your eyes. In this posting I'll describe the basic genetics of eye color based on two different loci. This is a standard explanation of eye color but, as we'll see later on, it doesn't explain the whole story. Let's just think of it as a convenient way to introduce the concept of independent segregation at two loci. Variation in eye color is only significant in people of European descent.

At one locus (site=gene) there are two different alleles segregating: the B allele confers brown eye color and the recessive b allele gives rise to blue eye color. At the other locus (gene) there are also two alleles: G for green or hazel eyes and g for lighter colored eyes.

The B allele will always make brown eyes regardless of what allele is present at the other locus. In other words, B is dominant over G. In order to have true blue eyes your genotype must be bbgg. If you are homozygous for the B alleles, your eyes will be darker than if you are heterozygous and if you are homozygous for the G allele, in the absence of B, then your eyes will be darker (more hazel) that if you have one one G allele.

Here's the Punnett Square matrix for a cross between two parents who are heterozygous at both alleles. This covers all the possibilities. In two-factor crosses we need to distinguish between the alleles at each locus so I've inserted a backslash (/) between the two genes to make the distinction clear. The alleles at each locus are on separate chromosomes so they segregate independently.^*


As with the ABO blood groups, the possibilities along the left-hand side and at the top represent the genotypes of sperm and eggs. Each of these gamete cells will carry a single copy of the Bb alleles on one chromosome and a single copy of the Gg alleles on another chromosome.

Since there are four possible genotypes at each locus, there are sixteen possible combinations of alleles at the two loci combined. All possibilities are equally probable. The tricky part is determining the phenotype (eye color) for each of the possibilities.

According to the standard explanation, the BBGG genotype will usually result in very dark brown eyes and the bbgg genotype will usually result in very blue-gray eyes. See the examples in the eye chart at the lower-right and upper-left respectively. The combination bbGG will give rise to very green/hazel eyes. The exact color can vary so that sometimes bbGG individuals may have brown eyes and sometimes their eyes may look quite blue. (Again, this is according to the simple two-factor model.)

The relationship between genotype and phenotype is called penetrance. If the genotype always predicts the exact phenotpye then the penetrance is high. In the case of eye color we see incomplete penetrance because eye color can vary considerably for a given genotype. There are two main causes of incomplete penetrance; genetic and environmental. Both of them are playing a role in eye color. There are other genes that influence the phenotype and the final color also depends on the environment. (Eye color can change during your lifetime.)

One of the most puzzling aspects of eye color genetics is accounting for the birth of brown-eyed children to blue-eyed parents. This is a real phenomenon and not just a case of mistaken fatherhood. Based on the simple two-factor model, we can guess that the parents in this case are probably bbGg with a shift toward the lighter side of a light hazel eye color. The child is bbGG where the presence of two G alleles will confer a brown eye color under some circumstances.

^*If the two genes were on the same chromosome this assumption might be invalid because the two alleles on the same chromosome (e.g., B + g) would tend to segregate together. Linked genes don't obey Mendel's Laws and this is called linkage disequilibrium.