Last week's molecule was cobalamin or vitamin B12. The structure was solved by Dorothy Crowfoot Hodgkin who won the Nobel Prize in Chemistry in 1964. There have been ten Nobel Prizes for work on vitamins and coenzymes. There were a lot of people who got this one right. The winner is Piotr Gasiorowski. The undergraduate winner is Jacob Toth [Monday's Molecule #218]. That makes four lunches that I owe Jacob. Right now, he's far away (British Columbia) but he may be coming to Toronto to collect. That may cut down on his chances of winning! 
Today's molecule is a very common enzyme found in all species (I don't know of any exceptions). It's part of a pathway that's familiar to all biochemistry students. The figure illustrates a classic "induced fit" mechanism of substrate binding where the binding of one substrate creates the binding pocket for the second substrate. In this case, it's the homodimeric animal version of the enzyme showing rotation of the small domain of one of the subunits. Name the enzyme and the reaction it catalyzes.
There's more. In order to win a free lunch you have to explain something else. It's related to the fundamental concepts that all biochemistry students should know. The standard Gibbs free energy change for the reaction catalyzed by this enzyme is ΔG°′ = -31.5 kJ mol-1. What does that mean if you are trying to understand the reaction that takes place inside the cell? Is there a reason why this reaction isn't coupled to synthesis of ATP? I'm interested in seeing how most Sandwalk readers understand the fundamental concept of reaction thermodynamics.
Email your answers to me at: Monday's Molecule #219. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.
There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)
In a recent post, I discussed the way Kevin Padian views evolution and why he thinks textbooks misrepresent evolution [see Misrepresentations of Evolution in Textbooks: Definition of Evolution According to Kevin Padian]. Now I want to quote his position on the conflict between science and religion.
Keep in mind that Kevin is President of the National Center for Science Education. He isn't speaking for NCSE in this paper but it's fair to say that his view is quite compatible with those of other members of the NCSE leadership.
Here's what Kevin writes under the subtitle "Avoid pitting science against religion, even though sometimes there are real conflicts" ...
Kevin Padian is a professor at the University of California, Berkeley and Curator of Paleontology at the University of California Museum of Paleontology. He is also President of the National Center for Science Education (NCSE).
He wrote an article for Evolution: Education and Outreach in which he describes misrepresentations of evolution in textbooks (Padian, 2013). Since he is a prominent leader in the fight against creationism, we need to pay attention when he tells us how evolution should be taught in public schools.
Before examining some of those "misconceptions," let's review some earlier papers in Evolution: Education and Outreach. The very first issue contained an article by John N. Thompson where he defined evolution as ...
Evolution is quite simply heritable change in the genetic structure of a population. There is nothing in this or any similar standard definition of evolution that requires that genetic change in the average size, shape, or any other trait be maintained for a hundred, a thousand, or a million years before it can truly be called evolution. (Thompson, 2007)
Unfortunately, Thompson is under the mistaken impression that natural selection is the only significant mechanism of evolution but that's not the point. The point it that he, and many others, see evolution as a continuous and ongoing process that includes the minor fluctuations that Kevin Padian dismisses.
The latest issue of BAMBED (Biochemistry and Molecular Biology Education) contains a series of articles on "Foundational Concepts and Assessment Tools for Biochemistry and Molecular Biology Educators." The goal is to get teachers to change their way of teaching undergraduate courses in biochemistry and molecular biology.
The first paper is an introduction to "Promoting Concept Driven Teaching Strategies in Biochemistry and Molecular Biology" (Mattos et al, 2013). The authors point out that ASBMB (American Society for Biochemistry and Molecular Biology) has been advocating concept driven teaching strategies for over a decade. What they don't mention is that this advocacy has been remarkably unsuccessful The majority of biochemistry and molecular biology courses are still taught in a memorize-regurgitate format. Most American courses are taught to the MCAT. Understanding concepts won't get you a good grade on the MCAT.
The idea of teaching fundamental concepts is useful if biochemistry and molecular biology are foundational courses designed as prerequisites for more advanced study. That's not how biochemistry is seen in most America colleges. Students usually don't take the course until their junior year and many don't take it until they are seniors! These courses are not generally seen as prerequisites for other courses in the biological sciences.
That's not how it works in Canada where biochemistry is a second year course and it is a prerequisite for many third year and fourth year courses. The importance of concept driven teaching should be more obvious in Canada. It isn't, in my experience. That doesn't mean we don't talk about it—or course we do. We all think that teaching concepts is a great idea. Problem is, we don't do it in our introductory courses.
This is one of the reasons why MOOCs are seen as a viable alternative to in-class biochemistry courses. You can spew out facts for multiple choice exams just as easily on a video as you do in a classroom. If, instead, we were actually teaching a concept driven course using a student-centered approach, then MOOCs would seem ridiculous.
Mattos et al. (2013) report that ASBMB developed a three pronged approach ...
- Building a network of scientists and educators focused on using and disseminating evidence-based teaching best practices.
- Fostering both an understanding of the use of appropriate assessment, and the creation of a network of educators focused on defining the foundational concepts of the discipline, identifying key cross-disciplinary principles, and incorporating the appropriate skills necessary for students to succeed in the practice of science into the curriculum and assessment of student outcomes.
- Promoting best practices in the education of our students by providing appropriate teaching and assessment resources for faculty.
They applied for, and received, a grant from the National Science Foundation (USA) to address these challenges. The results of those studies are ready to be published.
The next paper in this BAMBED issue describes the foundational concepts that all biochemistry & molecular biology instructors have to teach. Can you guess what they are before I post the answer? Put your best guesses in the comments.
Mattos, C., Johnson, M., White, H., Sears, D., Bailey, C. and Bell, E. (2013) Introduction: Promoting concept driven teaching strategies in biochemistry and molecular biology. Biochem. Mol. Biol. Educ. 41:287–288. [doi: 10.1002/bmb.20726]
Evolution News & Views (sic) will bring together David Klinghoffer and Stephen Meyer to discuss Darwin's Doubt on the Michael Medved show [The Closing of the Scientific Mind: Join Us on October 23 in the Medved Studio for a Special Edition of the Science & Culture Update]. The topic is the "closing of the scientific mind," surely an appropriate topic for three men who are not scientists.
Does science open minds, or close them? A "scientific view" is frequently taken as being basically synonymous with skepticism, questioning, and independent thinking. All good and wonderful things! Yet very often, self-proclaimed paladins of "science" are impatient with genuine skeptics, flee from debate, or find a variety of other creative ways to avoid having to confront challenges to their beliefs.
In the special October 23 edition of the Science & Culture Update on the Michael Medved Show, you'll have a chance to talk about science and skepticism, closed minds and open ones, live in the KTTH radio studio, with Mr. Medved, Darwin's Doubt author Dr. Stephen Meyer, and Evolution News & Views editor David Klinghoffer. All three are Discovery Institute senior fellows.
For the discussion, they'll take as a case in point the critical reception of Dr. Meyer's book, Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design, which has sparked furious debate -- and also a great deal of artful dodging of the relevant scientific issues by opponents of the theory of intelligent design. Why are critics of ID so determined to flee from a fair fight?
I think I'm going to try and listen in. I can't wait to hear how Medved, Meyer, and Klinghoffer respond to my scientific critique of Chapter 5: "The Genes Tell the Story?"
John G. West is Vice President for Public Policy and Legal Affairs of the Center for Science and Culture (CSC)—the most important Intelligent Design Creationism propaganda organization. He is upset because some reporters describe Intelligent Design Creationism as a form of creationism. I've taken an excerpt from his post at Attempting to Win the Debate over Intelligent Design through Stereotyping and changed just a few words so you can get the gist of his argument.
The really discouraging thing here is not that some reporters are critical of evolution. It is that so many of them apparently see nothing wrong with preventing evolutionary biologists from defining their own position. This is a very strange way to do journalism, and if journalists started to apply their approach to evolution to other topics, I think it would become manifestly clear how unfair it is. Imagine, for example, a journalist deciding to use "Marxist" as a neutral label for President Obama based on the views of certain right-wing academics and political activists. Would that be regarded as fair or impartial by most journalists? Of course not. What if a reporter redefined Marxist to mean anyone who supports more active government? Would that make applying the term to Obama in a news story more defensible? Hardly. Yet when reporters label evolutionary biologists as "Darwinists," they are essentially doing the same thing.
What is really going on here is censorship. When reporters use as a "neutral" description of evolution a polemical smear invented by its critics, they are effectively silencing evolutionary biologists by not allowing them to speak for themselves. They are poisoning the well so no one will be willing to listen to the actual views expressed by evolutionary biologists. Journalists who write about evolution should re-read the Society of Professional Journalists' Code of Ethics, especially the provisions calling for them to "Support the open exchange of views, even views they find repugnant" and to "Give voice to the voiceless...."
Whatever a news reporter's views on evolution, he or she has a professional duty not to simply spread stereotypes and caricatures. That duty means nothing if it only applies to news coverage of groups and positions with which the reporter agrees. The real test of fairness for reporters is how they treat those with whom they disagree. When it comes to evolution, sadly, many reporters are failing the test.
The week is half over and nobody told me it's Quackery Week. Perhpas that's because it's only Quackery Week in the USA. The US Senate passed a resolution ...
A resolution designating the week of October 7 through October 13, 2013, as “Naturopathic Medicine Week” to recognize the value of naturopathic medicine in providing safe, effective, and affordable health care.
Don't worry. Orac is on to it with: Naturopaths and vaccines.
But let's not forget that the Canadian College of Naturopathic Medicine makes their students take a course in Homeopathic Medicine and another im Asian Medicine and Acupuncture [Naturopathic "Doctors" Graduate from Convocation Hall on the University of Toronto Campus].
This is one more reason why we have to teach critical thinking in high school and in universities.
There are days when I think that Canadians will never, ever, become rational, scientifically literate, thinkers. Today is one of those days.
As of right now, 19,853 people have signed a petition asking the Girl Guides of Canada to take GMO ingredients out of girl guide cookies [Girl Guides of Canada: Take all GMO ingredients out of Girl Guide Cookies].
The petition is organized by Maya Fischer and Linda Cirella in Victoria, BC. Here's what they say ...
Our family tries to only buy food that is non-GMO or organic. The reason we're so concerned is because there have been no long-term studies showing that it is safe for people to eat or grow GMO foods. In fact, GMO studies on animals have shown infertility, immune system problems, accelerated aging, faulty insulin regulation, and changes in major organs and the gastrointestinal system. The American Academy of Environmental Medicine actually asks physicians to advise patients not to eat foods with GMO ingredients.
The really sad part is the message that those two women are sending to young girls across Canada. They're saying that science doesn't matter. You can just make up stuff to support your biases and prejudices.
UPDATE: Please read: With 2000+ global studies confirming safety, GM foods among most analyzed subjects in science.
A popular weapon used by those critical of agricultural biotechnology is to claim that there has been little to no evaluation of the safety of GM crops and there is no scientific consensus on this issue.
Those claims are simply not true. Every major international science body in the world has reviewed multiple independent studies—in some cases numbering in the hundreds—in coming to the consensus conclusion that GMO crops are as safe or safer than conventional or organic foods, but the magnitude of the research has never been catalogued.
Still the claim that GMOs are “understudied”—the meme represented in the quotes highlighted at the beginning of this article—have become a staple of anti-GMO critics, especially activist journalists. In response to what they believed was an information gap, a team of Italian scientists catalogued and summarized 1783 studies about the safety and environmental impacts of GMO foods—a staggering number.
The researchers couldn’t find a single credible example demonstrating that GM foods pose any harm to humans or animals. “The scientific research conducted so far has not detected any significant hazards directly connected with the use of genetically engineered crops,” the scientists concluded.
The research review, published in Critical Reviews in Biotechnology in September, spanned only the last decade—from 2002 to 2012—which represents only about a third of the lifetime of GM technology.
I snapped this picture on my way back from class. That's the science library on the left and the Medical Sciences Building on the far right. The tall buildings in the background are at the corner of College and Yonge in the heart of downtown Toronto.
I love being on a university campus.
Some people think it's important to define your terms before engaging in a debate. I am one of them and the term that most often leads to confusion is "evolution."
Let's look at an example. Ned Bowden is a chemistry professor at the University of Iowa. He published an article in the university magazine: Common ground: A case for ending the animosity between science and religion. Bowden said ...
It’s remarkably consistent how evolution and Genesis look at the process and tell the same stories using different words. Science can never prove or disprove God, but science can provide support for the existence of God and that is what the Big Bang and evolution can give us. There are, of course, holes in the theory of evolution that are big enough to drive a semi-truck through, but it is highly possible that evolution was the tool that God used to bring humans into being.
The Christians must be getting worried about all those atheist signs popping up on buses and billboards. Ken Ham and "Answers in Genesis" decided to strike back by hosting a 16 second video on an electronic billboard in Times Square, New York.
Watch the video if you dare.
I'm thinking that Young Earth Creationism and Christian fundamentalism aren't going to resonate too well with the average person in Times Square. This kind of publicity could really backfire by drawing attention to the large number of atheists in America.
Would this sort of thing ever have happened without Dawkins, Hitchens, Dennet, Harris and all those other obnoxious and disrespectful atheists who started making such a fuss just a few years ago? I think we're finally making progress and it's mostly due to them.
I've been having a discussion with Elizabeth Liddle in the comments to: Barry Arrington, Junk DNA, and Why We Call Them Idiots . I think it's important to understand why scientists first started thinking that most of our genome is junk. It's important to understand that these scientists were not Darwinists and their predictions were not based on an understanding of natural selection.
Let's look at a famous paper by Jack Lester King and Thomas Hughes Jukes.1 The title of the paper is "Non-Darwinian Evolution" and it was published 44 years ago in the May 16, 1969 issue of Science [read it at: Science 164:788-798].
The subtitle of the paper is "Most evolutionary change in proteins may be due to neutral mutations and genetic drift" but that's not what I want to talk about. This paper is among the first to predict the presence of large amounts of junk DNA in our genome. King and Jukes didn't call it "junk"—that term was introduced by Susumu Ohno in 1972—but that doesn't matter. When King and Jukes talk about "superfluous DNA" they mean "junk."
Here's the relevant part of the paper ...
Last week's molecule was α-tocopherol or vitamin E. You do not need vitamin E supplements and they may even be harmful. Lots of people got it right. The winner was Susan Heaphy [Monday's Molecule #217].
This is the week of Nobel Prize announcements so I've chosen an appropriate molecule. It is very complicated. So complicated, in fact, that there was a Nobel Prize for solving its structure. Name the molecule, the winner of the Nobel Prize, and the year it was awarded. You must get all three answers correct.
Email your answers to me at: Monday's Molecule #218. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.
There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)
Dr. Azor Betts (1740-1809) is a distant cousin of mine. His mother was Mary Beldon and I descend from another Mary Beldon who is a cousin of Dr. Azor Betts' mother. Our common ancestor is William Belden (1609-1655) of Wethersfield, Connecticut.
Dr. Betts' father was Nathan Betts and I'm also related to him through my ancestor Tama Betts (1754 - ).
Dr. Azor Betts was a physician in New York city at the beginning of the American Revolution in 1776. At the time there was a smallpox epidemic in the city and other parts of the colonies. George Washington had issued an order that no soldier of the Continental Army should be inoculated. In spite of this order Dr. Betts inoculated several officers at their urging.
The General presents his Compliments to the Honorable The Provincial Congress, and General Committee, is much obliged to them, for their Care, in endeavoring to prevent the spreading of the Small-pox (by Inoculation or any other way) in this City, or in the Continental Army, which might prove fatal to the army, if allowed of, at this critical time, when there is reason to expect thay may soon be called to action; and orders that the Officers take the strictest care, to examine into the state of their respective Corps, and thereby prevent Inoculation amongst them; which, if any Soldier should presume upon, he must expect the severst punishment.
Any Officer in the Continental Army, who shall suffer himself to be inoculated, will be cashiered and turned out of the army, and have his name published in the News papers throughout the Continent, as an Enemy and Traitor to his Country.
Upon the first appearance of any eruption, the Officer discovering of it in any Soldiers, is to give information to the Regimental Surgeon, and the Surgeon make report of the same, to the Director General of the hospital.
Dr. Azor Betts continued to give inoculations to officers of the Continental Army so he was arrested and imprisoned. He was freed when the British took over New York and the Continental Army retreated to New Jersey.
Dr. Betts became an officer in the Kings American Regiment (a Loyalist regiment) and later on was a surgeon in the Queen's Rangers. At the end of the war he moved his family to New Brunswick (Canada) and then to Nova Scotia where many of his descendants still live.
There are many ways to teach biochemistry. You can focus on the chemistry or emphasize biology. You can teach from a fuel metabolism perspective or you can teach to the MCAT. You can even teach biochemistry from an evolution perspective.
But here's one I'm not familiar with: The Science of ID: Biochemistry.
Maybe I'll give it a try.
