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.)

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

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.

The Emperor's New Clothes and the Courtier's Reply

I recently referred to the "Courtier's Reply", a term invented by PZ Myers to rebut the claims of believers who insist that their superstitious beliefs are ever so much more sophisticated than the simple version that Dawkins attacks.

PZ's response deserves much more publicity because it goes to the heart of the debate between rationalism and supersition. I'm going to post his original Courtier's Reply below (without permission, but I'm sure he'll understand) but before doing so I need to remind everyone about the original fairy tale [The Emperor's New Clothes].

THE EMPEROR'S NEW CLOTHESby Hans Christian Anderson

Once upon a time there lived a vain Emperor whose only worry in life was to dress in elegant clothes. He changed clothes almost every hour and loved to show them off to his people.

Word of the Emperor's refined habits spread over his kingdom and beyond. Two scoundrels who had heard of the Emperor's vanity decided to take advantage of it. They introduced themselves at the gates of the palace with a scheme in mind.

"We are two very good tailors and after many years of research we have invented an extraordinary method to weave a cloth so light and fine that it looks invisible. As a matter of fact it is invisible to anyone who is too stupid and incompetent to appreciate its quality."

The chief of the guards heard the scoundrel's strange story and sent for the court chamberlain. The chamberlain notified the prime minister, who ran to the Emperor and disclosed the incredible news. The Emperor's curiosity got the better of him and he decided to see the two scoundrels.

"Besides being invisible, your Highness, this cloth will be woven in colors and patterns created especially for you." The emperor gave the two men a bag of gold coins in exchange for their promise to begin working on the fabric immediately.

"Just tell us what you need to get started and we'll give it to you." The two scoundrels asked for a loom, silk, gold thread and then pretended to begin working. The Emperor thought he had spent his money quite well: in addition to getting a new extraordinary suit, he would discover which of his subjects were ignorant and incompetent. A few days later, he called the old and wise prime minister, who was considered by everyone as a man with common sense.

"Go and see how the work is proceeding," the Emperor told him, "and come back to let me know."

The prime minister was welcomed by the two scoundrels.

"We're almost finished, but we need a lot more gold thread. Here, Excellency! Admire the colors, feel the softness!" The old man bent over the loom and tried to see the fabric that was not there. He felt cold sweat on his forehead.

"I can't see anything," he thought. "If I see nothing, that means I'm stupid! Or, worse, incompetent!" If the prime minister admitted that he didn't see anything, he would be discharged from his office.

"What a marvelous fabric, he said then. "I'll certainly tell the Emperor." The two scoundrels rubbed their hands gleefully. They had almost made it. More thread was requested to finish the work.

Finally, the Emperor received the announcement that the two tailors had come to take all the measurements needed to sew his new suit.

"Come in," the Emperor ordered. Even as they bowed, the two scoundrels pretended to be holding large roll of fabric.

"Here it is your Highness, the result of our labour," the scoundrels said. "We have worked night and day but, at last, the most beautiful fabric in the world is ready for you. Look at the colors and feel how fine it is." Of course the Emperor did not see any colors and could not feel any cloth between his fingers. He panicked and felt like fainting. But luckily the throne was right behind him and he sat down. But when he realized that no one could know that he did not see the fabric, he felt better. Nobody could find out he was stupid and incompetent. And the Emperor didn't know that everybody else around him thought and did the very same thing.

The farce continued as the two scoundrels had foreseen it. Once they had taken the measurements, the two began cutting the air with scissors while sewing with their needles an invisible cloth.

"Your Highness, you'll have to take off your clothes to try on your new ones." The two scoundrels draped the new clothes on him and then held up a mirror. The Emperor was embarrassed but since none of his bystanders were, he felt relieved.

"Yes, this is a beautiful suit and it looks very good on me," the Emperor said trying to look comfortable. "You've done a fine job."

"Your Majesty," the prime minister said, "we have a request for you. The people have found out about this extraordinary fabric and they are anxious to see you in your new suit." The Emperor was doubtful showing himself naked to the people, but then he abandoned his fears. After all, no one would know about it except the ignorant and the incompetent.

"All right," he said. "I will grant the people this privilege." He summoned his carriage and the ceremonial parade was formed. A group of dignitaries walked at the very front of the procession and anxiously scrutinized the faces of the people in the street. All the people had gathered in the main square, pushing and shoving to get a better look. An applause welcomed the regal procession. Everyone wanted to know how stupid or incompetent his or her neighbor was but, as the Emperor passed, a strange murmur rose from the crowd.

Everyone said, loud enough for the others to hear: "Look at the Emperor's new clothes. They're beautiful!"

"What a marvellous train!"

"And the colors! The colors of that beautiful fabric! I have never seen anything like it in my life!" They all tried to conceal their disappointment at not being able to see the clothes, and since nobody was willing to admit his own stupidity and incompetence, they all behaved as the two scoundrels had predicted.

A child, however, who had no important job and could only see things as his eyes showed them to him, went up to the carriage.

"The Emperor is naked," he said.

"Fool!" his father reprimanded, running after him. "Don't talk nonsense!" He grabbed his child and took him away. But the boy's remark, which had been heard by the bystanders, was repeated over and over again until everyone cried:

"The boy is right! The Emperor is naked! It's true!"

The Emperor realized that the people were right but could not admit to that. He though it better to continue the procession under the illusion that anyone who couldn't see his clothes was either stupid or incompetent. And he stood stiffly on his carriage, while behind him a page held his imaginary mantle.

Here's how PZ Myers describes those people who claim to have a much more intellectual version of religion; one that can not be as easily dismissed as the "simple" version that Richard Dawkins addresses. These people seem to think that by dressing up their superstitious beliefs in fancy language with philosophical references they can escape the simple fact the the Emperor has no clothes.

The Courtier's Replyby PZ Myers

I have considered the impudent accusations of Mr Dawkins with exasperation at his lack of serious scholarship. He has apparently not read the detailed discourses of Count Roderigo of Seville on the exquisite and exotic leathers of the Emperor's boots, nor does he give a moment's consideration to Bellini's masterwork, On the Luminescence of the Emperor's Feathered Hat. We have entire schools dedicated to writing learned treatises on the beauty of the Emperor's raiment, and every major newspaper runs a section dedicated to imperial fashion; Dawkins cavalierly dismisses them all. He even laughs at the highly popular and most persuasive arguments of his fellow countryman, Lord D. T. Mawkscribbler, who famously pointed out that the Emperor would not wear common cotton, nor uncomfortable polyester, but must, I say must, wear undergarments of the finest silk.

Dawkins arrogantly ignores all these deep philosophical ponderings to crudely accuse the Emperor of nudity.

Personally, I suspect that perhaps the Emperor might not be fully clothed — how else to explain the apparent sloth of the staff at the palace laundry — but, well, everyone else does seem to go on about his clothes, and this Dawkins fellow is such a rude upstart who lacks the wit of my elegant circumlocutions, that, while unable to deal with the substance of his accusations, I should at least chide him for his very bad form.

Until Dawkins has trained in the shops of Paris and Milan, until he has learned to tell the difference between a ruffled flounce and a puffy pantaloon, we should all pretend he has not spoken out against the Emperor's taste. His training in biology may give him the ability to recognize dangling genitalia when he sees it, but it has not taught him the proper appreciation of Imaginary Fabrics.

Richard Dawkins on the Agenda

 
The Agenda with Steve Paikin is an interview show on TVO (TV Ontario). I watch it quite often.

Lately I've been more and more annoyed at Steve Paikin for his naive, simplistic views of religion and it's importance in the modern world. A few weeks ago he had an entire week of shows about the "resurgence" of religion in Canada. A resurgence that apparently only he and his fellow believers can see.

The show on Thursday night was just about the last straw for me. His interview with Richard Dawkins and the panel discussion afterwards were so bad that I'm going to stop watching the show. You can see the entire hour of the May 10th episode at [Richard Dawkins | Can We Live by Reason Alone?].

Pay close attention to Jordan Peterson in the panel discussion at the end. He's a Professor of Psychology at the University of Toronto. He accuses Dawkins of being very simplistic and naive about religion—and by implication he (Jordan Peterson) has the correct, deeply intellectual, understanding of religion that would trump Dawkins in a debate. Trouble is, nothing coming out of the mouth of Peterson convinces me that his reasons for believing in superstition are any better than the reasons Dawkins criticizes in The God Delusion. Or, am I missing some incredibly sophisticated version of the Courtier's Reply that's way over my head?

I especially like the claim that all hell will break loose if religion is abolished. The interesting part about such claims is that they come from people who are completely ignorant of what's going on in Europe. We're about to find out what happens when a country abandons religion because Sweden and other European countries are very close to that point. If the true believers are correct then these countries will soon become dens of iniquity and depravity—in sharp contrast to very religious countries like the USA. I can't believe that one of my colleagues would make such a stupid statement in public.

UPDATE: Read the comments on Dawkins.net

Biochemist Gregor Mendel Studied Starch Synthesis

Starch is the plant equivalent of glycogen. It consist of long branched chains of glucose residues. Starch is often stored in roots and tubers but it is also deposited in seeds where it can be mobilized following germination.

Mendel didn't know it at the time but he was dealing with the genetics of starch synthesis while crossing peas in his garden.

One of the genetic traits that Gregor Mendel studied was round ( R) vs. wrinkled ( r) peas. The wrinkled pea phenotype is caused by a defect in the gene for starch branching enzyme. Starch synthesis is very similar to glycogen synthesis. The main polymerization enzyme is starch synthase and it works just like glycogen synthase [Glycogen Synthesis]. Both starch and glycogen synthesis require an additonal enzyme to create new branches. In plants this enzyme is starch branching enzyme.

In the absence of this enzyme, starch synthesis is partially blocked and the developing peas have a higher concentration of sucrose. (In plants, glucose is transported as the disacharide sucrose.) This causes the mutant peas to absorb more water than normal peas and they swell to a larger size. When the seeds begin to dry out the peas with the defective enzyme lose more water and their outer surface takes on a wrinkled appearance. One copy of the active gene for starch branching enzyme is sufficient so the presence of one defective allele has no observable phenotype. When two mutant alleles are present the wrinkled phenotype is expressed because there's no active starch branching enzyme. The mutant allele is recessive to the wild type allele.

For some strange reason Mendel is more famous for discovering this simple genetic rule than for his contributions to understanding starch metabolism.

Bhattacharyya, M. K., Smith, A. M., Ellis, T. H., Hedley, C., and Martin, C. (1990) The wrinkled-seed character of a pea described by Mendel is caused by a transposon-like insertion in a gene encoding starch-branching enzyme. Cell 60:115-122.

[©Laurence A. Moran. Some of the text is from Principles of Biochemistry 4th ed. ©Pearson/Prentice Hall]

Gosling Relocation

 
Eva is a Ph.D. student in our department. She has a really cool blog called easternblot (get it?). You have got to see what she posted today [Annual gosling relocation at York University].

I've only got one small problem. Do we really need more Canada geese?

Regulating Glycogen Metabolism

Mammalian glycogen stores glucose in times of plenty (after feeding, a time of high glucose levels) and supplies glucose in times of need (during fasting or in “fight-or-flight” situations). In muscle, glycogen provides fuel for muscle contraction. In contrast, liver glycogen is largely converted to glucose that exits liver cells and enters the bloodstream for transport to other tissues that require it [The Cori Cycle]. Both the mobilization and synthesis of glycogen are regulated by hormones.

The regulation of glycogen metabolism is a good way to introduce the idea of signal transduction. This is a very popular part of modern biochemistry. It's basically a way in which signals from outside the cell are transduced through a chain of molecules to affect a particular biochemical reaction. In this case, we'll examine how the hormones glucagon, epinephrine, and insulin regulate glycogen synthesis and glycogen degradation.

Let's look at glycogen synthesis. Glycogen synthase is the enzyme responsible for adding UDP-glucose to a growing chain of glycogen. There are two forms of this enzyme. The inactive form is called glycogen synthase b and it is phosphorylated (P). The active form is called glycogen synthase a and it does not carry a phosphate group. The activity of glycogen synthase is controlled by covalent modification just like pyruvate dehydrogenase [Regulating Pyruvate Dehydrogenase].

The phosphorlation of enzymes is performed by kinases. In this case it's a very common cellular kinase called protein kinase A (PKA). The complete name of the enzyme is cyclic AMP-dependent protein kinase A because its activity is regulated by a messenger molecule known as cyclic AMP (cAMP). Cyclic AMP is made from ATP by the enzyme adenylyl cyclase and it is degraded by the action of an enzyme called phosphodiesterase

When cAMP is present inside the cell it binds to protein kinase A and activates it so that it can phosphorylate glycogen synthase. This shuts down glycogen synthesis by deactivating the enzyme. The key to hormonal regulation is the effect of the hormones on the production of cAMP. This takes place on the cell surface when the hormone binds to a cell surface receptor molecule.

Insulin, glucagon, and epinephrine are the principal hormones that control glycogen metabolism in mammals. Insulin, a 51-residue protein is synthesized by the cells of the pancreas. It is secreted when the concentration of glucose in the blood increases. Thus, high levels of insulin are associated with the fed state of an animal. Insulin stimulates glycogen synthesis in the liver. This makes sense since high concentrations of glucose indicate that it's time to store it as glycogen.

Glucagon, a peptide hormone containing 29 amino acid residues, is secreted by the cells of the pancreas in response to a low blood glucose concentration. Glucagon restores the blood glucose concentration to a steady-state level by stimulating glycogen degradation. Only liver cells are rich in glucagon receptors, so glucagon is extremely selective in its target. The effect of glucagon is opposite that of insulin, and an elevated glucagon concentration is associated with the fasted state.

The adrenal glands release the catecholamine epinephrine (also known as adrenaline) in response to neural signals that trigger the fight-or-flight response. Epinephrine stimulates the breakdown of glycogen to glucose 1-phosphate, which is converted to glucose 6-phosphate. The increase in intracellular glucose 6-phosphate increases both the rate of glycolysis in muscle and the amount of glucose released into the bloodstream from the liver. Note that epinephrine triggers a response to a sudden energy requirement; glucagon and insulin act over longer periods to maintain a relatively constant concentration of glucose in the blood.

Epinephrine binds to β-adrenergic receptors of liver and muscle cells and to α1-adrenergic receptors of liver cells. The binding of epinephrine to β-adrenergic receptors or of glucagon to its receptors activates the adenylyl cyclase signaling pathway. The second messenger, cyclic AMP (cAMP), then activates protein kinase A.

For now let's just take it as a given that glucagon and epinephrine trigger cAMP synthesis and this leads to shutting down of glycogen synthesis.


In addition to blocking glycogen synthesis, these hormones stimulate glycogen degradation. The glycogen degradation enzyme is called glycogen phosphorylase and it comes in two forms. Glycogen phosphorylase a is the active form and it's phosphorylated (it has an attached phosphate group). Glycogen phosphorylase b is the unphosphorylated form of the enzyme and it's inactive. Note the reciprocal relationship of the glycogen synthase and glycogen degradation enzymes. When both are phosphorylated, glycogen degradation is active and glycogen synthesis is not. When both are dephosphorylated, glycogen synthesis is active and glycogen degradation is blocked. This suggests a similar mechanism of regulation for the two enzymes.

The phosphorylation of glycogen phosphorulase is carried out by a kinase enzyme. In this case it's a specific kinase called phosphorylase kinase. Phosphorylase kinase is itself subject to activation by phosphorylation. The kinase that does this is our friend protein kinase A. Thus, epinephrine and glucagon will stimulate glycogen degradation in addition to stopping glycogen synthesis.



For every kinase there's a phosphatase that removes phosphate groups from proteins. Recall that insulin is released when glucose levels in the blood are high. The effect of insulin is the exact opposite of the effect of glucagon and epinephrine. Insulin binds to a cell surface receptor and triggers a pathway that leads to activation of protein phosphatase-1. This enzyme dephosphorylates the three enzymes shown above leading to activation of glycogen synthesis and deactivation of glycogen degradation. Insulin causes glucose to be stored as glycogen.



These kinds of kinase/phosphatase cascades are very common in eukaryotes. Believe it or not, this is one of the simpler examples.

Now, let's return to the effect of the hormone on cAMP synthesis. This is the key part of any signaling pathway and it's best illustrated by using a general model based on cAMP production. (There are other types of signaling pathways.)



The details aren't important unless you're seriously into signaling—like 50% of all biochemistry graduate students these days. Hormone binds to a cell surface receptor. The signal is transferred through the cell membrane to the inside part of the receptor molecule. This interacts with a G protein so that when hormone binds, the G protein is activated.

G protein then diffuses to the membrane bound adenylyl cyclase molecule and, when the two proteins connect, the activity of adenylyl cyclase is stimulated and cAMP is produced. This leads to activation of protein kinase A. The stimulatory effect of the signal transduction pathway is transient because cAMP is rapidly degraded by phosphodiesterase. Thus, hormone must usually be continuously present in order to get stimulation.

There are other hormones that inhibit cAMP production by activating different G proteins (G_i) that block adenylyl cyclase.

[©Laurence A. Moran. Some of the text is from Principles of Biochemistry 4th ed. ©Pearson/Prentice Hall]

Nicole Vienneau Has Gone Missing in Syria

 
Our friends are devastated because their niece, Nicole Vienneau, is missing in Syria. Her brother has a website with all the information [My Sister, Nicole Vienneau, Has Gone Missing in Syria].

My sister, Nicole Vienneau, has been missing in Syria since April 1st (40 days), near the town of Hama, while on a day-trip to see Qasr Ibn Wardan (a nearby castle) and the "Beehive Houses". We found her gear at the Cairo Hotel, but no sign of her after that.

If you have any details or contacts in the area, please contact me at mattv99@hotmail.com.

There's little chance that readers of Sandwalk can help but just in case please contact him immediately if you have any information.

Eye on DNA

 


Hsien-Hsien Lei, formerly of Genetics & Health, has a new blog called Eye on DNA. I've been reading it for a week or so and it looks really cool. Check it out.

Hsein-Hsein Lei (pronounced shen-shen lay) has a Ph.D. in epidemiology. She's ultimately interested in making everyone more healthy but she also wants everyone to know how your genes work. Right now she works out of London (UK) so North Americans can read her posting first thing in the morning!

City Lights Make Birds Sing at Night

 
Friday's Urban Legend: PROBABLY FALSE

BBC News reports that "Robins in urban areas are singing at night because it is too noisy during the day, researchers suggest" [City birds sing for silent nights].

Scientists from the University of Sheffield say there is a link between an area's daytime noise levels and the number of birds singing at night.

Until now, light pollution had been blamed because it was thought that street lights tricked the birds into thinking it was still daytime.

The findings are published in the Royal Society journal Biology Letters.

It turns out that it's not because of night lights that the birds are singing. It's because they can't make themselves heard over the din of city traffic so they wait 'till the dead of night to start singing. That way they get to annoy everyone around them.

I wonder if that's why people talk on cell phones when they're sitting on a quiet commuter train?