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Better BiochemistryThe American Society for Biochemistry and Molecular Biology (ASBMB) advocates for a concept-driven approach to teaching biochemistry and molecular biology. It set up a number of working groups to flesh out this approach. The results have been published in a series of papers in the latest issue of BAMBED (Biochemistry and Molecular Biology Education). The first paper (Mattos et al. 2013) discussed the strategy [see ASBMB Promotes Concept Driven Teaching Strategies in Biochemistry and Molecular Biology].
The second paper, by Tansey, et al., is the most important paper. It covers the results of a two-year study to define and describe the fundamental concepts that must be taught. The authors begin by explaining why it's important to agree on a core set of fundamental concepts.
Monday, October 14, 2013
Monday's Molecule #219
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.)
The Accommodationist View of Kevin Padian
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" ...
Misrepresentations of Evolution in Textbooks: Definition of Evolution According to Kevin Padian
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.
Friday, October 11, 2013
ASBMB Promotes Concept Driven Teaching Strategies in Biochemistry and Molecular Biology
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 ...
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.
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 ...
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.
- 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.
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]
Three Senior Fellows of the Discovery Institute Will Discuss Criticisms of Dawin's Doubt on a Radio Show on October 23
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.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?"
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?
- Darwin's Doubt: The Genes Tell the Story?
- The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes
- Stephen Meyer Says That Constant Mutation Rates Are a "Questionable Assumption"
- Stephen Meyer Says Molecular Data Must Be Wrong Because Different Genes Evolve at Different Rates
- Stephen Meyer Says Molecular Evidence Must Be Wrong Because Scientists Disagree About the Exact Dates
- Stephen Meyer Says that "Homology" Is a Problem in Molecular Evolution
Thursday, October 10, 2013
John G. West Speaks Out Against Using Derogatory Labels to Describe Your Opponents
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.
Wednesday, October 09, 2013
October 7-14th Is Quackery Week
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 ...
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.
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.
19,853 People Can't Be Wrong ... Can They?
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.
The Campus in October
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.
I love being on a university campus.
Tuesday, October 08, 2013
On the Importance of Defining 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.
Ken Ham Strikes Back
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.
Non-Darwinian Evolution in 1969: The Case for Junk DNA
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 ...
Monday, October 07, 2013
Monday's Molecule #218
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.)
Sunday, October 06, 2013
Dr. Azor Betts vs Smallpox and George Washington
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.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.
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. 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.
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