Monday's Molecule #120

 
This is a cartoon showing the genes present in a particular DNA molecule. Your task is to identify the kind of DNA molecule being depicted.

There is one Nobel Laureate who is most closely identified with this particular type of molecule. You have to identify the Nobel Laureate and what the prize was for.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are six ineligible candidates for this week's reward: Shumona De of Dalhousie University, Maria Altshuler of the University of Toronto, Mike Fraser of Toronto, Alex Ling of the University of Toronto, Laura Gerth of the University of Notre Dame, and Stefan Tarnawsky of the University of Toronto.

The Canadians continue their total dominance of the rest of the world. That's as it should be.

I still have one extra free lunch donated by a previous winner to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

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Theistic Evolution: How Does God Do It?

Theistic Evolution is a form of creationism that limits God's involvement in the creation event. The chief limitation is that most of God's activity have to be consistent with the facts of evolution.

Francis Collins has created a website devoted to his concept of BioLogos, which, it turn out, is just another word for Theistic Evolution. The website is funded by a grant from the John Templeton Foundation.

Many of us have difficulty understanding how a personal God can be involved in guiding evolution without violating the laws of physics and chemistry. In other words, how is Theistic Evolution/BioLogos compatible with science? This is a key question since we know that major scientific organizations (AAAS, NAS, NCSE) support the notion that science and religion are compatible. In fact, they explicitly support Francis Collins and Theistic Evolution.

Let's see how science and religion are compatible by looking at Question 14 on the BioLogos website [What role could God have in evolution?].

Divine Action is defined as God’s interaction with creation. Due to the understanding that evolution accounts for the diversity of present life forms, it might appear God played no role in the process of evolution. (See Question 26 about The Complexity of Life.) Clearly this contradicts the central doctrine of creation for many faiths. Christianity, for example, professes a God actively involved in creation. Many faiths share the concept of an interactive God, or theism. The opposing belief — the belief in an uninvolved, disinterested God — is deism.

Collins sees this a a major problem. According to him, Christians believe in creation and a strictly scientific explanation of evolution seems incompatible with this belief.

Elsewhere on the website, Collins makes it clear that theism is not deism and his view of Theistic Evolution/BioLogos is not deistic. So how does he solve the problem?

Any God worthy of the name has to be capable of miracles, and each of the great Western religions attributes a number of very special miracles to their conception of God. What can science say about a miracle? Nothing. By definition, the miraculous is beyond explanation, beyond our understanding, beyond science.

Ken Miller in "Finding Darwin's God" p. 239Well, it's not very clear to me. There is some hand-waving and some backhanded suggestions but nothing specific is described. In this sense, the Francis Collins version of Theistic Evolution is similar to that of Ken Miller in Finding Darwin's God. Here's the BioLogos version..

Even before Darwin’s contribution to biology, the scientific revolution in physics marked a tremendous advance in our understanding of the world. Scientists discovered that the world’s behavior could be explained and predicted with great accuracy on the basis of physical laws. Nature, as understood at the time, appeared to reliably follow a set of fundamental rules. For example, the motion of planets could be explained as a necessary result of their obedience to the force of gravity. This understanding of the world lent itself to the belief in a rational, consistent creator.

But, as Polkinghorne puts it, these laws might also come across as “a gift from the Greeks.”5 Given a second look, they challenge basic theism. For as much as these laws signify a rational creator, their trustworthiness could also imply God’s absence. After all, if the laws of nature can explain almost any phenomenon, how is God involved? In order to understand how God could take an active role, or how the world could have any inherent freedom, the laws of nature must be somehow open or flexible. The world’s future cannot be entirely determined or predictable from any given moment.

This is the potential area of conflict. If science says that evolution obeys the laws of physics and chemistry then there's no room for an interventionist God without violating those rules. And if your God does that then there's a conflict between science and religion. They are not compatible.

What to do? Miller and Collins, and many other theists, opt for a solution where God can intervene at the quantum level without ever being detected. Thus, nature only appears to obey the fundamental laws of physics and chemistry because God is clever enough to disguise his interventions.

The mechanical worldview of the scientific revolution is now a relic. Modern physics has replaced it with a very different picture of the world. With quantum mechanical uncertainty and the chaotic unpredictability of complex systems, the world is now understood to have a certain freedom in its future development. Of course, the question remains whether this openness is a result of nature’s true intrinsic chanciness or the inevitable limit to humans’ understanding. Either way, one thing is clear: a complete and detailed explanation or prediction for nature’s behavior cannot be provided. This was already a problem for Newtonian mechanics; however, it was assumed that in principle, science might eventually provide a complete explanation of any natural event. Now, though, we see that the laws of nature are such that scientific prediction and explanation are ultimately limited.

It is thus perfectly possible that God might influence the creation in subtle ways that are unrecognizable to scientific observation. In this way, modern science opens the door to divine action without the need for law breaking miracles. Given the impossibility of absolute prediction or explanation, the laws of nature no longer preclude God’s action in the world. Our perception of the world opens once again to the possibility of divine interaction.

Despite the uncertainty and unpredictability of the world, we are not forced to reject the earlier understanding of God’s creation as consistent and reliable. After all, the world still exhibits the same orderly behavior that inspired so many faithful scientists of earlier centuries. Regardless of the irregularity of tiny,quantum mechanical, or complex, chaos theoretical, systems, the sun stills rises and sets, the tides ebb and flow, and objects fall to the ground. Nature is reliable enough to reflect God’s faithfulness yet flexible enough to permit God’s involvement.

So this is how to make science and religion compatible. Let's restate it so that everyone can grasp the argument,

"... modern science opens the door to divine action without the need for law breaking miracles. Given the impossibility of absolute prediction or explanation, the laws of nature no longer preclude God’s action in the world.."

On the surface it seems to work since, by definition, all of God's interventions and guidance are undetectable. Therefore, there can't be any obvious conflict between the purely modern scientific view of evolution and creationism.

Personally, I don't think you can have your cake and eat it too. Once you start attributing events to God's intervention you are conflicting with a strictly materialistic interpretation of those same events. It doesn't matter whether your God is extremely careful to fool scientists into thinking that evolution is natural. The very act of postulating divine intervention in the natural world is not compatible with the scientific way of knowing.

Here's the bottom line, according to Francis Collins.

Our modern understanding of physical laws combined with a proper understanding of God’s relationship to time can be synthesized into a robust theistic worldview. Darrel Falk provides the following perspective:

“The Bible tells us that God created, but it does not tell us how, and we need to be careful that we do not force the God of the Universe into one of our human molds. […] What do we learn about the nature of God’s activity from studying the Bible? One thing we learn is that God builds freedom into His creation. […] Just as God builds freedom into our lives today, so freedom may well be a central component of God’s biological world as well. This is not to say that God is not playing a supervisory role in creation in a manner resembling the role God plays in my life and yours. But there is no a priori scriptural reason to assume that the biological world was created one species at a time by the God of the Universe “pushing creation buttons” each time he wanted a new species. […] God’s spirit guides the progression of life. His presence is never far from creation, just as it is never far from the events of my life. Nonetheless God respects my freedom and (I suspect) values freedom in the rest of creation as well.”

This is how evolution and creationism are compatible. This idea that "God’s spirit guides the progression of life" is the view that major scientific organizations and the NCSE endorse as being compatible with science.

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[Photo Credit: Francis Collins discusses “The Language of God”]

What American Science Teachers Can't Say

 
John Pieret is a pain in the lawyer. He has something to say about a recent court case [Accommodating the Law].

The latest ruling on the religion-science front is by a Federal judge in California holding that a public school teacher who called creationism "religious, superstitious nonsense," violated a creationist student's First Amendment rights.

Since John has been following the debate on the blogs, he realizes the implications.

The lesson is not restricted to such blatant cases, however. It is clear that a government teacher could not teach that philosophical naturalism is true, as that would clearly render most religions false. And it is more than doubtful that a public school teacher could teach that science was true while, at the same time maintaining that it was in conflict with most religions, since that which is in conflict with the truth is, necessarily, false.

This is pretty much what I thought. High school science teachers cannot say that the deluge never happened and they cannot say that the idea of a 10,000 year-old Earth is wrong.¹ That would violate the American Constitution.

God Bless America.

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1. I don't understand how they can get away with saying that evolution is true, since that statement is logically equivalent to saying that many forms of creationism are superstitious nonsense.

The Accommodationist Postion in Academic Matters

 
Margaret Somerville has written an essay on Facing up to the dangers of the intolerant university: Bird on an ethics wire. It is published in Academic Matters, the publication of the Ontario Confederation of University Faculty Associations (OCUFA).

Here's her brief biography as published in the journal.

Margaret Somerville is Samuel Gale Professor in the Faculty of Law and a professor in the Faculty of Medicine at McGill University and is the founding director of the McGill Centre for Medicine, Ethics and Law. In 2004, she received the UNESCO Avicenna Prize for Ethics in Science and in 2006 delivered the prestigious Massey Lectures.

I agree with a lot of what Somerville has to say about rampant political correctness in the universities.

That is where political correctness enters the picture. It excludes politically incorrect values from the “all values are equal” stable. The intense moral relativists will tolerate all values except those they deem to be politically incorrect—which just happen to be the ones that conflict with their values.

Political correctness operates by shutting down non-politically correct people’s freedom of speech. Anyone who challenges the politically correct stance is, thereby, automatically labeled as intolerant, a bigot, or hatemonger. The substance of their arguments against a politically correct stance is not addressed; rather people labeled as politically incorrect are, themselves, attacked as being intolerant and hateful simply for making those arguments. This derogatorily -label-the-person-and-dismiss-them-on-the-basis-of-that-label approach is intentionally used as a strategy to suppress strong arguments against any politically correct stance and, also, to avoid dealing with the substance of these arguments.

However, I also agree with Jeffrey Shallit that she applies her own standards inconsistently, such as when she insists that physicians are being "forced" to act against their conscience when treating certain patients [Margaret Somerville in "Academic Matters"].

Shallit is an expert on the difference between real free speech and its imposters.

I'd like to focus on another part of Somerville's essay.

Sixth, not only can we, but we must, cross the secular/religious divide, the science/religion divide and the divide between religions, if we are to find a shared ethics. This is where I believe both the fundamentalist religious people and the fundamentalist neo-atheists are wrong because they demand that we choose between religion and science. We must accommodate both.

Some would like to reduce religion to being seen as nothing more than a personal fantasy or superstition. But that’s not realistic. At best it will fail; at worst it will do serious harm because it will exacerbate the acrimony of the values conflicts and make it more likely, not less likely, that religion will become a focus of serious conflict. Also, because culture and religion are linked, even within democratic, multicultural, pluralistic Western societies, it will increase the number and intensity of the current values clashes and may contribute to culture wars.

I'm not sure what this means. I believe that religion is a superstition and I advocate a non-religious society. According to Somerville the "best" thing that could happen is that I will fail to convince people. The worst thing that will happen is that I will succeed but the result will make religion the focus of serious conflict. What a strange choice. The second option is exactly my goal.

I suppose the politically correct thing to do is to accommodate because we certainly can't have a situation where religion is challenged, can we?

Somerville says that religion and culture are linked. That's correct. It's an attitude that I want to change and there's lots of evidence that it is changing in other countries. Did this lead to "culture wars"? Yes, it did in some places—notably the Canadian province of Quebec in the 1960's. What Somerville fails to address is whether the culture wars are a good thing or a bad thing. She seems to be implying that we should not criticize religion because religious people might be upset. Don't we have a word for that kind of thinking?

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[Photo Credit: The Catholic Registrar]

Vanier Canada Graduate Scholarships

 
There are 166 winners of Vanier Canada Graduate Scholarships. Of these, 34 are from the University of Toronto and several will be in the labs of my close colleagues. Congratulations to all the winners.

The scholarships will be administered by the three granting councils and each one is worth an astonishing $50,000 per year. That means that these scholarships amount to twice the level of funding of a typical graduate student at my university.

There's no sound logic behind awarding such a sum. T. Ryan Gregory points out that if the scholarships had been for $25,000 per year, the excess could have funded 73 research grants at an average of $34,000 per year. I agree that this money could have been better spent.

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Gary Goodyear Explains Canada's Science Policy

 
Gary Goodyear, you might recall, is Canada's Minster of State (Science and Technology). He is a chiropractor who doesn't accept the scientific view of evolution.

The policy of the Conservative Party is to cut funding to the major granting agencies (SSHRC, NSERC, CIHR) by $148 million over the next few years. This will have a disastrous effect on basic research in Canada.

At a recent meeting in Washington (USA), Goodyear explained how Conservative ideology is driving science funding [Canadian research may hold key to ‘clean coal:' Goodyear].

Only days after Mr. Obama delighted America's scientific community by saying the “days of science taking a back seat to ideology are over” – a clear reference to the eight years George W. Bush was president – Mr. Goodyear made a point of claiming Canada's Conservative government took science seriously.

“Canada sees the role of science and technology in contributing to global economic growth and recovery,” he said. “We know that the jobs of tomorrow are found in the discoveries of today, so we look at research funding as investment — investment in innovation, in scientific discovery, in job creation, and as a hedge against tough economic conditions.”

But he also said the government's role in funding science went beyond backing pure research. Ottawa's science spending reflects “our government's emphasis on commercializing research and improving the processes that help get innovative ideas to the marketplace,” Mr. Goodyear told a two-day AAAS forum on science and technology.

“Commercialization is one area in which public policy makers play a huge role in enabling the private sector to do what it does best — turn knowledge into innovation, and innovation into greater wealth and well-being for people.”

I wish I were an American. President Obama seems to know the difference between science and technology and he seems to understand where real creativity and innovation can be found—it's not in technology development, it's in curiosity motivated basic research.

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Don't Like Evolution in Alberta?

 
Let's say you live in Alberta and you oppose evolution because it conflicts with your religion. Is this a problem if your kids attend public school?

Maybe it is right now but if the Alberta government passes its new bill you will be able to take your kids out of class whenever evolution is discussed [Evolution classes optional under proposed Alberta law].

"This government supports a very, very fundamental right and that is parental rights with respect to education," said Premier Ed Stelmach.

Although Stelmach has confirmed the bill will give parents the authority to exclude their kids from classes if the topic of evolution comes up, Education Minister Dave Hancock said it won't change anything.

"With respect to values, religion and sex education have always been areas of concern for parents, and they've always been areas parents have had the right to be notified about and to exempt their students from," Hancock said.

I can't imagine why a parent would want to keep their children from learning about evolution. Are they so insecure about the strength of their religion that a lesson or two about evolution could turn their children into atheists?

Hopefully, this bill won't pass without being amended. If it does, then Alberta will look even more like some of the hick states in the USA that have tried to ban evolution in the schools.

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Nobel Laureate: Paul Ehrlich

 

The Nobel Prize in Physiology or Medicine 1908

"in recognition of their work on immunity"

Paul Ehrlich (1854 - 1915) won the Noble Prize in 1908 for his contributions to understanding immunology. His co-recipient was Ilya Ilyich Mechnikov.

Ehrlich was already a well-known scientist at the time he received that Nobel Prize and he subsequently went on to achieve even greater fame for synthesizing a drug to treat syphilis [Monday's Molecule #119].

Although Ehrlich's specific contributions to immunology aren't mentioned in the presentation speech, they mostly concern the discovery of antibodies. Here's how his contribution is described ...
THEME:
Nobel Laureates

An endless series of questions now arises: Why are antibodies only built up against some substances and not against all substances which are foreign to the organism? Where are the antibodies formed? By what process are they formed? What is the nature and constitution of these antibodies? How do they react on the microorganisms and their poisons? And various other questions which are important as regards the development and practical utilization of the theory of immunity. It is also a matter of great interest that connecting links have been found between the theory of immunity and the normal physiological processes.

A great deal of intensive and very fruitful work has been devoted to these questions in the last one and a half decades. A large number of research scientists have served the cause of science well by their discoveries and achievements. It is not possible here to report on the extent to which the questions have been answered, neither is it possible to describe the separate accomplishments of individual scientists in this field.

A man who has been responsible for important scientific progress as organizer and leader in this field deserves to be mentioned among the first of those who have dedicated themselves to a study of immunity, is the research scientist Paul Ehrlich, already famous for his other biological work, and the Professorial Staff of the Caroline Institute wishes to honour him too with this year's Nobel Prize for his work in the sphere of immunity.

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[Photo Credit: Wellcome Trust Photographic Library]

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

NCSE v National Association of Biology Teachers

There's been a lot of discussion recently about the proper role of scientific organizations, such as the American Association for the Advancement of Science (AAAS), The Royal Society, and the National Academies of Science (NAS), in the conflict between science and religion. Many people, including me, think that these scientific organizations should remain neutral on the issue of possible conflict between sceince and religion.

The situation with respect to the National Center for Science Education (NCSE) is more complicated. I believe that NCSE should also avoid taking a stand in favor of some religions over others, and in favor of religious versus non-religious interpretations of the conflict.

It's worth reminding people of how this issue has played out in the past so I'm posting a brief summary of an incident that took place over ten years ago.

In 1995, the National Association of Biology Teachers issued the following statement.

The diversity of life on earth is the result of evolution: an unsupervised, impersonal, unpredictable and natural process of temporal descent with genetic modification that is affected by natural selection, chance, historical contingencies and changing environments.

A number of theologians and theistic evolutionists objected to the inclusion of "unsupervised," "impersonal," and "unpreditable" since this clearly conflicted with their religious beliefs.

In 1997, NABT reviewed their statement in light of these complaints and rejected them, voting to keep the original statement. At that point, Eugenie Scott, the Executive Director of NCSE stepped in and persuaded the teachers to drop "unsupervised" and "impersonal" from the statement.

Why did NCSE support the theologians and theistic evolutionists against the biology teachers? It's because Genie draws a line between materialistic naturalism and philosophical naturalism and she thinks the biology teachers stepped over that line (see National Association of Biology Teachers incident for a description of the event). She believes that science cannot know whether evolution is unsupervised and/or impersonal.

I suppose she would have been comfortable with the following statement ....

The diversity of life on earth is the result of evolution: a natural process of temporal descent with genetic modification that is affected by natural selection, chance, historical contingencies and changing environments. Science is unable to tell whether evolution was unsupervised and impersonal or whether it was supervised by a personal god.

That's what she and her allies really want the teachers to say even though they don't insist upon it.

I disagree. I think that scientific evidence points overwhelmingly to a life that was not designed for a purpose. I think there's no evidence whatsoever to suggest that evolution was guided and I don't think we should censor ourselves from saying this.

I think Genie and NCSE are making too big of a distinction between methodological naturalism and philosophical naturalism. Saying that there is no evidence of purpose and direction is a perfectly good methodological statement and the conclusion that, therefore, evolution is unsupervised and unguided is rational based on what we know about science.

It was wrong of NCSE to pressure the biology teachers to change their statment.

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Some scientists are astrologers, therefore science and astrology are compatible

 
Most people would laugh at you if you were to say that, "Some scientists are astrologers, therefore science and astrology are compatible." There's a serious logical flaw in that statement. It probably has a name but I can't think of it right now.

Chris Mooney sides with the accommodationists in the fight over how scientific organizations should behave Atheists for Common Cause With the Religious On Evolution. That's fine, he's entitled to his opinion.

What he's not entitled to is blatantly illogical arguments like the following.

First, I don’t see anything particularly “philosophical” about the accommodationist stance. Rather, holding that there is no necessary conflict between faith and science is an empirical matter: There are a vast number of different religions traditions in the world, and a still more vast number of ways in which different people profess and live out their faiths. In some of these traditions, and for some of these people, there is stark conflict with science; in other traditions, and for other people, there isn’t. That’s just a fact, and one that can be demonstrated simply by identifying any number of scientists who are religious, any number of religious leaders and denominations which embrace evolution, and so on.

There are religious people who are scientists. That's a fact, but it doesn't necessarily mean what Chris Mooney thinks it means.

It means the same thing as saying that some Intelligent Design Creationists are scientists. That's also a fact.

Please, let's stop using illogical arguments in this discussion. We can all agree that there are Theistic Evolutionist scientists, Young Earth Creationist scientists, Intelligent Design Creationist scientists, and scientists who believe in astrology and homeopathy. There are even scientists, as Chris knows, who deny global warming.

You can't draw any conclusion from those facts about whether science is compatible with all those beliefs.

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[Image Credit: Astrology]

Head Growth and Tail Growth

There are many examples of polymerization reactions in biochemistry: DNA/RNA synthesis, protein synthesis, carbohydrate synthesis and fatty acid synthesis. In some cases the polymer consists of a string of identical monomers (e.g. some carbohydrates, fatty acids) while in other cases the polymer can be a mixture of several different kinds of monomers (e.g. nucleic acids, proteins).

There are two basic strategies of polymerization: head growth and tail growth. The basic concept is often presented in the textbooks when DNA synthesis or protein synthesis is described.

I posed a simple question yesterday and got some comments on the blog and in my email [Are You as Smart as a Second Year University Student? Q6]. Some people didn't have a clue what the question was about and some people declared that the question was silly. One commenter said, "Sounds like a stupid question that has something to do with memorizing someone's silliness and nothing to do with understanding biochemistry."

Let's see if you agree that this is a silly question that has nothing to do with understanding biochemistry.

In head growth the head of the growing polymer is "activated"—it carries the energy for the addition of the next monomer. This "activation" energy is depicted below as a red bond. Each of the incoming monomers is also "activated" but the energy of the activated bond will be used for the next addition once the monomer is added to the growing polymer.

The classic example of head growth is protein synthesis. Fatty acids are also made in this way.

In tail growth the head of the growing polymer is not activated. The energy for the addition of each monomer is supplied by the incoming activated monomer.

The best examples of tail growth strategy are nucleic acid synthesis, where the activated monomers are nucleoside triphosphates, and synthesis of storage polysaccharides, where the activated monomer is UDP-glucose.

Why is it important to understand the difference between head growth and tail growth? Because one type is unidirectional whereas the other type is compatible with both lengthening and shortening of the polymer.

Let's look at the process of error correction as seen in the proofreading reaction of DNA biosynthesis. Imagine that the replication complex makes a mistake and adds the wrong nucleotide to the growing DNA molecule. The incorrect nucleotide is subsequently removed by the proofreading activity of DNA polymerase. Since DNA synthesis is a tail growth mechanism, the removal of the most recently added monomer doesn't change the chemical reactivity of the growing end of the chain so the reaction can now continue in the direction of lengthening as shown by the green check mark in the figure.

If DNA synthesis utilized a head growth mechanism, then proofreading would not have evolved since removal of the last monomer also removes the activated head of the growing chain.¹ That's why there's no proofreading in protein synthesis.

The synthesis of storage carbohydrates such as starch and glycogen doesn't involve proofreading but there's still a very good reason why the mechanism is tail growth. Recall that starch and glycogen are polymers of glucose and their role is to store glucose as a potential carbon source in time of need. When the need arises, the ends of the polysaccharide chains are nibbled back releasing glucose molecules (as glucose-6-phosphate). These molecules enter the glycolysis pathway.

The degradation reaction terminates when the immediate need for glucose has been met. Later on, in time of plenty, the starch and glycogen chains can be re-extended by adding more glucose residues. The reason why this is possible is because starch and glycogen synthesis is an example of tail growth just like nucleic acid synthesis. If nibbling the ends of the polysaccaride chains removed the activated head, as it would in the case of head growth, then the synthesis reaction could not occur. Thus, the fundamental reason why tail growth evolved in both nucleic acid synthesis and glycogen synthesis is the same.


One of the other reasons for discussing this concept in introductory biochemistry classes is that it gets students thinking about the big picture. Rather than focusing on the details of any one type of polymerization reaction they are encouraged to think about general strategies and they are stimulated to compare and contrast different types of reactions. Unfortunately this approach is rapidly disappearing from introductory biochemistry courses because they are often taught in sections where the lecturer in each section is a specialist in information flow, carbohydrate metabolism, or protein structure. These lecturers often don't know enough about the other subjects to make the relevant comparisons.

That wouldn't matter a great deal as long as the introductory biochemistry textbooks did the job for them. There are two reasons why that doesn't seem to work. First, many team-taught courses don't use a textbook because the individual experts in each section think they know everything they need to know and the students can just rely on the lecture notes.

Second, the comparative biochemistry concepts and principles are disappearing from the textbooks. This is partly because of the way courses are taught and the way students are examined—once the exam on carbohydrate metabolism is over, students don't have to remember anything about carbohydrates while preparing for the next test on lipids and membranes. It's also partly because some biochemistry courses don't cover all aspects of biochemistry in a single course. Many introductory biochemistry courses, for example, separate information flow (DNA replication, transcription, translation) from the rest of biochemistry.

Because of the negative feedback from the customers (Professors) my textbook does not mention head growth and tail growth. The concept is also missing in all of the other introductory biochemistry textbooks.

I'm putting it back in the next edition of my book even if it means losing some adoptions.

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1. Admittedly, one could imagine evolving ways around this limitation; by re-activating the end in a separate reaction, for example.

Are You as Smart as a Second Year University Student? Q6

 
Are You as Smart as a Second Year University Student?

Question 1
Question 2
Question 3
Question 4
Question 5
Today was the final exam in my introductory biochemistry course. It was kinda sad because it's the last year I'll be teaching this course.

Here's a variation on one of the questions. How many of you know the answer?

There are two basic strategies in polymerization reactions: head growth and tail growth. For each of the following polymerization reactions identify whether it is an example of head growth or tail growth.

a) DNA synthesis
b) starch synthesis
c) fatty acid synthesis
d) protein synthesis

Bonus points for Sandwalk readers if you can explain why it's important for some polymerization reactions to use a tail growth strategy.

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Monday's Molecule #119: Winners

 
The molecule is arsphenamine or Salvarsan—also known as compound 606 or "magic bullet." It is the first synthetic drug developed specifically to treat syphilis. It was discovered in Paul Ehrlich's lab in 1909. Ehrlich had already receive the Nobel Prize for his pioneering work on antibodies.

The discovery of arsphenamine was the subject of a 1940 movie called Dr. Ehrlich's Magic Bullet starring Edward G. Robinson as Dr. Ehrlich.

This week's winner is Laura Gerth of the University of Notre Dame. She identified the molecule, the Nobel Laureate, and even got the correct name of the movie! Laura has already agreed to donate her free lunch to a starving undergraduate.

The undergraduate winner is Stefan Tarnawsky of the University of Toronto. He took time off yesterday when he should have been studying for this morning's final exam in Biochemistry! I hope he didn't regret it.

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This is a very famous molecule. There was even a Hollywood movie about it! Can you name it?

There is one Nobel Laureate who is most closely identified with this particular molecule, although it had nothing to do with the awarding of the Nobel Prize. You have to identify the Nobel Laureate and what the prize was really for.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are six ineligible candidates for this week's reward: Peter Horwich from Dalhousie University, Devin Trudeau from the University of Toronto, Shumona De of Dalhousie University, Maria Altshuler of the University of Toronto, Mike Fraser of Toronto, and Alex Ling of the University of Toronto.

The Canadians continue their total dominance of the rest of the world. That's as it should be.

I still have one extra free lunch donated by a previous winner to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

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

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Monday's Molecule #119

 
This is a very famous molecule. There was even a Hollywood movie about it! Can you name it?

There is one Nobel Laureate who is most closely identified with this particular molecule, although it had nothing to do with the awarding of the Nobel Prize. You have to identify the Nobel Laureate and what the prize was really for.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are six ineligible candidates for this week's reward: Peter Horwich from Dalhousie University, Devin Trudeau from the University of Toronto, Shumona De of Dalhousie University, Maria Altshuler of the University of Toronto, Mike Fraser of Toronto, and Alex Ling of the University of Toronto.

The Canadians continue their total dominance of the rest of the world. That's as it should be.

I still have one extra free lunch donated by a previous winner to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

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Brandon Thinks I'm Illogical

 
Brandon writes on Siris: Moran and the 'Courtier's Reply'.

Larry Moran suffers what looks like a complete lapse of critical thought in a recent post on the so-called 'Courtier's Reply'. As he puts it:

Atheists and theists often discuss the existence of God. Unfortunately, these discussions often degenerate into classic Christian apologetics where the main goal of the theist is to rationalize why his or her god doesn't conflict with rationality.

Before long they are rambling on about how to resolve the problem of evil or why god doesn't reveal herself. These problems only exist once you've accepted the premise that there is a god/spirit. This sort of apologetics has nothing to do with the fundamental question of whether god exists in the first place.

Now, Moran is usually pretty reasonable; but this argument is so thoroughly absurd and irrational that he should be ashamed to have put it forward. Let's abstract from the situation a bit to show why. Take a position, A, and a contrary position, B. Now suppose that A gives an objection to B. To this objection, B responds with an argument, whether good or bad, that the objection fails. To which A replies, "This sort of apologetics has nothing to do with the fundamental question of whether B is true in the first place." But this is demonstrably false, of course; B's argument was dealing with an objection put forward by A. What A is trying to do is irrational: he's trying to rig the argument so that his objections are never answered, independently of whether they can be, by dismissing any answer that might be made to them as 'apologetics that have nothing to do' with the original question.

So it is here. The reason theists talk about the problem of evil or the problem of hiddenness is that atheists typically raise these as objections to theism.

I don't talk about the "problem of evil" when I'm discussing the possible existence of supernatural beings and neither do many other atheists.

The point of the Coutrier's Reply is that theists bring up these "problems" when they should be discussing whether gods exist.

The Courtier's Reply does not apply when atheists engage in discussions about the problem of evil or any other problem that theists have when they're trying to reconcile superstition and rationality. It only applies when theists try moving the goalposts—which they do all the time.

It's unfortunate, too, because it makes Moran seem more unreasonable than he probably is. He ends by saying that he would be happy to discuss evidence for theism. This would sound somewhat more sincere if he hadn't just finished giving an argument for why he doesn't have to listen to any responses to any objections he might raise against this purported evidence.

I said I'd be happy to discuss any evidence for the existence of a spiritual world and I stand by that statement.

Brandon, if you or anyone else wants to debate the existence of the supernatural then, by all means, give it your best shot. Give me the evidence for the existence of god(s) and I promise to listen. Maybe I misunderstood your "evidence." Are you saying that the presence of evil in the world is evidence that god(s) exist?

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