How to Make a Scientific Argument

The debate over the amount of junk in our genome is a genuine scientific debate. There are legitimate scientific points of view on both sides although the weight of evidence and logic is tilting heavily in favor of junk DNA. It looks more and more like most (~90%) of our genome is junk.

The problem with the debate is that the scientific literature is full of papers attacking junk DNA while there are very few papers promoting it. This is partly because there haven't been any new discoveries in favor of junk DNA. On the other hand, there have been quite a few discoveries showing that some small part of the genome that was thought to be junk might have a function. Even though these discoveries make an insignificant contribution to the big picture, they are often blown up out of all proportion and promoted as an end to junk DNA.

A recent paper in PLoS Genetics illustrates the problem.

Monday's Molecule #207

Last week's molecule was N-acetylmuramic acid (MurNAc) one of the components of the polysaccharide in bacterial cell walls [Monday's Molecule #206]. The winner was Michael Florea. He should contact me by email to collect his winnings.

Today's (Tuesday's) molecule is a new addition to biochemistry textbooks because its structure was only solved a few years ago. There are plenty of hints in the figure. You have to identify the molecule AND each of the seven activities that are labelled. Bonus points for the PDB identification number and the species.

Email your answers to me at: Monday's Molecule #207. 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.)

Evolution vs God

It's Ray Comfort and he's going to destroy Richard Dawkins. Bet you can hardly wait to see this movie. PZ Myers is in it. Read what he has to say at: Lie harder, little man.

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A Philosopher Trashes Junk DNA

I am one of those scientists who think that the discipline of "philosophy of science" is catering to some pretty stupid philosophers. Dan Graur found one of them, his name is Max Andrews and he's a graduate student in philosophy at the University of Edinburgh, Scotland ["I’ve Got a Little List" & “Let the Punishment Fit the Crime"].

You can read Max Andrews' blog posting at: Junk DNA Isn’t Junk. Be careful, you might find it very difficult to see the connection between this philosophy student's view of biology and anything you might recognize as real science.

It goes without saying that Max Andrews gets the Central Dogma wrong—many scientists make the same mistake. But here's a taste of what else he gets wrong.

The argument from junk DNA suggests that a designer would be maximally efficient in his use of information. There appears to be some information that does not execute or have any meaningful coding. Darwinism takes this issue and uses it as the result of the prediction that there would be left over information not being used due to natural selection and random mutation. However, it doesn’t appear that all junk DNA is actually junk.

Genome organization is patterned to be maximally informative. The overlapping codes observed are known to be evolutionarily costly, because random mutations will likely have a deteriorating effect, not an instructing role So the complex specified information entailed by any genomic region is orders of magnitude higher than previously suspected by, say, Dembski. Any seemingly random aspect of chromosome sequence arrangement is not. A case in point involves endogenous retroviruses (ERV’s). This implies that the taxonomically-specific formatting, indexing, punctuation, etc., of genomes were precisely written. Morphogenetic information is not reducible to the genotype—though it is strongly dependent upon it. Therefore, changes in DNA do not equal changes in the information that structures the body plan.

I wonder who his supervisor is? Maybe Dan or I could be external reviewer on his Ph.D. oral?

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On the Misuse of the Term "Genetic Code"

Dan Graur is fed up with journalists who don't know the difference between the "genetic code" and the sequence of a genome. He's not alone. But, unlike the rest of us, Dan has a solution. It may be a little difficult to enforce ...

See: An Artistic Inspiration for Putting an End to the Misuse of the Term “Genetic Code”.

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Will There Be a Junk DNA Debate in Chicago?

Quite a few people think that there's going to be a serious debate about junk DNA at the SMBE meeting in Chicago next week. One of the sessions has a provocative title, "WHERE DID 'JUNK' GO?", but if you look at actual session titles it doesn't look like there's going to be much of a debate.

It's true than the session organizer, Wojciech Makalowski, advertised the session as a dicussion about junk DNA ....

Keep Calm and Ask About Onions

Nick Matzke is going to the SMBE (Society for Molecular Biology and Evolution) meeting in Chicago next week. He's created a T-shirt for supporters of junk DNA [KEEP CALM and ASK ABOUT ONIONS].

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Get Science Right in Canada

Get Science Right

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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.”

The Best Enzyme

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.

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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 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

"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."

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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'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.)