Theme
Better BiochemistryWhile I was collecting posts on biochemistry, I came across one that I wrote almost five years ago. It was about a new record for catalytic proficiency. As you know, enzymes speed up reactions that occur naturally and spontaneously. The difference between the spontaneous rate and the rate catalyzed by an enzyme is called the catalytic proficiency.
That old post [Enzyme Efficiency: The Best Enzyme] had a nice graphic showing the spontaneous rates of some reactions that take place quickly inside a cell.
Here it is ....
And here's how the information in that 2008 post got incorporated into the latest edition of my textbook.
This is a "Theme" post where I collect all previous posts on teaching biochemistry and molecular biology.
March 22, 2015
On the handedness of DNA
March 5, 2015
Don't misuse the word "homology"
January 28, 2015
Vision and Change
January 28, 2015
Evidence-based teaching
January 15, 2015
The Nature of Science (NOS)
January 11, 2015
Why can't we teach properly?
January 8, 2015
Evolutionary biochemistry and the importance of random genetic drift
January 3, 2015
Thinking critically about the Central Dogma of Molecular Biology
December 9, 2014
On the meaning of pH optima for enzyme activity
December 9, 2014
On the specificity of enzymes
December 4, 2014
How to revolutionize education
October 20, 2014
How not to teach biochemistry
October 3, 2014
Metabolism first and the origin of life
September 11, 2014
The mystery of Maud Menten
August 8, 2014
Historical contingency and the evolution of the glucocorticoid receptor
July 28, 2014
Finding the "perfect" enzyme
Jun 2, 2014
"Flipping the classroom": what does that mean?
April 25, 2014
ASBMB Core Concepts in Biochemistry and Molecular Biology: Molecular Structure and Function
April 24, 2014
ASBMB Core Concepts in Biochemistry and Molecular Biology: Biological Information
March 21, 2014
ASBMB Core Concepts in Biochemistry and Molecular Biology: Homeostasis
March 5, 2014
The crystal structure of E. coli RNA polymearse σ70 holoenzyme
January 10, 2014
How not to teach biochemistry at memorize.com
December 9, 2013
Monday's Molecule #226
December 6, 2013
Die, selfish gene, die!
December 6, 2013
Do you understand this Nature paper on transcription factor binding in different mouse strains?
December 2, 2013
Monday's Molecule #225
November 12, 2013
David Evans Says, "Teach What the Vast Majority of Scientists Affirm as Settled Science"
November 5, 2013
Stop Using the Term "Noncoding DNA:" It Doesn't Mean What You Think It Means
October 30, 2013
Time to Re-Write the Textbooks! Nature Publishes a New Version of the Citric Acid Cycle
October 29, 2013
The Khan Academy and AAMC Teach Evolution in Preparation for the MCAT
October 29, 2013
The Khan Academy and AAMC Teach the Central Dogma of Molecular Biology in Preparation for the MCAT
October 29, 2013
The Khan Academy and the Association of American Medical Colleges (AAMC) Team Up to Teach Evolution and Biochemistry for the New MCAT
October 24, 2013
ASBMB Core Concepts in Biochemistry and Molecular Biology: Matter and Energy Transformation
October 15, 2013
ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution
October 14, 2013
Fundamental Concepts in Biochemistry and Molecular Biology
October 11, 2013
ASBMB Promotes Concept Driven Teaching Strategies in Biochemistry and Molecular Biology
Another curious aspect of the theory of evolution is that everybody thinks he understands it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually, as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology. Jacques Monod (1974)October 8, 2013
On the Importance of Defining Evolution
October 6, 2013
Teaching Biochemistry from an Intelligent Design Creationist Perspective
October 1, 2013
The Many Definitions of Evolution
September 30. 2013
The Problems With The Selfish Gene
September 18, 2013
Breaking News!!! Wikipedia Is Wrong! (about the Central Dogma)
September 13, 2013
Sean Carroll: 'What Is Science?"
September 13, 2013
Better Biochemistry: Teaching ATP Hydrolysis for the MCAT
September 12, 2013
Better Biochemistry: Teaching to the MCAT?
June 27, 2013
The Best Enzyme
April 16, 2013
Where Do Organisms Get Their Energy?
April 10, 2013
Spontaneous Degradation of DNA
March 18, 2013
Estimating the Human Mutation Rate: Biochemical Method
Last week's molecule was myricyl palmitate, the major component of beeswax [Monday's Molecule #205]. The winner was Bill Chaney. There was no undergraduate winner.
Today's molecule is a very common molecule shown in a somewhat unusual conformation. (It's the conformation of the molecule when it's bound to a certain enzyme.) Identify the molecule (common name only). Can you describe the conformation?
Email your answers to me at: Monday's Molecule #206. I'll hold off posting your answers for 24 hours. The first one with the correct answer wins. I will only post 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.)
Laurence Hurst is a Professor of Evolutionary Genetics in the Department of Biology and Biochemistry at The University of Bath (United Kingdom). He did his graduate studies under W.D. Hamilton at Oxford so it's safe to assume that he has adaptationist leanings.
Hurst wrote a comment in BMC Biology where he criticized the logic employed by those of us involved in the junk DNA debate [Open questions: A logic (or lack thereof) of genome organization]. Here's part of what Hurst says about logic ...
As a graduate student I was advised that if you don’t understand why an animal does what at first sight looks like behavior contrary to its best interests, then you should presume that it is you, not the animal, that is stupid. Look harder, the wisdom goes, and you will discover natural selection’s cunning logic.
That's bad advice, as Stephen Jay Gould and Richard Lewontin pointed out 35 years ago [The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme]. But, like many adaptationists, Hurst is willing to concede that this kind of reasoning may not apply at the molecular level.
While this may be good advice to those studying organismic behavior or anatomy, when we approach genomic anatomy and behavior it will not do.
Indeed, typically when thinking about genomes people often make the opposite presumption. Intergenic DNA was dismissed as irrelevant junk and many transcripts are presumed to be just so much noise. Synonymous mutations have been assumed to be neutrally evolving and where in a genome a gene sits is considered to be largely irrelevant. But are these assumptions more witness to a lack of understanding rather than robust statements about how genomes function and evolve? You are, after all, alive reading this, testament to the fact that your genome is doing something right.
So then, what features of our and other genomes are functionally relevant and which just so much noise? More importantly, when selection does act, why is it acting?
Hurst seems to be assuming that we know nothing about most of the genome and he makes the erroneous assumption that junk DNA advocates dismiss all intergenic DNA as junk. These are the hallmarks of someone who is uniformed about the debate over junk DNA. There is strong positive evidence for junk and those arguments need to be addressed (e.g. genetic load, C-Value Paradox). There is also strong evidence for functional intergenic sequences (origins, centromeres. telomeres, SARs, regulatory regions, etc.) and that evidence is part of the debate. None of the advocates of junk DNA claim that all intergenic DNA is junk.
We know that half of our genome is composed of bits and pieces of defective transposons. That's not ignorance. Broken genes are ... broken genes. They don't work. They are junk. We know enough about genes to recognize the difference between active functional transposons and those that carry lethal mutations of are missing large pieces of their coding region. It's logical to conclude that about half of our genome is junk based on those facts alone.
We know enough about transcription to know that spurious transcription and production of junk RNA transcripts are an inevitable consequence of the basic biochemistry of DNA binding proteins. That's not ignorance.
We know enough about nearly neutral mutations and molecular evolution to know the the existence of an approximate molecular clock means that most synonymous mutations and amino acid substitutions are fixed by random genetic drift. That's not due to a lack of understanding. Hurst has published evidence that some of these seemingly neutral mutations affect function but he ignores the evidence that most behave as if they were neutral.
The fact that you are alive does, indeed, mean that your genome is doing something right. It's good enough for survival of our species. It does not mean that all of your genome is functional.
To his credit, Hurst recognizes that the ENCODE scientists were wrong and that the null hypothesis is NOT natural selection.
The challenge is difficult. Assuming that sites involved in interactions are all functional isn’t good enough. By this, the logic employed by ENCODE, following a collision between a car and a pedestrian, a car’s bonnet would be ascribed the 'function' of projecting a pedestrian many meters and the pedestrian would have the 'function' of deforming the car’s bonnet. Similarly, we expect, for example, accidental transcription factor-DNA binding to go on at some rate, so assuming that transcription equals function is not good enough. The null hypothesis after all is that most transcription is spurious and alternative transcripts are a consequence of error-prone splicing. Conversely, assuming unbound sequence, such as nucleosome-free regions, to be lacking in function can mislead, as they can be critical for the proper control of gene expression.
I get the feeling that Hurst is uncomfortable with the idea that most of our genome is junk [see Hacking the Genome] but he's at least on the right track when he recognizes that there's still a legitimate scientific debate.
Hat Tip: Dan Graur: Laurence Hurst’s Error: The Inability to Distinguish between a Stupid Animal, a Dead Animal, and the Elephant in the Room
Dan Graur has written a post on The Evolution of "Evolutionist". He points out that the term "evolutionist" and "evolutionism" used to refer to those who accept the fact of evolution and support evolutionary theory.
However, he also notes that ...
Since 2000, it is impossible to find the terms “"evolutionist" and "evolutionism" used by anyone except by creation apologists.... I would greatly like to know when exactly was the evolution of "evolutionist" completed and the term acquired its present negative connotation.
I prefer the term "evolutionary biologist" to describe scientists who are experts on evolution. For those non-experts who accept the basic principles of biology, chemistry, physics, geology etc. we don't need a term other than "rational." It's silly to describe them as "gravitationists" or "plate tectonicists" or "thermodynamicists."
Do you ever refer to yourself as an evolutionist?
The National Center for Science Education (NCSE) is looking for a new executive director to replace Eugenie Scott [Help wanted: executive director].
It's gonna be tough filling those shoes.
PZ Myers has discovered an article published in Christian News. The title of the article is: Groundbreaking Genetic Discoveries Challenge Ape to Human Evolutionary Theory. Here's the opening paragraph ...
Fresh findings in the field of genetics have directly challenged yet another key evolutionary hypothesis by showing that the differences between humans and apes cannot be easily accounted for under the theory of evolution.
The paper they are referring to is Farré et al. (2013) and it shows the exact opposite of what the creationists claim. The paper demonstrates reduced recombination rates in those parts of the human and chimp chromosomes where genomic rearrangements have occurred. That's exactly what has been observed for the past 75 years. (See my post on balancer chromosomes, which describes artificial Drosophila chromosomes that were constructed to supress recombination.)
Read PZ's post on the subject to see just how stupid the creationists can be: Do the creationist shuffle and twist!.
I really don't get it. Why does the creationist movement publish material that is blatantly wrong? Even though I mock them repeatedly, I don't really think that every one of them is stupid. Where are the smart ones who review articles like the one published in Christian News? Will we see a retraction or an apology now that their error has been exposed by PZ and by some of the people who commented on the Christian News website?
Farré, M., Micheletti, D., Ruiz-Herrera, A. (2012) Recombination Rates and Genomic Shuffling in Human and Chimpanzee--A New Twist in the Chromosomal Speciation Theory. Mol. Biol. Evol. 30:853-864.
There are dozens of trees like this in Venice, California (USA) in the neighborhood where my grandchildren live. Can you name this tree (common name and species name)?
Can you come up with an adaptationist explanation for why this tree is so different from most other trees and bushes?
RMS Queen Mary first sailed across the North Atlantic on May 27, 1936. At the time she was one of the largest ocean liners.
Now she lives in "retirement" as a tourist attraction in Long Beach, California (USA) where I took this photo yesterday.
The Canadian College of Naturopathic Medicine is not affiliated with the University of Toronto but naturopath students do study anatomy in my building (Medical Sciences Building) on the downtown campus. The College rents Convocation Hall for their graduation ceremonies. The latest graduation ceremonies were on May 23, 2013 (see Graduation Day!.
In order to graduate, students at the Canadian College of Naturopathic Medicine need to pass courses in a number of areas. Here are two of the things they study ...
Asian Medicine/Acupuncture
Students learn about the philosophy and principles of Asian medicine: Yin and Yang theory, the meridians and channels system, the five-element theory and the symptoms and signs involving the 12 master meridians. Applying these principles in the context of patient assessment and treatment is emphasized, with acupuncture and therapeutic botanicals being the main approaches.
Homeopathic Medicine
The history, principles and philosophy of homeopathy are discussed in depth. Practical application of homeopathic principles in patient assessment and management is emphasized for acute and constitutional cases. Skills are developed in case analysis, repertorization, materia medica search, remedy differentiation and selection and prescribing the appropriate posology.
This is pseudoscience and quackery. The University of Toronto should not be lending its implicit stamp of approval to such nonsense.
I realize that the university rents out Convocation Hall for all kinds of events but most of them are so detached from the university that no one will mistake the event as an endorsement by the university. This is different. Convocation Hall is where the university's own graduation ceremonies take place (the name is a clue!). The average person will assume that the University of Toronto supports the Canadian College of Naturopathic Medicine and that our faculty has no problem with graduating quack "doctors."
This practice should stop.
Back in the late 1980's, I read Molecular Evolutionary Genetics by Masatoshi Nei. He introduced me to the concept that the history of life is driven by mutation and that the old-fashioned view of mutationism needs to be looked at more carefully. A decade later, Arlin Stoltzfus took up the cause and he has published a number of papers on the topic.
If you want to read more about mutationism then you can't find a better source than the series of posts by Arlin on Sandwalk from 2010. The last one, The Mutationism Myth VI: Back to the Future, contains links to all of the others. Be warned, it will be hard to resist the idea of mutationism after you read Arlin's explanation. It will hurt your brain.
I just learned that Masatoshi Nei is about to publish a new book called Mutation-Driven Evolution. Here's the description on Amazon ...
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MutationThe purpose of this book is to present a new mechanistic theory of mutation-driven evolution based on recent advances in genomics and evolutionary developmental biology. The theory asserts, perhaps somewhat controversially, that the driving force behind evolution is mutation, with natural selection being of only secondary importance. The word 'mutation' is used to describe any kind of change in DNA such as nucleotide substitution, gene duplication/deletion, chromosomal change, and genome duplication. A brief history of the principal evolutionary theories (Darwinism, mutationism, neo-Darwinism, and neo-mutationism) that preceded the theory of mutation-driven evolution is also presented in the context of the last 150 years of research. However, the core of the book is concerned with recent studies of genomics and the molecular basis of phenotypic evolution, and their relevance to mutation-driven evolution. In contrast to neo-Darwinism, mutation-driven evolution is capable of explaining real examples of evolution such as the evolution of olfactory receptors, sex-determination in animals, and the general scheme of hybrid sterility. In this sense the theory proposed is more realistic than its predecessors, and gives a more logical explanation of various evolutionary events.
Mutation-Driven Evolution is suitable for graduate level students as well as professional researchers (both empiricists and theoreticians) in the fields of molecular evolution and population genetics. It assumes that the readers are acquainted with basic knowledge of genetics and molecular biology.
I can't wait to get my hands on a copy of this book. Look for a review in a few months.
Let's look at a recent post on Evolutin News * Views (sic): From Discovering Intelligent Design: Opposition from the Scientific Establishment. As the title suggests, this is an excerpt from one of the books being heavily promoted by the IDiots.
They have a problem. How do the IDiots explain why 99.9% of biologists oppose Intelligent Design Creationism? It's because they all have a materialistic bias that prevents them from following the evidence wherever it may lead. Read this bit ...
ID challenges a reigning scientific paradigm. But as sociologist Steve Fuller says, ID is not anti-science, but rather anti-establishment. ID theorists want more scientific investigation, not less. They simply want the freedom to follow the evidence without harassment or philosophical restrictions.
An ID-based view of science promises to open new avenues of scientific investigation. Without materialist paradigms governing science, perhaps more scientists would have sought function for structures like "junk" DNA and vestigial organs, rather than assuming they were non-functional evolutionary relics.
Let me remind you that the presence of junk DNA in our genome was not anticipated by those who believed in the importance of natural selection. What happened was that the evidence became too substantive to ignore so scientists had to accept the presence of junk DNA in spite of the fact that most of them expected selection to eliminate it.
Now if you insist on believing in an intelligent design paradigm then you simply can't follow the evidence wherever it may lead because junk DNA isn't part of your worldview. In other words, the example used by the IDiots in this post is the exact opposite of the point they are making.
Oops!
Now you know why we call them IDiots.
