Last week's molecule was 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU). It is an intermediate in the degradation pathway from uric acid (or urate) to carbon dioxide and ammonia. Uric acid is the main breakdown product in purine catabolism. Humans have lost activity of all of the enzymes of this pathway so they excrete urate. Most other species excrete ammonia, although in other animals some of the terminal enzymes have been lost.
Some textbooks do not show the uric acid degradation pathway since it doesn't occur in humans and those textbooks aren't interested in an evolutionary approach to biochemistry (e.g. Berg, Tymoczko, and Stryer). The other majors textbooks (Voet & Voet, Garrett & Grisham, Nelson & Cox [Lehinger]) all show uric acid converted directly to allantoin via urate oxidase. This reaction was shown to be incorrect about 15 years ago. The actual pathway from uric acid to allantoin involves two intermediates; 5-hydroxyisourate and OHCU.
Image Credit: Moran, L.A., Horton, H.R., Scrimgeour, K.G., and Perry, M.D. (2012) Principles of Biochemistry 5th ed., Pearson Education Inc. page 568 [Pearson: Principles of Biochemistry 5/E] © 2012 Pearson Education Inc.
The winner, for the second week in a row, is Jean-Marc Neuhaus. [Monday's Molecule #220]. Jean-Marc lives in Switzerland so I've made arrangements to fly over there to visit him and treat him to two fondues at the Pinte de Pierre-à-Bot in Neuchatel. 
Jean-Marc was kind enough to send me a menu [PDF]. There are about 30 different fondues to choose from. If you would like to join us you can leave a comment on last week's post.
This week's molecule is related to a discussion we are having on the How Do the IDiots Explain the Origin of Life? post. Can you identify this molecule? You have to be very specific.
Email your answer to me at: Monday's Molecule #221. 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.)
Theme Genomes & Junk DNAI happened to stumble on this video where Trace Dominguez (@trace501) promotes the idea of junk DNA based on the C-value Paradox—a version of the Onion Test. It's good that he tells the general public about junk DNA but it's bad that he equates "noncoding DNA" with "junk DNA." It's really silly to tell people that the only important part of your genome is the 2% that codes for proteins.
Just so you know, some of the important known functions of "noncoding DNA" are [What's in Your Genome?] ....
- Genes for functional RNAs like ribosomal RNA, tRNA, and a host of others.
- Regulatory sequences that control expression of all genes.
- Part of intron sequences.
- Origins of replication;specific sites where DNA replication begins.
- Telomeres.
- Centromeres.
- SARS or scaffold attachment regions; sites required to organize chromatin.
- Functional transposons or "selfish DNA."
- Functional DNA and RNA viruses.
Scientists believe that about 2% of our genome encodes proteins and about 8% has other functions. It is not true that all noncoding DNA is junk. No knowledgeable scientist ever said that.
I realize that the kind of presentation shown in this video doesn't lend itself to a detailed description of noncoding DNA functions but surely we can do better than this? Why not say that scientists have determined that genes make up about 2% of our genome and about 8% contains information necessary for the proper functioning of genes and chromosomes? The rest, about 90%, is thought to be junk?
98% of your DNA is junk
Attanasio et al. (2013) published a paper in Science where they identified several thousand possible enhancers that were active in the facial area of developing mouse embryos. About 200 of them appear to be controlling genes that determine the size and shape of the face. (Recall that there are about 20,000 protein-encoding genes in mammals.)
Lynn Yarris of Lawrence Berkeley National Laboratory in California (USA) wrote up the press release [What is it About Your Face?]. It's a really good press release that fairly represents the published work and explains some of the significance. There's no mention of junk DNA in the press release or the published paper.
This is what it looks like when science correspondent Alok Jha published it in The Guardian.
Faces are sculpted by 'junk DNA'
Though everybody's face is unique, the actual differences are relatively subtle. What distinguishes us is the exact size and position of things like the nose, forehead or lips. Scientists know that our DNA contains instructions on how to build our faces, but until now they have not known exactly how it accomplishes this.
Visel's team was particularly interested in the portion of the genome that does not encode for proteins – until recently nicknamed "junk" DNA – but which comprises around 98% of our genomes. In experiments using embryonic tissue from mice, where the structures that make up the face are in active development, Visel's team identified more than 4,300 regions of the genome that regulate the behaviour of the specific genes that code for facial features.
It's pretty clear that science correspondent Alok Jha doesn't understand what he's writing and it's about time we started publicizing the names of those science writers who mislead the public about science. The consensus among knowledgeable scientists is that at least 80-90% of our genome is junk. It's time for science writers to admit that the science favors junk.
Scientists have known for decades that a lot of noncoding DNA is functional. The idea that all noncoding DNA (98%) is junk is false. No knowledgeable scientist ever made such a claim. It is a myth perpetuated, in part, by ignorant science writers; albeit, aided and abetted by ignorant scientists. Scientists have known for fifty (50!!) years that gene expression is controlled by regulatory sequences in noncoding DNA. Scientists have known for at least that length of time that during embryogenesis different genes are turned on and off and that this is due, in part, to binding of transcription factors to those regulatory sequences (enhancers). Scientists have known for one hundred years that the morphological features of mammals, including humans, are controlled by genes.
Move along folks. There's nothing to see here.
Attanasio, C. et al. (2013) Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers. Science 342: Oct. 25, 2013 [doi: 10.1126/science.1241006]
This is the view from the window just outside my office on the fifth floor.
Theme
Better BiochemistryTansey et al. (2013) have described the five core concepts in biochemistry and molecular biology. These are the fundamental concepts that all biochemistry instructors must teach and all biochemistry students must understand.
The five core concept categories are:
- evolution [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution ]
- matter and energy transformation [ASBMB Core Concepts in Biochemistry and Molecular Biology: Matter and Energy Transformation]
- homeostasis [ASBMB Core Concepts in Biochemistry and Molecular Biology: Homeostasis]
- biological information [ASBMB Core Concepts in Biochemistry and Molecular Biology: Biological Information]
- macromolecular structure and function [ASBMB Core Concepts in Biochemistry and Molecular Biology: Molecular Structure and Function]
I like the idea of teaching biochemistry from a concept-driven perspective and I like the five categories. However, I was not too pleased with the description of the core concept of evolution [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution]. It's one thing to identify the main categories but you also have to get the concepts right if you are going to advocate teaching them!
Let's see how they do with the second core concept.
Matter and Energy Transformation
The Many Forms of Energy Involved in Biological Processes
The energetics of a biological system or process—be it an ecosystem, an organism, a cell, a biochemical reaction—conforms to and is understood in terms of the fundamental laws of thermodynamics. Biological systems capture and process energy from the environment in many forms including that emanating directly from the sun (photons through photosynthesis), heat from the environment (kinetic energy), and energy rich compounds produced by geothermal processes (e.g. sulfur compounds) or other organisms (e.g. carbohydrates). Energy from all sources is chemically converted into useful chemical and physical work in a controlled and regulated fashion. The potential
energy stored in chemical bonds can used to generate motion, light, heat, and electrochemical gradients; likewise, electrochemical gradients can be used to generate motion and new chemical bonds. The input of energy from the environment allows living systems to exist in a state of nonequilibrium with their environment. The discussion of energy and matter conversions in biological systems makes use of the physical concept of changes in Gibbs free energy, or ΔG.
I think we can all agree that a basic understanding of thermodynamics is an important core concept. However, I would have worded this paragraph somewhat differently.
First, I would have mentioned that organisms can capture energy from simple inorganic compounds such as H2 or those containing Fe2+. These are energy sources for many chemoautrophic bacteria. If you are teaching biochemistry from an evolutionary perspective, it's important that students understand how these organisms capture energy. That's the process that is most like the mechanism found in the earliest living cells.1
Second, I would have put more emphasis on using captured energy in biosynthesis pathways. The paragraph mentions that energy can be used to generate new chemical bonds but that doesn't convey the importance of the process. Think about bacterial cells growing and dividing in the ocean or plants growing from a single seed. Most of the energy goes into making proteins, nucleic acids, lipids, and carbohydrates.
Third, I would drop the reference to cells being in "a state of nonequilibrium with their environment." That conceptt is covered under "homeostasis."
Catalysis
Biologically relevant energy and matter interconversions do not occur rapidly enough (often by many orders of magnitude) to support life. In living systems, biological catalysts called enzymes facilitate these reactions. Enzymes are macromolecules, usually proteins or RNA molecules with a catalytic function. Enzymes do not alter reaction equilibria; instead, they lower the activation barrier of a particular reaction so that reactions proceed much more rapidly. The presence of powerful enzymatic catalysts is one of the key conditions for life itself.
Description of the rates of enzymatic reactions represents the subdiscipline enzyme kinetics. Key concepts of kinetics, including the definitions of the terms vo, Vmax, Km, and kcat, constitute a common language for biochemists and molecular biologists in discussing the properties of enzymes.
Students should be able to apply their knowledge of basic chemical thermodynamics to biologically catalyzed systems, quantitatively model how these reactions occur, and calculate kinetic parameters from experimental data.
This is pretty good. I would only add that there are some fundamental concepts of enzyme mechanisms that need to be covered. The idea of a transition state is important. I put a lot of emphasis on oxidation-reduction reactions as a core concept in biochemistry.
Coupling Exergonic and Endergonic Processes
Biochemical systems couple energetically unfavorable reactions with energetically favorable reactions to allow for a wider variety of reactions to proceed.
Students should be able to discuss the concept of Gibbs free energy, and how to apply it to chemical transformations, be able to identify which steps of metabolic pathways are exergonic and which are endergonic and relate the energetics of the reactions to each other.
I have a problem with this section. I don't think that the concepts of "exergonic" and "endergonic" processes are very important in biochemistry and I don't use them in my textbook. They're not found in many other textbooks, either. Also, the idea of "coupled" reactions is very poorly taught in biochemistry courses. It's almost never true that enzymes simply link up two independent reactions, one of which is "favorable" and the other "unfavorable." What usually happens is that a completely new reaction is catalyzed. For example, ATP is not hydrolyzed but, instead, a group transfer reaction is created. This important concept is covered in the next section but the authors do not appear to have grasped its significance.
Not only that, what does it mean to say that a reaction is "energetically unfavorable"? Usually this refers to the standard Gibbs free energy (ΔG°′) but one of the most important concepts in biochemistry is the difference between the standard Gibbs free energy change and the actual Gibbs free energy change (ΔG) inside the cell. In most cases ΔG = 0.
It's true that there are potential "endergonic" reactions occurring inside cells. Think about ATP hydrolysis, for example. The concentration of ATP is maintained at a high level relative to ADP and Pi so the Gibbs free energy change in the direction of hydrolysis is actually more negative that even the standard Gibbs free energy change. What this means is the the reverse reaction is extremely "endergonic."
However, it is simply not true that there are steps in metabolic pathways that are "endergonic" as the authors state. That statement reflects a profound misunderstanding of a fundamental concept in biochemistry. There will not be any flux in the "forward" direction of a metabolic pathway as long as even one reaction is "endergonic." All reactions have to be near-equilibrium reactions or reactions with a negative ΔG that's maintained because the enzyme activity is regulated to prevent the reaction from reaching equilibrium.
The important concept is "flux" or flow of metabolites in one direction along a metabolic pathway. There are many pathways where flux can occur in either direction as in the central part of the gluconeogenesis/glycolysis pathway or the citric acid cycle. Students need to understand what controls flux in one direction or another. They should know that, like water, metabolic flux cannot flow uphill.
The Nature of Biological Energy
In biological systems, chemical energy is stored in molecules with high group transfer potential or strongly negative free energy of hydrolysis or decomposition. These molecules, particularly ATP, provide the free energy to drive otherwise unfavorable biochemical reactions or processes in tightly coupled and highly controlled fashion. Most frequently, the free energy needed for a process or metabolic pathway is provided by group transfer rather than by hydrolysis. In this way, efficient energy transfer is optimized, while inefficient energy transfer to the environment (in the form of heat for example) is minimized.
Students should be able to show how reactions that proceed with large negative changes in free energy can be used to render other biochemical processes more favorable.
The essence of these statements is correct but it is not explained very well. The important concept is not that you "couple" a "favorable" reaction like ATP hydrolysis to an "unfavorable" reaction like synthesis of glutamine from glutamate and ammonia (ΔG°′ = +14 kJ mol-1).
The point is that the enzyme (glutamine synthetase) catalzyes a completely different reaction—a phosphoryl group transfer reaction—with a negative standard Gibbs free energy change of ΔG°′ = −18 kJ mol-1.
[see Moran et al. (2011): Introduction to Metabolism]
If there were an enzyme that catalyzed the first reaction involving only glutamate and ammonia then this reaction could easily occur inside the cell in spite of the positive ΔG°′. It would be a near-equilibrium reaction with steady-state equilibrium concentrations of glutamate that were very much higher than the concentration of glutamine.
It's likely that the concentration of glutamine would then be too low to support all the reactions that require it. That's why the reaction involving ATP is more useful. It means that the steady-state concentration of glutamine can be maintained a much higher concentration. This requires regulation of glutamine synthetase in order to prevent the reaction from reaching equilibrium.
It seems to me that the authors (Tansey et al.) have not thought about the fundamental core concepts. They are promoting widespread misconceptions about thermodynamics and metabolism and they are missing some important concepts. I've already mentioned flux. The other missing concept is oxidation-reduction reactions (electron transfer) and the importance of reduction potentials. NADH, NADPH, and QH2 are important energy currencies inside the cell—just as important as ATP.
There's something seriously wrong with biochemistry teaching if ASBMB educators can't even correctly explain foundational concepts like "evolution" and "matter and energy transformation."
1. I believe that all introductory biochemistry students should be able to explain where chemoautrophs get their energy. If they can't do it, they haven't been taught the fundamental concepts.
Tansey, J.T., Baird, T., Cox, M.M., Fox, K.M., Knight, J., Sears, D. and Bell, E. (2013) Foundational concepts and underlying theories for majors in “biochemistry and molecular biology”. Biochem. Mol. Biol. Educ., 41:289–296. [doi: 10.1002/bmb.20727]
We don't know how life on Earth originated. We're not completely ignorant because we have a good idea of basic biochemistry and we know which enzymes and pathways had to be present in the earliest cells. We're pretty sure that the first life forms captured energy by oxidizing inorganic molecules. We're pretty sure that the first cells formed in the ocean.
We also know from the fossil record that the first organisms were single-celled organisms that resemble modern bacteria in size and shape. We know that they appear more than 3 billion years ago and there were no complex organisms for another billion years. We know that the idea of a primordial soup is nonsense and that speculations about an RNA world are not helpful.
Other than that, all we have is informed speculation. The correct answer to the question of how did life begin is "I don't know."
Denyse O'Leary asks: Origin of life: How are we doing?. She is shocked to learn that scientists have not figured out all the details of how life began. She acts like she knows the answer. She acts like she has an explanation that accounts for all of the data and for the subsequent history of life.
Why isn't she sharing that information? How do the IDiots explain the origin of the first primitive cells more than 3 billion years ago?
Minda Berbeco once taught evolution and she was surprised that her students wanted to talk about religion. She decided to consult with Peter Hess, the director of religious community outreach at the National Center for Science Education (NCSE). Her blog post is on the NCSE website at: When Students Ask about Religion.
Peter Hess mentioned that many people see a conflict between science and religion so Minda asked him what she should say to such people. Hess replied ...
I would recommend citing examples from the numerous scientists who have integrated current science into their religious worldviews, scientists such as Kenneth Miller, Francis Collins, Robert Russell, and Father George Coyne.
Another tack would be to cite statements from theological figures, such as Pope Benedict’s statement in Communion and Stewardship (2002), when he was still Cardinal Ratzinger:
Converging evidence from many studies in the physical and biological sciences furnishes mounting support for some theory of evolution to account for the development and diversification of life on earth, while controversy continues over the pace and mechanisms of evolution. While the story of human origins is complex and subject to revision, physical anthropology and molecular biology combine to make a convincing case for the origin of the human species in Africa about 150,000 years ago in a humanoid population of common genetic lineage.
Let me be clear: I’m not suggesting that you cite the views of such scientists and theologians as authoritative. There’s a wide range of religious reactions to evolution, from rejection to embrace, and you may not feel comfortable in endorsing any of them. (Indeed, a teacher in the public schools is required not to endorse any of them in the classroom.) But many people who reject evolution for religious reasons are ignorant about, or have never been seriously exposed to, the range of religious reactions to evolution. It may come as a complete surprise to them that devout religious people—perhaps even people of the same faith—have no theological objection to evolution. And opening people’s horizons is part of what education is all about, isn’t it?
There's so much wrong with this advice that I hardly know where to begin.
First, Hess seems to assume that Minda Berbeco is a Christian because otherwise his advice makes no sense. Surely, he wouldn't expect an atheist like me to tell students that the Pope is an authority on evolution? What if the teacher is a Muslim, a Buddhist, or a Hindu? What should they say? (Peter Hess is Roman Catholic.)
Second, he says that the views of these scientists (and the Pope) should not be cited as authoritative but if he really believes that then why cite them at all? Why not cite those religious scientists who think there really is a conflict between evolution and their religious beliefs?
Third, just because some scientists have been able to rationalize their acceptance of evolution with their Christian beliefs does not mean that there's no conflict. That is not a very good way to teach students how to think critically. After all, there are scientists who believe in homeopathy and astrology but that doesn't mean there's no conflict between real science and those pseudosciences, does it?
Fourthly, I agree that opening people's horizons is an important part of education. That's why I would tell students that, yes, there is a very real conflict between science and religion. It's quite likely that your faith will be severely challenged if you learn about evolution and science. Many students have never been seriously exposed to the atheist position. Somehow I don't think that's what Peter Hess has in mind when he talks about "opening people’s horizons."
Peter Hess recommends that students visit the Christian accommodationist webpages on the NCSE website [Science and Religion]. So, fifthly, I recommend that NCSE offer a more balanced view of this issue where they point out that there are many scientists who believe the conflict is very real. (I would be happy to write something.) NCSE should also expand their discussion to include non-Christian views of evolution.
The purpose of a grant, after all, is to facilitate research. But the rationale has become curiously inverted: now the purpose of one’s research seems to be to get a grant ...
Jerry CoyneThis is a post for scientists and those who would be scientists.
Wake up!!! Science is in trouble! If you don't believe me, read How science goes wrong and Trouble at the lab. Both articles were published in the October 19th edition of The Economist.
It likely that you've heard all this before but the magnitude of the problem just hasn't registered with you. Well, it's time to start paying attention.
Jerry Coyne has written an excellent commentary on these articles [Science is in bad shape]. Read it. Now.
These articles and commentaries focus on research but let's not forget teaching. There are far too many science teachers—expecially at the university level—who are doing a terrible job of teaching evolution and biochemistry. (And probably lots of other subjects but those are the ones I'm familiar with.)
We have to do something about this.
Dan Graur discovered that the term "junk DNA" was commonly used in the 1960's—long before Susumu Ohno used "junk" in the title of his 1972 paper. This makes a lot of sense. Apparently the term was quite commonly used in Cambridge by people like Francis Crick and Sydney Brenner. (Perhaps you've heard of them?)
Graur found a 1963 paper that refers to "junk" DNA. This is the earliest known refencee to junk in the scientific literature. Read about his sleuthing at: The Origin of Junk DNA: A Historical Whodunnit.
Meanwhile, a person named "ShadiZl" commented on one my posts and pointed me to a letter from Thomas Jukes to Francis Crick in 1979. Jukes, you might recall, was no Darwinian. He was a proponent of Neutral Theory and random genetic drift. The letter is archived on the National Library of Medicine (USE) site under a section devoted to The Francis Crick Papers: Letter from Thomas H. Jukes to Francis Crick.
The letter is interesting because it reveals how casually the "insiders" talked about junk DNA and about the adaptationist misconception even as far back as 1979. This was when Gould and Lewontin published the "spandrels" paper. It also reveals how misguided the creationists are when it comes to the history of junk DNA. They still think that it was "Darwinists" who "predicted" junk DNA based on their view of natural selection. (Do not read this letter if you are irony-deficient. It will only confuse you.)
December 20, 1979
Dear Francis:
I am sure that you realize how frightfully angry a lot of people will be if you say that much of the DNA is junk. The geneticists will be angry because they think that DNA is sacred. The Darwinian evolutionists will be outraged because they believe every change in DNA that is accepted in evolution is necessarily an adaptive change. To suggest anything else is an insult to the sacred memory of Darwin.
This additive is so pervasive that if no reason can be found for an evolutionary change, it is necessary to invent one. Kimura points out that one author attributed the pink color of flamingos to protective coloration against the setting sun. This type of thinking carries over into people who sequence mRNA. They claim that differences between rabbit and human globin mRNAs are because each species has its own requirements for secondary structure.
Various people have tried to think up possible functions for the regions of DNA that do not code for anything as far as is known. Roy Britten says that such DNA has a regulatory function.
Actually, the scheme proposed by Britten about ten years ago was that occasionally events of saltatory duplication, took place, so that a great many copies of a short piece of DNA were made. As time went by, the composition of a family of identical copies became changed by drift, until the copies no longer closely resemble each other. Figure 55 of the article by Britten shows a diagram of a sort of "junk DNA generating system". I note that he says on page 105 "the rate of increase in DNA content per cell resulting from saltatory replication alone may prove to be embarrassingly large and a mechanism for the loss of DNA may have to be invoked". I gather that you agree with this.
I quoted you on drift in DNA in a talk that I gave at the symposium for Emil Smith (see enclosure). Your concept of "junk DNA" presumably includes this idea. I shall look forward to hearing more about it, and I have been asked by Die Naturwissenschaften to write an article on silent changes, so I hope I can include mention of your new manuscript when I start to write mine.
With best regards,
Thomas H. Jukes
The title of this post suggest a story that's about as interesting as the proverbial "Dog Bites Man" story [see Man Bites Dog]. Nevertheless, from time to time it is amusing to see how the creationist mind works.
Michael Egnor is upset about the fact that the American Society for Biochemistry and Moleclar Biology (ASBMB) picked "evolution" as an important concept that should be covered in a biochemistry or molecular biology course. He doesn't like my post: ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution. He decided that he better convince his fellow creationists than biochemists don't know what they are talking about [Is Darwinian Evolution "Indispensable" to Biology?].
Here are some excerpts for your amusement.
Last week's molecule was citrate synthase, one of many enzymes that show considerable amounts of structural change during binding. It looks like the "induced fit" mechanism is a general feature of substrate binding and not something that is limited to just a few examples. That part of the question was easy but the second part was hard. Jean-Marc Neuhaus is this week's winner because he has a copy of my book and was able to look up the explanation. The important point to keep in mind when you are thinking about the thermodynamics of biochemical reactions is that most reactions are near-equilibrium reactions where ΔG = 0. In the case of the citrate synthase reaction, ΔG°′ = -31.5 kJ mol-1, in the direction of citrate formation. What this means is that the equilibrium concentrations of the products are very much higher than the concentrations of the substrates. These concentrations would be closer to being equal if the reaction was coupled to substrate level phosphorylation (e.g. ATP formation). This would be a problem since the concentration of oxaloacetate (substrate) inside the cell is very low. (Because the standard free energy change of the malate dehydrogenase reaction is ΔG°′ = +30 kJ mol-1) [Monday's Molecule #219]. Jean-Marc lives in Switzerland so I've made arrangements to fly over there to visit him and treat him to fondue at the Pinte de Pierre-à-Bot in Neuchatel.
Today's molecule is one of those molecules that students should never be asked to memorize. It's an intermediate in a very important pathway. Identify the molecule and the pathway. You have to give me the full name and the common abbreviation. Email your answer to me at: Monday's Molecule #220. 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.)
Intelligent Design Creationists are upset when I call them IDiots. They don't realize that the easiest way to make me stop is for them to stop acting like ... well, idiots.
The IDiots are fond of pointing out that they are all good Christians who would never stoop so low. They are all kind and gentle people who treat their opponents with respect and dignity. That's why they get so upset when we insult them.
Denyse O'Leary and the people who comment on Uncommon Descent have made these points repeatedly. They are the good guys and we are the bad guys when it comes to describing your opponents.
Let's look an example of how Christian IDiots behave. Denyse O'Leary recently wrote a post about The racist implications of Darwin’s theory.
She quotes a passage from Dawrin's The Descent of Man, and Selection in Relation to Sex.
The break between man and his nearest allies will then be wider, for it will intervene between man in a more civilised state, as we may hope, even than the Caucasian, and some ape as low as a baboon, instead of as now between the negro or Australian and the gorilla.
The quote is from page 201.
Denyse then says,
Darwin’s racism was not adopted out of bad will but simply as the logic of Darwinism. That is the point that every Darwinist wants to miss or downplay.
They have demanded that we all understand that the greatest man who ever lived wasn’t a racist and we are all misquoting or misunderstanding him or are bad, bad people or whatever for even bringing this stuff up.
Okay so we’re really awful here at Uncommon Descent. As our name implies, we don’t espouse any theory that says that humans are merely evolved animals or that we must inevitably form separate species as a result of isolation. Heck, we don’t even espouse a theory that says that separate species usually form that way. The evidence is mixed.
His believers are therefore stuck in the awkward position of having to pretend that what is obviously racist isn’t, and denouncing any of us who read the plain sense of it correctly.
Do you see the problem. Those poor IDiots are being criticized unjustly for seeing the obvious; namely, that all Darwinists are racists.
Doesn't your heart go out to them? Poor, poor IDiots.
Theme
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.
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.
Some of us spend a lifetime trying to understand evolution. We read books, go to meetings, study the scientific literature, and consult experts. It's a difficult subject.
Gil Dodgen is a software engineer who wrote a program that plays checkers. He also plays the piano quite well. He didn't struggle at all over the concept of evolution [Philosophical Repugnancy].
For me, despite 43 years of indoctrination in atheistic materialism and Darwinian orthodoxy, it was a very simple logical exercise to conclude that living systems are the product of intelligent design.
The simplest living cell includes highly sophisticated, functionally integrated information-processing machinery, with error-detection-and-repair algorithms and their implementation.
The notion that random errors, whether filtered by natural selection or not, can produce such technology, is a transparently absurd proposition.
It’s really just that simple.
A few nights ago, Jerry Coyne and Richard Dawkins had an intimate conversation in front of one thousand people at Northwestern University. It was moderated by Hemant Mehta (Friendly Atheist).
I would dearly loved to have been there. I greatly admire all three men. Watch this clip to see Richard Dawkins at his best. You don't have to agree with everything he says (I don't) but you do have to admire his intellect (and his humor).
You're really not going to believe what's going on over at Uncommon Descent. Not only are we witnessing the meltdown of Barry Arrington, but we may also be witnessing the beginning of the end of Intelligent Design Creationism. The IDiots are manoeuvring themselves into such an extreme position that no intelligent person can possibly support them. Just read the comments.
I'm reminded of the word "pathos" but I had to look it up to make sure I got it right. It means something that causes people to feel pity, sadness, or even compassion. It's the right word to describe what's happening. It's also similar to the word "pathetic."
Here's what's happening.
As you know, Barry Arrington claimed that the IDiots made a prediction. They predicted that there's no such thing as junk DNA. They predicted that most of our genome would turn out to have a function [Let’s Put This One To Rest Please]. That's much is true. It makes perfect sense because an Intelligent Design Creator wouldn't create a genome that was 90% junk.
A few days ago I mentioned that definitions were important and I asked my students to look at twenty definitions of "evolution" [The Many Definitions of Evolution]. I was surprised to discover that some of you don't think it's very important to agree on how we define important terms and concepts.
David Klinghoffer agrees with me. He recently posted an article on Evolution News & Views (sic) where he called for clear definitions [Terry Mattingly: In the Evolution Debate, Clear Definitions Are Among the Casualties]. Let's see what he has to say ...
The point cannot be hammered home too often: In media coverage of the evolution debate, a standard trick, the one that stands out the most for slipperiness, is the refusal to define common terms. What is "evolution," or "creationism," or "intelligent design"? Readers may think they know. The reporter may think he knows. Usually, the shades of meaning get blurred, with the suspiciously consistent effect of casting evolution skeptics into a bad light.
Oh dear. Klinghoffer thinks that we are guilty of using definitions that make creationists look bad. He quotes from an article by Terry Mattingly who says ....
[T]he committee that produces the Associated Press Stylebook needs to urge mainstream journalists to be more careful when using the words "evolution" and "creationism." Each of those terms has a half dozen or so finely tuned definitions, depending on who is using them at any given moment.
For example, a person who accepts a creation narrative with a "young earth" and a timeline with seven 24-hour days will certainly embrace the creationist label. But what about a person who believes that creation unfolded over billions of years, involved slow change over time, a common tree of descent for species and ages of micro-evolutionary change?
That's simple. Both are creationists [On Describing IDiots as Creationists] [Creationism Continuum] [What Is Creationism?] (The last two posts attempt to deal with some Sandwalk readers who think that their preferred definition is the only correct definition.)
Mattingly then tackles a more difficult definition ....
Similar things happen with the term evolution, which as the Blessed Pope John Paul II once observed, is best discussed in terms of different schools of evolutionary thought, some of which are compatible with Christian faith and some of which are not...
The word "evolutionist" certainly applies to someone who believes life emerged from a natural, materialistic, random process that was without design or purpose. But what about someone who accepts that theory on the biological front, but believes that there is scientific evidence that our universe was finely tuned to produce life? What about someone who says that creation contains evidence best thought of as the signature of its creator (Carl Sagan, for example). What about people who insist they are doctrinaire Darwinists, but still see cracks in the old neo-Darwinian creeds? Are "theistic evolutionists" really believers in "evolution" in the eyes of the truly secular academic powers that be? And so forth and so on.
This is definitely a problem. As we see, Mattingly is terribly confused about the meaning of "evolution" and the difference between it and "evolutionary theory." I agree that we need to be clear about what we mean and I've tried to do that [What Is Evolution?]. (BTW, "theistic evolutionist" is just a euphemism for a particular kind of "creationist.")
Mattingly doesn't give us an answer. I guess he was too busy complaining.
Let's see what Klinghoffer has to say since he's convinced that this is an important issue. How do the IDiots define "evolution" and "Darwinism" and what do they have to say about modern evolutionary theory? How do they define "creationist"?
Waiting .........
Jean-Marc was kind enough to send me a menu [PDF]. There are about 30 different fondues to choose from. If you would like to join us you can leave a comment on last week's post. 
