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Friday, June 28, 2013

Get Science Right in Canada

Get Science Right

John Mattick on the Importance of Non-coding RNA

John Mattick is a Professor and research scientist at the Garvan Institute of Medical Research at the University of New South Wales (Australia). He received an award from the Human Genome Organization for ....
The Award Reviewing Committee commented that Professor Mattick’s “work on long non-coding RNA has dramatically changed our concept of 95% of our genome”, and that he has been a “true visionary in his field; he has demonstrated an extraordinary degree of perseverance and ingenuity in gradually proving his hypothesis over the course of 18 years.”

Thursday, June 27, 2013

The Best Enzyme


Better Biochemistry
While 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.

Better Biochemistry

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

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

Tuesday, June 25, 2013

"Reasons to Believe" in ENCODE

Fazale "Fuz" Rana is a biochemist at Reasons to Believe". He and his colleagues are Christian apologists who try to make their faith compatible with science. Fuz was very excited about the ENCODE results when they were first published [One of the Most Significant Days in the History of Biochemistry]. That's because Christians of his ilk were very unhappy about junk DNA and the ENCODE Consortium showed that all of our genome is functional.1

Fuz is aware of the fact that some people are skeptical about the ENCODE results. He wrote a series of posts defending ENCODE.
  1. Do ENCODE Skeptics Protest Too Much? Part 1 (of 3)
  2. Do ENCODE Skeptics Protest Too Much? Part 2 (of 3)
  3. Do ENCODE Skeptics Protest Too Much? Part 3 (of 3)
The first post is merely a list of the objections many of us raised.

One of the Most Significant Days in the History of Biochemistry

Reasons to Believe is "where science and faith converge." It's the organization founded by creationist Hugh Ross, a graduate of the University of Toronto. One of his leading minions is Fazale ("Fuz") Rana, a biochemist.

Fuz says that "September 5, 2012 marks one of the most significant days in the history of biochemistry."

Marc Kirschner Defends Basic Science

Marc Kirschner is Chair of the Department of Systems Biology at Harvard Medical School. He's a very smart man and a well-respected scientist.1 He has an editorial in the June 14th issue of Science: A Perverted View of “Impact” [see also: In search of big breakthroughs: why attempts to predict ‘significant’ research might backfire in The Boston Globe]

Kirschner says that the emphasis on "significance" and "impact" in making funding decisions is "misleading and dangerous." Nobody can really predict how fundamental research will affect the future. He writes ...

Monday, June 24, 2013

Monday's Molecule #206

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 Discusses Junk DNA

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

Are You an Evolutionist?

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?

Wednesday, June 19, 2013

Get a Job! ... at NCSE

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.

More Creationist Stupidity

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.

Saturday, June 08, 2013

Name this tree!

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

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.

Friday, June 07, 2013

Naturopathic "Doctors" Graduate from Convocation Hall on the University of Toronto Campus

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.

Saturday, June 01, 2013

Mutation-Driven Evolution

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 ...

The 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.