Michael Egnor Keeps Digging

When you find yourself in a hole, stop digging.
Will RogersI favor teaching biochemistry from an evolutionary perspective and I was pleased to see that ASBMB considers evolution to be one of the fundamental concepts in biochemistry and molecular biology [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution]. (ASBMB screws up their description of evolution but at least their heart's in the right place.)

Unless they understand evolution, students can't really understand why some parts of a protein are the same in all species and other parts are quite variable. They certainly can't understand why you can construct a phylogenetic tree from sequences and why this tree closely resembles those trees made from comparing anatomy/embryology. They won't know why those molecular trees are consistent with a fossil record unless they understand evolution.

Monday's Molecule #221

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.)

Trace Dominguez of Discovery News Says 98% of Your Genome Is Junk

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?] ....

1. Genes for functional RNAs like ribosomal RNA, tRNA, and a host of others.
2. Regulatory sequences that control expression of all genes.
3. Part of intron sequences.
4. Origins of replication;specific sites where DNA replication begins.
5. Telomeres.
6. Centromeres.
7. SARS or scaffold attachment regions; sites required to organize chromatin.
8. Functional transposons or "selfish DNA."
9. 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

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How to Turn a Simple Paper into a Scientific Breakthrough: Mention Junk DNA

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.

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Attanasio, C. et al. (2013) Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers. Science 342: Oct. 25, 2013 [doi: 10.1126/science.1241006]

Oops!

This is the view from the window just outside my office on the fifth floor.

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ASBMB Core Concepts in Biochemistry and Molecular Biology: Matter and Energy Transformation

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:

1. evolution [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution ]
2. matter and energy transformation [ASBMB Core Concepts in Biochemistry and Molecular Biology: Matter and Energy Transformation]
3. homeostasis [ASBMB Core Concepts in Biochemistry and Molecular Biology: Homeostasis]
4. biological information [ASBMB Core Concepts in Biochemistry and Molecular Biology: Biological Information]
5. 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 v_o, V_max, K_m, and k_cat, 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 P_i 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."

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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]

How Do the IDiots Explain the Origin of Life?

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?

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Peter Hess of NCSE Tells Us About How to Make Evolution Compatible with Christianity

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.

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The Trouble With Science

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.

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Jukes to Crick on Junk DNA

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

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Evolution Is Irrelevant to Michael Egnor

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.

Monday's Molecule #220

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.)

ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution

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:

1. evolution [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution ]
2. matter and energy transformation [ASBMB Core Concepts in Biochemistry and Molecular Biology: Matter and Energy Transformation]
3. homeostasis [ASBMB Core Concepts in Biochemistry and Molecular Biology: Homeostasis]
4. biological information [ASBMB Core Concepts in Biochemistry and Molecular Biology: Biological Information]
5. macromolecular structure and function [ASBMB Core Concepts in Biochemistry and Molecular Biology: Molecular Structure and Function]

Darwinists Are Racists?

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.

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Fundamental Concepts in Biochemistry and Molecular Biology

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.