Some of the articles that are published in Biochemistry and Molecular Biology Education (BAMBED) are a little bit difficult to understand. Here's one from the latest issue....
Laura Miralles, Paloma Moran, Eduardo Dopico and Eva Garcia-Vazquez (2013) DNA Re-EvolutioN: A game for learning molecular genetics and evolution. BAMBED 41:396-401 [doi: 10.1002/bmb.20734]
The abstract explains that the goal is to teach evolution.
Evolution is a main concept in biology, but not many students understand how it works. In this article we introduce the game DNA Re-EvolutioN as an active learning tool that uses genetic concepts (DNA structure, transcription and translation, mutations, natural selection, etc.) as playing rules. Students will learn about molecular evolution while playing a game that mixes up theory and entertainment. The game can be easily adapted to different educational levels. The main goal of this play is to arrive at the end of the game with the longest protein. Students play with pawns and dices, a board containing hypothetical events (mutations, selection) that happen to molecules, “Evolution cards” with indications for DNA mutations, prototypes of a DNA and a mRNA chain with colored “nucleotides” (plasticine balls), and small pieces simulating t-RNA with aminoacids that will serve to construct a “protein” based on the DNA chain. Students will understand how changes in DNA affect the final protein product and may be subjected to positive or negative selection, using a didactic tool funnier than classical theory lectures and easier than molecular laboratory experiments: a flexible and feasible game to learn and enjoy molecular evolution at no-cost. The game was tested by majors and non-majors in genetics from 13 different countries and evaluated with pre- and post-tests obtaining very positive results.
I would be embarrassed to present this game to students at the University of Toronto. It seems more suitable for adolescents who are just learning about evolution in high school.
What do you think? Is this a suitable class experience for students at your university?
The latest issue of Biochemistry and Molecular Biology Education (BAMBED) has a list of "Websites of Note." One of them is Memorize.com. Here's what the BAMBED says about this site ...
You may be impressed or appalled that this site reduces biochemistry to the basics for rote learning. Type biochemistry into the search box associated with Learn on the home page. You will then discover numerous pages created by individual students who have listed prompts and answers to help in their biochemistry studies. Mostly the tabulations of pathways and facts are excellent and accurate. Try Laura Wright's page at memorize.com/biochemistry-metabolism-1/laurawright. The memorization protocol is simple, but effective. After declaring that you have memorized a table you will be tested and at the prompt you answer mentally or on paper, not by entering an answer. You then get to reveal the answer and tell the program whether your recall was correct. Continue as required until all propositions are memorized and can be answered correctly. Pavlov and Skinner would endorse the approach. If a student is pestering with the question "what else can I do to prepare for the exam?" then recommending this site may be the answer.
I was more than a little surprised that an education journal would advertise such a site especially since ASBMB (American Society of Biochemistry and Molecular Biology has come out strongly in favor of concept driven teaching [see ASBMB Promotes Concept Driven Teaching Strategies in Biochemistry and Molecular Biology]. The last issue of BAMBED had a series of articles on the proper way to teach biochemistry.
Theme
Better BiochemistryA concept driven course is incompatible with rote memorization and regurgitation of facts. No respectable teacher—and no reader of BAMBED—should ever send students to the memorize.com website.
According to ASMBM the The five core concept categories are:
- Evolution
- matter and energy transformation
- homeostasis
- biological information
- macromolecular structure and function
While I disagree with the way the evolution concept is described [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution], I agree that it is important to teach biochemistry from an evolutionary perspective. I'm interested in knowing how biochemistry is taught at other schools and that's why I often look at websites such as memorize.com where students post what they think is important.
What I see at memorize.com is appalling. It's clear that students who are posting there have taken courses that focus exclusively on rat liver metabolism and human biochemistry. There's no evolutionary approach visible in any of the student websites. Not only that, many of these students seem to be fixated on something called the "rate-limiting step" in various pathways. Where does that come from? Is there a textbook that teaches like that?
There are people out there who actually think that as soon as an undergraduate finishes a biochemistry course they become an expert. This is the only explanation for all the favorable references to biochemistry websites constructed by teenagers who don't even have an undergraduate degree. (Many of them are directed at pre-med students who are preparing for the MCAT.)
Let's look at a few things that Laura Wright (Oxford University, UK?) says on her page at memorize.com [Biochemistry - Metabolism 1].
The first box tells us where various pathways are located in the cell. Of course, we're talking about animal cells, not bacteria or plants (photosynthesis isn't mentioned). We learn that protein synthesis takes place in the "RER.". I had to look that up ... it means "rough endoplasmic reticulum." I'd love to know who taught her that. Only a small subset of proteins enter the endoplasmic reticulum. The vast majority of protein synthesis takes place in the cytoplasm.
Students taking a rote memorization course often have to memorize the number of ATP equivalents produced when glucose is oxidized to CO2. This number is 32 ATP equivalents in bacteria and less in eukaryotes. It depends on a number of estimates, especially the number of ATP equivalents produced when electrons from NADH pass through the membrane-associated electron transport system (should be 2.5). Laura Wright says,
32 from malate-aspartate shuttle (heart and liver) vs only 30 from glycerol-3P shuttle (muscle)
This is not what I teach in my textbook but the point is that the "correct" answer on a multiple choice test will not depend on what I think or what Laura Wright thinks. She thinks that the citric acid cycle produces 24 ATP equivalents, I think it produces 20 ATP equivalents, and who know what YOUR professor thinks.
If biochemistry is properly taught from concepts then every student would understand the problems with these estimates and would be able to explain the assumptions behind the calculations.
It's sad to see the sorts of things that students have to memorize. Apparently, many of them have to memorize the names of metabolic diseases (e.g. Niemann-Pick disease) and the symptoms. I think they're also expected to memorize the names of enzymes.
This is not how biochemistry should be taught.
The Clergy Letter Project is sponsoring the 9th annual "Evolution Weekend" on February 7-0 2014. This is a weekend where clergy talk to their congregations about science and evolution. Here's how they describe the event ...
Evolution Weekend is an opportunity for serious discussion and reflection on the relationship between religion and science. An ongoing goal has been to elevate the quality of the discussion on this critical topic, and to show that religion and science are not adversaries. Rather, they look at the natural world from quite different perspectives and ask, and answer, different questions.
Maybe it's just me, but I thought that "serious discussion and reflection" means that all aspects of the conflict between science and religion would be considered. This includes the possibility that the conflict is very real and cannot be accommodated.
I was wrong. If you are a member of the Clergy Letter Project your mind is already made up.
Because religion and science use different methodologies to understand the world, and because religion and science ask very different questions, there is no reason to view them in conflict. One important facet of Evolution Weekend 2014, therefore, is to explore the questions each ask and to examine the different ways of knowing embodied in each.
There's not going to be any serious discussion about different ways of knowing and which ones are successful.
One of the most important lessons of science is that life evolved from simple primitive organisms over a period of at least three billion years. The history of life can be fully explained by natural causes without any need for miracles or divine intervention. We have learned that the evolution of life on this insignificant planet, in an ordinary galaxy, in a vast universe, has no purpose or goal.
There aren't many religions that can accommodate those facts.
[Hat Tip: Panda's Thumb]
My department is in a Faculty of Medicine and the main source of research funding for biomedical sciences in Canada is the Canadian Institutes of Health Research (CIHR). The current Conservative Government has been consistently underfunding CIHR over the past six years so that the number of grants available for basic research (e.g. biochemistry and molecular biology) has been falling.
This is the time of the year when my colleagues hear the results of the latest grant competitions. It's been a sad couple of days because four labs failed to get funding for their main research projects. Eight other labs failed to get additional funding for ongoing projects that were not part of their main grant.
What does this mean? Let's think about the consequences for labs that lose their grants. In the short term, the lab will survive until the next application deadline but it means that the Professor running the lab can't take on any new graduate students or post-docs no matter how brilliant they might be. In some cases, the department, or the university, might have to provide "bridging" funds in order to pay the salaries and stipends of people in the lab. If the Professor manages to get the grant back in the next competition then a recovery is possible but a lot of damage has already been done.
However, in many cases the second or third attempts to recover funding are not successful and the lab must shut down. That's the situation we face in our department with several active research groups that have disappeared or are about to disappear.
The first people to be let go are the post-docs who are funded from the grant. They have to scramble to find a new position and this isn't easy. It could be the end of their career.
The most expensive people in the lab are the research technicians ($50-60,000 per year1). They have to be put on notice and they will be fired. These are scientists with advanced degrees who are the heart and soul of a research lab. They are mostly women in mid-career. Many of them will never find another position that pays as well.
Graduate students who are close to finishing can usually be helped but those at the beginning of their studies have to switch to another lab and start a new project. This may not be possible.
Our research labs have two or three undergraduate students doing research projects as part of their degree requirements. As we lose more and more active labs, we also lose the ability to train undergraduates. We also hire undergraduate to work in labs over the summer and this provides invaluable experience in preparation for graduate school. If you don't have a funded lab you can't hire students. If you lose part of your funding, the easiest way to save money is not to hire anyone.
The groups that are losing their grants are the backbone of Canadian research infrastructure. The typical lab has three or four graduate students, a post-doc, and a research technician (research associate, lab manager). It takes about $150,000 per year to sustain such a lab. The Professor who runs the lab is usually between 30 and 40 years old (mid-career). The lab is producing several papers a year in respectable journals. These labs would easily have been funded a decade ago when the success rate on grant applications was 25% but now that it's down to 15% they are being cut out of the system.
Even those labs that are still funded are affected when a colleague loses a grant. That's because there's a lot of sharing of equipment and resources and expertise. We can foresee a time when the department falls below a critical mass of active research labs and when that happens everyone will lose their grants. Morale is already at an all-time low. Students and faculty are more worried about survival than science.
A generation of mid-career scientists is being destroyed by the policies of the Canadian government. Graduate students, post-docs, technicians, and undergraduates are being affected. It might take another generation to recover if funding were to return to appropriate levels. We might never recover if something isn't done soon.
Here at the University of Toronto we used to talk about becoming a world-class research centre. We don't talk about that very much any more.
1. Salary plus benefits.
This month's Carnival of Evolution is hosted by a group of "foreigners"1 at The Geneological World of Phylogenetic Networks. David Morrison at Uppsala, Sweden wrote the post. Read it at Carnival of Evolution, No. 67 — Wallace centenary edition.
Charles Darwin's Tree of Life metaphor (from 1859) has become world-famous. However, Alfred Russel Wallace, who independently developed the idea of evolution by means of natural selection, had already used a very similar image in 1855, when he noted: "the analogy of a branching tree [is] the best mode of representing the natural arrangement of species ... a complicated branching of the lines of affinity, as intricate as the twigs of a gnarled oak ... we have only fragments of this vast system, the stem and main branches being represented by extinct species of which we have no knowledge, while a vast mass of limbs and boughs and minute twigs and scattered leaves is what we have to place in order, and determine the true position each originally occupied with regard to the others".
This past year has been one in which many people commemorated the death of Wallace (1823-1913), and so it seems appropriate to join them for the final summary of 2013's posts at the Carnival of Evolution.
The next Carnival of Evolution will be at Byte Size Biology. Nobody has volunteered to host the February edition.
If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.
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1. That's anyone who isn't Canadian. It's a very large group.
This post is about a paper recently published in Science (Dec. 13, 2013) by John Stamatoyannopoulos and his collaborators at the University of Washington in Seattle, Washington, USA.
Stergachis, A.B., Haugen, E., Shafer, A., Fu, W., Vernot, B., Reynolds, A., Raubitschek, A., Ziegler, S., LeProust, E.M., Akey, J.M. and Stamatoyannopoulos, J.A. (2013) Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution. Science 342:1367-1372. [doi: 10.1126/science.1243490] [Abstract] [PDF]
Stamatoyannopoulos is one of the ENCODE workers. He recently gave a talk at the University of Toronto where he defended the idea that pervasive transcription and pervasive transcription factor binding are evidence of widespread function in the human genome. This paper looks at transcription factor binding sites in exon sequences (coding sequences) and finds lots of them. What this means is that stretches of coding region contain codons AND transcription factor binding sites (duh!).
Glenn Branch of NCSE alerted me to this book: 1001 Ideas the Changed the Way We Think. He wrote some of the articles [see Creationism and Evolution in 1001 Ideas].
The last great idea that changed the way we think (#1001) is written by Simon Adams, a "historian and writer living and working in London." Simon Adams thinks that the discovery that most of our genome is not junk counts as a big idea. To his credit, Glenn Branch realizes that this is somewhat controversial.
That's putting it mildly. Knowledgeable scientists agree that most (~90%) of our DNA is junk in spite of what the ENCODE publicity campaign might have said back in September 2012. I'm reproducing the article that Simon Adams wrote to show you just how successful that publicity campaign was and how difficult it is for the corrections and rebuttals to make an impact on a gullible public. With apologies to Glenn, whose articles are probably accurate, you should not buy a book that makes such a serious mistake by allowing an amateur to write about genomes, a subject he knows nothing about.
NOT-JUNK DNA
Far more of the human genome has vital functions than was first realized
The ribbons of DNA (deoxyribonucleic acid) in our cells carry instructions for building proteins and thus continuing life, but it was long believed that stretches of them are useless. The idea of "junk DNA" was first formulated by the Japanese-American geneticist Susumu Ohno (1928-2000), writing in the Brookhaven Symposium in Biology in 1972. He argued that the human genome can only sustain a very limited number of genes and that, for the rest, "the importance of doing nothing" was crucial. In effect, he dismissed 98 percent of the total genetic sequence that lies between the 20,000 or so protein-coding genes.
Yet scientists always thought that such junk must have a purpose. And indeed, a breakthrough in 2012 revealed that this junk is in fact crucial to the way our human genome, that is the complete set of genetic information in our cells, actually works.
After mapping of the entire human genome was completed in 2003, scientists focused on the so-called junk DNA. Nine years later, in 2012, the international ENCODE (Encyclopedia of DNA Elements) project published the largest single genome update in Nature and other journals. It found that, far from useless, the so-called junk contained 10,000 genes—around 18% of the total—that help control how the protein-coding genes work. Also found were 4 million regulatory switches that turn genes on and off (it is the failure of these switches that leads to diseases such as type 2 diabetes and Crohn's disease). In total, ENCODE predicted that up to 80 percent of our DNA has some sort of biochemical function.
The discovery of these functioning genes will help scientists to understand common diseases and also to explain why diseases affect some people and not others. If that can be achieved, drugs can be devised to treat those diseases. Much work still needs to be done, but the breakthrough has been made.
The editor of this book is Robert Arp, a philosopher specializing in the philosophy of biology and evolutionary psychology. I assume that he approved of the article by Simon Adams, which means that even philosophers of biology were duped by the ENCODE leaders.1
The book was published on Oct. 29, 2013. That means there was plenty of time to read the critiques of the ENCODE publicity campaign and even the scientific articles that were published last winter and early spring. There's really no excuse for making such a mistake.
We're in Washington D.C. for a wedding. Our hotel is the Ritz-Carleton in Arlington, Virginia, right next door to the Pentagon City Mall.
This is a photo of the food court in the mall. I was here with my children 20 years ago (August 1993) when I discovered "Panda Express" and orange chicken for the very first time. Of course I had to celebrate this anniversary by having some more. (I just finished.) I think that orange chicken is my number one fast food dish. I'm pretty sure that my daughter likes it too since she eats it at least once a week.
We have a nice view from our room of some big odd-shaped building.
It's always difficult to pin down an intelligent design creationist. They demand detailed "naturalistic" explanations of everything before they will accept them but, on the other hand, they won't ever give you their explanation. For example, we know they have doubts about the evolution of bacterial flagella but have you ever heard them describe their hypothesis? Like who made the first flagellum? When? Why?
It's also difficult to tell the difference between the various creationist cults. Clearly there are Young Earth Creationists who support the Intelligent Design Creationist movement but sometimes the IDiots say that YEC is inconsistent with Intelligent Design Creationism. Isn't that strange?
Most IDiots define their movement in very broad terms but they get really upset with Theistic Evolution Creationists. Apparently, you can't believe in theistic evolution and still be an IDiot. Who knew?
Now Granville Sewell comes to the rescue by describing what Intelligent Design Creationists actually believe [Granville Sewell: Intelligent design shouldn't be dismissed]. A link was posted on Uncommon Descent under the title "Introduction to ID."
Here's the important part of Sewell's article.
So what do ID proponents believe?
Perhaps the best way to answer this question is to state clearly what you have to believe to not believe in intelligent design. Peter Urone, in his 2001 physics text "College Physics" writes, "One of the most remarkable simplifications in physics is that only four distinct forces account for all known phenomena."
The prevailing view in science today is that physics explains all of chemistry, chemistry explains all of biology, and biology completely explains the human mind; thus physics alone explains the human mind and all it does. This is what you have to believe to not believe in intelligent design, that the origin and evolution of life, and the evolution of human consciousness and intelligence, are due entirely to a few unintelligent forces of physics.
Thus you must believe that a few unintelligent forces of physics alone could have rearranged the fundamental particles of physics into computers and science texts and jet airplanes.
Contrary to popular belief, to be an ID proponent you do not have to believe that all species were created simultaneously a few thousand years ago, or that humans are unrelated to earlier primates, or that natural selection cannot cause bacteria to develop a resistance to antibiotics.
If you believe that a few fundamental, unintelligent forces of physics alone could have rearranged the basic particles of physics into Apple iPhones, you are probably not an ID proponent, even if you believe in God. But if you believe there must have been more than unintelligent forces at work somewhere, somehow, in the whole process: congratulations, you are one of us after all!
This is a very broad definition. If you believe in God then you pretty much have to be an IDiot unless you are a strict deist. Every single religious person that I know believes that "there must have been more than unintelligent forces at work somewhere, somehow, in the whole process."1 Therefore, every Roman Catholic and every evangelical Christian is an IDiot, according to Granville Sewell. This includes Ken Miller and Francis Collins. In fact, it includes every religious scientist.
Not bad, eh?
For the record, I do not "believe" that " ... a few fundamental, unintelligent forces of physics alone could have rearranged the basic particles of physics into Apple iPhones." I think it's the most reasonable explanation. I don't know of any other explanation that is supported by evidence.
1. Yes, I know about atheist Buddhists. That doesn't count as a "religion" in my book.
We had a big ice storm in Southern Ontario last weekend. There are still thousands or people without power and many are unlikely to have power restored before Christmas (tomorrow).
We got off fairly lightly. We were never without power (underground wires) and the roads were cleared pretty quickly. However, lots of trees in our neighborhood suffered and some were almost completely destroyed by the weight of the ice. A large branch of the ash tree in our front yard cracked but did not fall. It was hanging over our driveway so we had to move our cars. We called Davey Tree on Sunday and they showed up yesterday to remove the broken branch.
It was quite a production. The woman in charge had to park this huge truck in our driveway and maneuver the cherry picker trough the branches. As you can imagine, it attracted an audience from the neighboring houses. When the job was done they swept up all the debris and turned it into sawdust in a wood chipper. There are more photos at: Uh Oh!. We have a daughter and a granddaughter who would love this job!
The Princeton Guide to Evolution is a collection of 107 articles on various aspect of evolution. The editors felt they should address the obvious conflict between evolution/science and religion. There are at least five different approaches they could have taken.
- An atheist perspective on the incompatibility of evolution/science and religion. Richard Dawkins or Jerry Coyne would be good choices.
- An atheist perspective on the compatibility of science and religion (the accommodationist view). Michael Ruse or Nick Matzke are obvious choices.
- A theist view of the incompatibility of evolution and religion. Phillip Johnson could have explained this view but so could a number of other creationists.
- A theist explanation of the compatibility of evolution/science as long as they stick to their proper magisteria. Francis Collins, Ken Miller, and several other religious scientists could present their case.
- The editors could have published four articles representing the main viewpoints or commissioned a single article that would have covered all the angles.
The big advantage of an atheist perspective is that it fairly represents the views of a majority of evolutionary biologists. Having a theist write the article would not be as fair. I think we can all agree that option #5 is by far the best choice.
Before reading any further, take a minute to decide what you would do if you were the editors of The Princeton Guide to Evolution.
One of the problems in most debates and discussions in the problem of definitions. It's common for two opponents to end up talking past one another because they don't agree on what they are arguing about. That's why an important component of critical thinking is to define your terms so that everyone knows what you are defending (or attacking).
But there's more. If you are going to be a good critical thinker, then you have to be aware of other points of view. If there are other, equally valid, definitions out there then you MUST acknowledge them and incorporate them into your argument. You can't, for example, just make up your own definition of words like "noncoding," "junk," or "function," and declare that you are right. Since you know that there are other definitions out there, you are obliged to show why YOUR definition is the only correct one. That's a crucial part of the debate.
If you don't even know that there are other valid definitions then you are not an expert and you should not be pretending to be an authority on the subject. This is why I object to people who argue against the Central Dogma of Molecular Biology without understanding what Francis Crick actually said.
Let's look at a video of Elliott Sober lecturing on "Some Questions for Atheists to Think About." He begins by asking the members of his audience whether they are atheists or agnostics. Apparently, most members of the audience are atheists and ony a few are agnostics.
Next, he defines his terms ...
Theism = God exists
Atheism = God does not exist
Agnosticism = We don't know whether God exists
The lecture is about something called "evidentialism." Elliott Sober claims that the following proposition is true ...
For any proposition, you should believe it only if you have evidence that it is true and you should disbelieve it only if you have evidence that it is false.
He then goes on to show that we can never have evidence that God does not exist. Therefore, "If 'God exists' is untestable, you ought not to be an atheist. You should be an agnostic."
He suggests that all the atheists in the audience should become agnostics because of evidentialism. If I had been in the audience, I would have pointed out that MY definition of atheist is that an atheist is someone who doesn't believe in god(s). My definition is such a common definition that it's part of the Wikipedia article on Atheism. Since I do not need "evidence" to not believe in something, I'll remain an atheist, thank-you very much. My position is perfectly consistent with the proposition about evidentialism.
Here's the problem. Elliott Sober is a prominent philosopher. Doesn't he realize that his argument relies entirely on his definition of "atheism"? Doesn't he realize that his argument is completely useless if an atheist is simply someone who doesn't buy into the God delusion? This sort of thing makes me livid and it makes me wonder whether there's something seriously wrong with modern philosophy.1
1. I am not suggesting that Sober's definition is wrong. He should not be ignoring the fact that many members of his audience don't agree with his definition and that's why they are atheists.
A few days ago, I asked the following questions, Is the "Modern Synthesis" effectively dead?, and What do they mean when they say they want to extend the Modern Synthesis?. The point I was trying to make was that there are many different views on evolutionary theory and it's often difficult to figure out which version of evolutionary theory someone is defending.
For example, which version of evolutionary theory is compatible with the "selfish gene" as a metaphor for evolution? Or for adaptation? Which version of the "Modern Synthesis" is being attacked in the book edited by Massimo Pigliucci and Gerd Müller? Is it the version defended by Ernst Mayr? Does it incorporate Neutral Theory and random genetic drift?
Here are the questions on yesterday's exam for students in my course. Students will be graded on their explanations and not so much on the actual answer they give. The idea is to reward critical thinking and that includes the ability to see both sides of an issue and recognize problems with whatever side you choose to defend.
- Assuming that the technology is safe and effective, should we, or should we not, have laws forbidding the cloning of humans?
- What is the best definition of a "gene"? Explain why you choose that definition and give examples of possible "genes" that don’t fit your definition.
- Elliott Sober is a highly respected philosopher. He explains that theistic evolution is a reasonable hypothesis because God could easily cause mutations to occur in a way that scientists would not be able to detect. In other words, a specific, directed, mutation would be indistinguishable from a random mutation. Thus, it would appear that evolution was an entirely naturalistic process while, in fact, its direction was being guided by God. Do you think this is a reasonable argument in support of theistic evolution? Why or why not?
- In his book, The Myth of Junk DNA, Jonathan Wells writes.
According to intelligent design (ID), it is possible to infer from evidence in nature that some features of the world, and of living things, are better explained by an intelligent cause than by unguided natural processes.
What sorts of positive arguments do ID proponents use to support this inference from evidence in nature? Are they effective?
