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.

I Agree With Denyse O'Leary!

 
Calm down. The world has not come to an end. I don't agree with everything Denyse O'Learly says but there's one issue where we can see eye-to-eye.

Denyse thinks that Theistic Evolution is a cop-out [Theistic evolutionism and the new militant atheism]. She claims that Theistic Evolutionists have to surrender too much of their religion.

However, much of what is called theistic evolution today is simply an attempt to sell Darwinism, the creation story of materialism, to people who are not materialists. I call that "accommodationist" theistic evolution - it attempts to accommodate spiritually directed institutions to rule by materialists....

Usually, Christians (or other theists or people who accept that there is meaning and purpose in the universe) are urged to "accept" - in broad terms - "evolution." Darwinism, which nakedly refutes everything the theist believes, is the form of evolution that the sponsors are actually interested in promoting, to judge from their other activities. But they do not spell out its implications with the candor that the anti-God Darwinists do.

I agree that the middle ground position of Theistic Evolution is untenable [Theistic Evolution: The Fallacy of the Middle Ground]. In my case it's not because the Theistic Evolutionists (e.g., Ken Miller, Francis Collins, Simon Conway-Morris) are giving up too much religion; it's because they are giving up too much of science.

In typical IDiot fashion, Denyse O'Leary continues to use the term "Darwinism" to define her enemy. But if we overlook that particular bit of dissembling for the moment, she has a point. Science in general, and evolutionary biology in particular, tells us that there's no meaning or purpose in the universe. Theistic Evolutionists say that there is but they have no evidence to back up their claim. That's anti-science.

Denyse and I agree that Theistic Evolutionists are trying to have their cake and eat it too.

The Felt Effect of Gravity

 
Phil Plait answers the question, "Just how strong is the gravity from the Moon compared to someone right next to you?". The answer will probably surprise you. It certainly surprised me.

As a bonus, you'll find out the most distant start you can see with the naked eye. An even greater bonus is finding out whether astrology is true. I won't reveal the answer. You'll have to watch the video.

Monday's Molecule #15

 
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.

President of University of Toronto Receives Order of Canada

 
David Naylor is the President of the University of Toronto. He's one of the best Presidents we've had for several decades. A few weeks ago he received the Order of Canada in recognition of his work in Medicine and the University.

That's our Governor General Michaelle Jean beside him in the picture. As the Queen's representative in Canada she is our Head of State. The awards ceremony was at her house, Rideau Hall, in Ottawa.

It's comforting to know that Conservative Prime Minister Stephen Harper can't do a lot of damage to the country as long as Michaelle Jean is Governor General and the Rt. Hon. Chief Justice of Canada is Beverley McLachlin.

What Kind of "Intelligent" Am I?

 

Your Dominant Intelligence is Logical-Mathematical Intelligence

You are great at finding patterns and relationships between things. Always curious about how things work, you love to set up experiments. You need for the world to make sense - and are good at making sense of it. You have a head for numbers and math ... and you can solve almost any logic puzzle. You would make a great scientist, engineer, computer programmer, researcher, accountant, or mathematician.

What Kind of Intelligence Do You Have?

Jan Betker Loses to Kelley Scott

 
My (distant^*) cousin Jan Betker from Saskatchewan just lost the final of the Scotties Tournament of Hearts to last year's champion Kelly Scott of British Columbia, playing as Team Canada.

Too bad. Well done Jan and good luck next year.

Jan is a three time Canadian champion (1993, 1994, 1997), a three time World champion (1993, 1994, 1997) and an Olympic Gold Medal winner in 1998.

^* Jan's grandfather was my grandmother's brother. Does this make her a second cousin or a third cousin?

More on the Marcus Ross Case

 
Read what Janet Stemwedel has to say in Scientific and unscientific conclusions: now with pictures!.

It's going to take me a while to figure out how to respond but I think she's make a big step toward clarifying the issue. What it boils down to is this. Is it possible to be a scientist and hold "beliefs" that flatly contradict scientific evidence? Janet suggests that it is possible because your "beliefs" can be entirely separated from doing good science.

But, it seems to me that the aim of the scientific enterprise is to find ways to draw inferences that move beyond the beliefs of any individual scientist. Leaving the "belief" boxes out of the flowchart doesn't seem to remove any of the steps required for building sound scientific conclusions. Scientific conclusions may well affect the belief structures of individual scientists, but that's a matter of their own personal growth, not required step in the construction of the shared body scientific knowledge.

I wonder if this point of view can be extended to philosophy? Janet talks about Popper in her posting. She doesn't mention Kuhn. Lets imagine a philosophy student who is preparing a thesis in epistemology. Assume that the student writes all the right things about Popper and Kuhn in her thesis. Assume that this students then gives public lectures where she claims that Popper advocated scientific revolutions and Kuhn was really a proponent of falsifiability. In other words, points of view that are contrary to fact.

Is it fair to ask this student about her "beliefs" during her Ph.D. oral? Is it fair to say that she is a good philosopher as long as she keeps her strange contrary-to-fact beliefs separate from the work she does on campus?

What Kind of English Do YOu Speak?

 
Canadian doesn't seem to be one of the choices. (I wonder which 10% of my English is "Dixie"!)

Your Linguistic Profile:

45% General American English

35% Yankee

10% Dixie

5% Upper Midwestern

0% Midwestern

What Kind of American English Do You Speak?

Canada's Supreme Court Strikes Down Anti-terror Law

 
Reuters reports that Canada's top court strikes down anti-terror law. It's all over the radio stations and in all the newspapers (Toronto Star, Globe and Mail).

The decision was unanimous. As Thomas Walkom puts in it the Toronto Star,

Canada is on its way to becoming a civilized country again. The Supreme Court has ruled that if the government wants to lock up people indefinitely without charge, it has to at least let them muster a defence.

In the post-9/11 world, this counts as progress.

Yesterday's court ruling deals with what are known as security certificates. These are ministerial orders that allow the government to jail non-citizens without charge and then deport them.

But it's worth noting that the court did not invalidate the entire security certificate regime. It just told the government it has to be more respectful of the Constitution. More important, the top court has yet to address the most controversial element of Canada's immigration laws – the question of what to do to those that the government wants to deport as security risks even though it knows they will almost certainly face torture in their homelands.

That question is due to be addressed by a lower court, probably later this year.

Still, yesterday's decision does go some way to clearing up a law that has become a searing embarrassment for Canada.

Since 2001, it has allowed the government to jail any foreigner, whether legally or illegally in the country, that it deems a security risk.

The reason this decision is important is because the Americans are holding Canadian citizens without charging them. Canada has been in a weak position to criticize this practice since we have also been violating the rights of foreigners.

The Supreme Court declared that the six terrorist suspects who are now in detention must be allowed their day in court. Chief Justice Beverley McLachlin wrote the unanimous decision, which said that the present law violates the fundamental right to a fair trial that's part of Canada's constitution.