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Friday, August 17, 2012

Disproving Evolution

Elsewhere on the internet there's a discussion about whether evolution can be disproved by simply finding a fossil out of order.

Here's what I said on Facebook ...
The statement is untrue. If we discover that a given species is older than we thought then we will just revise our view of the history of life on Earth. It will not disprove the fact of evolution and it will have no effect on evolutionary theory. It is a mistake to link the truth of evolution to our current understanding of the history of life. That history can be easily changed without threatening evolution.


Thursday, August 16, 2012

R. Elsiabeth Cornwell Talks About Social Networks

R. Elisabeth Cornwell is Executive Director of the Richard Dawkins Foundation (US). She has a Ph.D. in psychology and her day job is Professor at the University of Colorado at Colorado Springs.

Here's Cornwell giving a talk at TAM2012. It makes me cringe but is it just me? Apparently not if you read the comments at YouTube.


She talks a lot about bullies and their presumed psychiatric problems but she doesn't give any examples. Who is she thinking about? Jonathan Wells? PZ Myers? Margaret Thatcher? Rush Limaugh? Stephen Jay Gould? Jerry Falwell? Ken Miller? Ann Coulter? Christopher Hitchens? Thomas Huxley? Rachel Maddow? Richard Dawkins?

It would have been nice to see the difference between pre-internet "bullies" and those on the internet. Are there any example of people who were "civilized" before they got on the internet but became bullies once they started a blog?


Stipends for Graduate Students

Here's what we pay our slaves graduate students while they are working toward their degrees. How does it compare with other biochemistry departments?

Biochemistry Graduate Student Stipends for 2012-2013

M.Sc. students

Domestic Students
$17,000 living allowance plus tuition ($7,160.00) and incidental fees ($1,241.52) = $25,401.52

International Students
$17,000 living allowance plus tuition ($16,886.00) and incidental fees ($1,241.52) AND UHIP ($684.00) = $35,811.52

Ph.D. students

Domestic Students
$19,000 living allowance plus tuition ($7,160.00) and incidental fees ($1,241.52) = $27,401.52

International Students
$19,000 living allowance plus tuition ($16,886.00) and incidental fees ($1,241.52) AND UHIP ($684.00) = $37,811.52

(UHIP is the University Health Insurance Plan)

My graduate student stipend in 1968 was $3000, which is $19,500 in 2012 dollars. I don't remember how much tuition and the health plan cost. We lived in subsidized housing, The rent was $56 per month.

We have about 140 graduate students in our department. Many of them are in the photo along with several much older "students" who earn a lot more money.


Wednesday, August 15, 2012

Donald E. Nicholson (1916 - 2012)

Donald Nicholson died last May. He was 96 years old.

Nicholson was a professor of biochemistry at the University of Leeds in the United Kingdom. He started drawing metabolic charts back in 1955 and they gradually evolved into the works of art that you have seen in all the textbooks and on the walls of labs in offices in biochemistry departments around the world. I doubt that there's a single biochemist that hasn't studied these charts at some time during their undergraduate experience.

Lately his metabolic charts have been the property of the International Union of Biochemistry and Molecular Biology (IUBMB) but many of them have been marketed by Sigma-Aldrich [Metabolic Pathways].

Recent additions have included several minimaps of specific pathways such as those involved in lipid metabolism, glycolysis, the urea cycle etc. It's sad that we won't see any additions to this collection or any updates.



A Sophisticated Theologian Explains Why You Should Believe in God

Modern atheists are often accused of being ignorant of the most up-to-date arguments for the existence of god(s).1 We are told that there's a very sophisticated group of theologians out there who shouldn't be ignored.

Whenever we ask for those "sophisticated" arguments for the existence of god(s) we are directed to various Courtier's Replies discussing how to rationalize the properties of various gods. They all begin with the assumption that god(s) exist. As I pointed out earlier, there's no reason why an atheist should care about things like the problem of evil. It makes about as much sense as debating the cut of the Emperor's new clothes or the stylishness of his new hat.

Alvin Plantinga is one of these "sophisticated" theologians. Listen to him explain why atheists should believe in god(s). Is this really the best they can do?



1. The second most common complaint is that we don't even have good arguments for atheism—at least not as good as those thinkers of the 20th century who were full of angst over not having a god to believe in. Apparently modern atheists aren't very sophisticated unless they are contemplating suicide.

[Hat Tip: Jerry Coyne: Plantinga on why he believes in God, dislikes the New Atheists, and finds naturalism and evolution incompatible.]

Monday, August 13, 2012

Monday's Molecule #181

Last week's molecule was an intermediate in some amino acid biosynthesis pathways and the enzyme that makes it is the target of Roundup®. Replacing this enzyme with a Roundup® resistant version yields genetically modified food plants [Monday's Molecule #180].

This week's molecule is a lot more complicated. You need to identify the specific type of molecule. Defective metabolism of this molecule is associated with a famous disease. Name the disease.

Post your answers as a comment. I'll hold off releasing any comments 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 comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is ganglioside GM2. Defects in ganglioside synthesis are responsible for a number of genetic diseases in humans including Tay-Sachs disease. This is the same molecule featured in Monday's Molecule #162 back on March 19, 2012. There was no winner that time.

This week's winner is Matt McFarlane, an undergraduate. He lives in Canada but he's quite far away and probably won't make it for lunch.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia
July 23: Raul A. Félix de Sousa
July 30: Bill Chaney and Raul A. Félix de Sousa
Aug. 7: Raul A. Félix de Sousa
Aug. 13: Matt McFarlane


An Example of "Directed" Mutation and an Idiotic "Gotcha"

There's nothing in modern evolutionary theory that allows for mutations that arise specifically because they will produce a future benefit. That's why we say that mutations are "random" with respect to outcome.

There's nothing in the known history of life that suggests it has a purpose or direction. In particular, there's nothing to suggest that 3.5 billion years of evolution were just advanced preparation for the appearance of Home sapiens. That's why we say that evolution appears unguided and purposeless [Is "Unguided" Part of Modern Evolutionary Theory?]. And that's why anyone who says that life shows evidence of purpose is not being scientific.

Creationists aren't happy about this so they will go to extraordinary lengths to wiggle out of the inescapable conclusion based on solid evidence. The usual excuse is to postulate that god is very sneaky. He/she/it makes a huge effort to hide his/her/its manipulations so that it only appears that evolution is unguided and purposeless. The clever creationists aren't fooled by this sneaky god; they can detect its deception, but scientists can't.

Saturday, August 11, 2012

Humanities Aren't Science? More's the Pity

Science is a way of knowing that is evidence based and requires rational thinking and healthy skepticism. It's the only successful way of knowing that has ever been invented.

Whenever investigators in the humanities discover new knowledge it turns out that they have been using a scientific approach. They've been thinking like a scientist. What else could they be doing?

Maria Konnikova is a graduate student in psychology at Columbia University. She writes in Scientific American that Humanities aren’t a science. Stop treating them like one.

Well, it's certainly true that many disciplines in the humanities are very unscientific—evolutionary psychology comes to mind—but this is one of the first times I've ever heard someone be proud of the fact that they don't think scientifically. Why in the world would she say that?

Turns out she's confused about what science is and what it isn't. She thinks that science requires lots of quantitative data and lots of mathematics and statistics.
Sometimes, there is no easy approach to studying the intricate vagaries that are the human mind and human behavior. Sometimes, we have to be okay with qualitative questions and approaches that, while reliable and valid and experimentally sound, do not lend themselves to an easy linear narrative—or a narrative that has a base in hard science or concrete math and statistics. Psychology is not a natural science. It’s a social science. And it shouldn’t try to be what it’s not.
Hmmmm ... that might explain a lot. I guess if you are seeking knowledge in the social sciences it's okay to use a non-scientific approach to gain knowledge. I wonder what approach they follow? Do they pray for guidance? Use a Ouija board? Or do they just make stuff up?

Maybe Konnikova is just saying that humanities disciplines are not chemistry, physics, biology or geology? Nah, that's too obvious. It doesn't merit an article in "Scientific" American. Maybe we'll find out what she really means when her book comes out in January. It's title is: Mastermind: How to Think Like Sherlock Holmes. Did Sherlock Holmes think like a scientist or did he think like someone in the humanities?


[Hat Tip: Mike the Mad Biologist]

Science and Christianity—Different Ways of Finding Truth?

Chris Mulherin is an Anglican Minister who studies the relationship of science and religion. In this video he claims that science and religion are compatible. Specifically, science and Christianity are compatible.

UPDATE: Eric MacDonald does an excellent job of taking down Chris Mulherin in Science and Religion Again!. MacDonald is a former Anglican priest. (Hat Tip: Jerry Coyne.

He doesn't explain how rising from the dead, miracles, souls, heaven, and a Bible full of lies are compatible with science. Instead, he concentrates on the old saw of different magisteria. Christianity answers different questions than science and discovers different truths.


Id' like to echo the challenge I made some years ago and the one Jerry Coyne issues today [Do both science and faith produce truth?]. Can anyone give us an example of a "truth" discovered by religion—one that we all recognize as genuine knowledge? Name a "why" question that religion answers in a way that we all accept as meaningful and true.1

Those who think that science and religion are compatible like to accuse us of not understanding the serious philosophical issues. I don't think that's correct but, if it is, here's a chance for the serious courtier theologian to set us straight.

Waiting .....


1. It's not good enough to say that if only Christians accept the answer as true, then Christianity has discovered truth. If that were the case then astrology and homeopathy are also valid ways of finding truth even if astologers and homeopaths are the only ones who believe the answers. I'm guessing that no serious philosopher would defend such a ridiculous position.

Is "Unguided" Part of Modern Evolutionary Theory?

Creationists are unhappy with the claim that the evolution of life on Earth appears unguided and purposeless. Casey Luskin would like to think that it's a fundamental part of "the theory of Darwinian evolution" [Unguided or Not? How Do Darwinian Evolutionists Define Their Theory?].
An argument we are increasingly hearing from theistic evolutionists is that the "unguided" or "random" aspects of Darwinian evolution are merely "philosophical gloss" or an "add-on" promoted by new atheists who use bad philosophy. Jay Richards covered this question in his recent dialogue with Alvin Plantinga--see here, here, here, and here for the series. While many new atheists undoubtedly make poor philosophers, the "unguided" nature of Darwinian evolution is not a mere metaphysical "add on." Rather, it's a core part of how the theory of Darwinian evolution has been defined by its leading proponents. Unfortunately, even some eminent theistic and intelligent design-friendly philosophers appear unaware of the history and scientific development of neo-Darwinian theory.
This is wrong in many ways.

Here's the simple explanation ... so simple that even an IDiot should be able to understand it.

Modern evolutionary theory consists of many parts including the mechanisms of evolution. The main mechanisms are natural selection and random genetic drift and those two mechanisms act on populations containing variation. The variation is due to the presence of mutations and mutations arise "randomly" with respect to ultimate purpose or goal.

There are tons of experiments proving that mutations are essentially random. (Let's not get into quibbling about the meaning of "random.")

Now let's look at the history of life on Earth. This is a completely separate subject from evolutionary theory. It's like the difference between the theory of gravity and how and when our particular solar system formed.

Looking all the evidence used to reconstruct the probable history of life we see no evidence whatsoever that it was guided in any particular direction or that there was any underlying purpose. That's why we conclude that the evolution of life on Earth appears unguided. It's a tentative conclusion based on fact and observation and not on "the theory of Darwinian evolution."

While it is true that evolutionary theory doesn't allow for a "guided" mechanism, it isn't true that the history of life has to be devoid of purpose or guidance. There could well be evidence that god intervened or that particular organisms were preferred over others and the history was tilted in one direction. But there's no evidence that this is the case—with the possible exception of beetles.

The history of life looks exactly like it should if it were the result of accident, contingency, and evolution. There's no evidence of god(s). That's what makes the creationists upset, not evolutionary theory.


Friday, August 10, 2012

Only Young Scientists Overthrow Old Concepts?

Max Planck once said ...
A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.
This does not conform to my experience in the biological sciences.

I think that what usually what happens is that a new way of thinking is promoted by well-established investigators. Gradually other scientists are convinced by the evidence to change their minds and the new scientific truth spreads within the community.

When a substantial number of scientists are converted, they start teaching the new concept in graduate and undergraduate courses. This produces a young generation who never heard of the old "truth."

If I'm correct then a new generation of scientists grows up familiar with the new scientific truth but only because the established scientists converted and started training the next generation properly.

When it comes to challenging old established concepts in a discipline I find that initially the younger scientists are often quite conservative unless they just happen to be working on that problem. This shouldn't be a surprise since our young investigators have their hands full just establishing themselves in their field. They don't have time to think about what's going on in the rest of the discipline. In fact, it might be detrimental to their careers to challenge most established concepts.

As I'm writing this I'm having trouble coming up with examples in biology. Most of the conceptual shifts that come to mind are ongoing controversies where it still isn't clear that the new scientific truth will replace the old one. I'm thinking of evo-devo, challenges to evolutionary theory, junk DNA, chemiosmotic theory, metabolism & thermodynamics, the tree of life, photosynthesis, and even new ways of teaching.

Can anyone think of examples were the shift has been completed so we can test the Max Planck hypothesis?

How about the shift from thinking that genes were proteins to genes are DNA?


Thursday, August 09, 2012

Still Digging: Part II

Bet you thought that this horse had been beaten to death when you read Still Digging: Part I.

Ha! You don't know why we call them IDiots!

Here's the latest contribution from lawyer non-scientist David Klinghoffer: Why We Call the Myth of Junk DNA a "Myth"

Still Digging: Part I

Believe it or not, the IDiots are still trying to weasel out of the mistakes they've made in attacking junk DNA.

Here's the problem. Jonathan Wells wrote an entire book on The Myth of Junk DNA. Wells says that back in the early 1970s a substantial number of scientists—he calls them Darwinists—said that all noncoding DNA was junk.

44 Years Ago Today


We got married forty-four years ago today.

Ms. Sandwalk hasn't changed a bit.


"Curiosity" Driven Science

The engineers and technicians have done their job, and what a fantastic job they did! "Curiosity" is now on the surface of Mars and it's time for the science to begin.

Have you been wondering about the scientific mission? The search for life is getting all the publicity but, let's face it, the chances of success are slim.

What about the other missions? Rebecca Ghent of the Dept. of Earth Sciences at the University of Toronto explains why she's interested in the data that "Curiosity" will collect [Curiosity: planetary science and the latest Mars mission].
One of the things I'm interested in is the physical characteristics of planetary regoliths - the surface layer of broken rock, dust, etc., that covers planetary surfaces. It's important to understand how this layer formed and has evolved, because it holds a record of the geological processes that have occurred on each planet. Mars has a very complex surface geological record involving the actions of wind, volcanism, impact cratering, and possibly, water; so this new information about the composition and physical characteristics of the rocks at the Curiosity landing site will provide valuable new insights into the roles of these various processes in forming Mars' surface rocks.
For scientists, the best is yet to come. I hope the science journalists can keep the public focused on the real mission and the importance of the data.


Wednesday, August 08, 2012

Charles Darwin at the London 2012 Olympics

Those Brits know what's important! (They also had a picture of some other scientist, I think his name was Isaac.)



[Hat Tip: Ms. Sandwalk]

TED: Alexander Tsiaras, "It was hard not to attribute divinity to it"

Some of you aren't familiar with TED talks so the recent criticism doesn't make sense (e.g. The Trouble with TED). Here's an example of one of the problems with TED talks. This is a "gosh, gee whiz" kind of talk that's almost completely devoid of information.1

The talk has pretty pictures of the developing human embryo/fetus accompanied by the kind of music that evokes mystery and awe. The author of the video talks of the mystery and why it makes him think of divinity.

The first divinity-inspiring observation concerns collagen. Most collagen molecules form fibers (see Collagen) but those in the eye form sheets in the basal lamina. This is because the eye collagen is a different type of collagen. Here's what Wikipedia says [Collagen IV] ...
Type-IV collagen is a type of collagen found primarily in the basal lamina. The type IV collagen C4 domain at the C-terminus is not removed in post-translational processing, and the fibers link head-to-head, rather than in parallel. Also, type-IV lacks the regular glycine in every third residue necessary for the tight, collagen helix. This makes the overall arrangement more sloppy with kinks. These two features cause the collagen to form in a sheet, the form of the basal lamina.
Does that make you think of god(s)?

Would you pay several thousand dollars to hear this TED talk?



1. Recall that the theme of TED is "Ideas worth spreading." Which ideas in this talk are worth spreading?

Tuesday, August 07, 2012

Changing Ideas About The Origin Of Life

I recommend this article by Enrico Uva: Changing Ideas About The Origin Of Life.

Here are the main points—but you should read the whole thing.

  1. Primordial catalysts were probably not proteins nor RNA
  2. First Energy Source Likely Involved Proton Gradients
  3. Knowledge of New Bacterial Kingdoms Downplays Role of Fermentation In First Cells
You should also read The beginnings of life: Chemistry’s grand question by Ashutosh Jogalekar. Here's an excerpt.
While Miller and his fellow “soupists” blazed the initial paths in origins of life research, a startling new era dawned in the 80s with the discovery of potential life-sustaining factories in the most unlikely environments. The finding that life thrives in deep hydrothermal vents opened a whole new chapter in the field, again avowedly chemical. Black smoker chimneys located miles beneath the ocean have for millions of years been orchestrating a tumultuous union of hot, metal-rich, acidic chemicals arising from volcanic vents with cool alkaline waters. The unholy meeting of these two chemical opposites leads to a violent precipitation of minerals including the silicate mineral olivine, one of the most ubiquitous components of our planet’s rocky landscape. The precipitation of these minerals results in chimney like structures that can be miles high. The convecting thermal currents in these chimneys provide an abundant source of life’s sine qua non – energy. The metals can act as catalysts for simple reactions which involve sulfur, carbon monoxide and water. In recent years, because of the sheer energy hidden inside them, their capacity to catalyze key reactions like the Krebs cycle and concentrate reactants and products in microscopic pores and the uncanny resemblance of some of the iron and sulfur compounds to crucial iron-sulfur cores found in proteins, these mighty smokers have been considered by many scientists to precede or at least accompany the origin of life on the surface. Prominent among the “smokers” are scientists like Nick Lane and the patent attorney Günter Wächterhäuser who moonlights in the field as a “hobby”. These theories provide the “metabolism first” counterpart to the “replication first” camp. Together they may account for both genetic inheritance and chemical metabolism.
It doesn't matter whether you're a soupist or a smoker but you'd better be aware of the controversy. Too many scientists think that the primordial soup is still the best, and only, game in town in spite of its severe problems.


Note to David Klinghoffer, When You find Yourself in a Hole, Stop Digging

Some of you might recall the recent Chromosome 2 kerfuffle. It started when Carl Zimmer asked David Klinghoffer a simple question. Zimmer asked him to describe the evidence to support his claim that the fusion site didn't look like it should if two primitive ape chromosomes had fused to produce human chromosome 2.

Rather than simply answer the question, the IDiots circled the wagons then went into attack mode. Eventually, after a lot of pressure, they got around to answering the question; apparently there is no evidence to support their claim [And Finally the Hounding Duck Can Rest].

Of course by then they were so deep in their hole that the sun don't shine.

Monday's Molecule #180

It's Tuesday, so it must be time for Monday's Molecule.... Oops.1

Last week we looked at an important intermediate in the Calvin cycle—the main pathway for fixing carbon dioxide in many species [Monday's Molecule #179]. Today we're going to look at the intermediate in another pathway. Name the molecule, the common name will do.

Discovery of this molecule, and the pathway it's involved in, was an important contribution to understanding basic metabolism in most cells. The enzyme that makes it has been characterized. It's now one of the most widely studied enzymes in biochemistry. The pathway is essential for all species, with a few minor exceptions.

This knowledge has been exploited by technology to an extent never imagined only 50 years ago. Name the technology and how it makes use of what we know about the enzyme and the pathway. For extra bonus points, explain how the molecule got it's root Japanese name.

Post your answers as a comment. I'll hold off releasing any comments 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 with a very famous person, or me.

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 comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.

Comments are invisible for 24 hours. Comments are now open.

UPDATE:The molecule is 5-enolpyruvylshikimate 3-phosphate an intermediate in the chorismate pathway and the synthesis of tryptophan, phenylalanine, and tyrosine. The enzyme that produces this product is EPSP synthase and some bacterial versionsof this enzyme are resistant to glyphosate, the active ingredient in the herbicide Roundup®.

The gene for the resistant enzyme can be inserted into crop plants making them resistant to Roundup®.

The winner would have been Ben but I can't identify that person. The winner is Raul A. Félix de Sousa.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia
July 23: Raul A. Félix de Sousa
July 30: Bill Chaney and Raul A. Félix de Sousa
Aug. 7: Raul A. Félix de Sousa


1. I got confused because yesterday was Simcoe Day.

Newsgroups, Blogs, Twitter, Facebook, and Google+

Blogging is fun. I love it when a serious discussion breaks out in the comments. Sometimes I love it even when the discussion is not serious.

Back in the olden days I used to love the newsgroups, especially talk.origins but I don't read it much any more. (Don't worry, I won't shut off the talk.origins server.)

Lately I've been spending more time on Twitter, Facebook and Google+ to see if there's anything there worth reading. It seems to be a mixed bag. The ratio of interesting vs non-interesting stuff seems to be a problem.

Perhaps that's just because I'm not following the right people?

Let me know if you find something worthwhile. My Twitter account is @larryon sandwalk, you can reach me on Facebook at Laurence A. Moran, and on Google+ I'm Laurence A. "Larry" Moran.


Monday, August 06, 2012

The Trouble with TED

An awful of of people seem to waking up to the idea that TED talks are not what they're supposed to be. They attract a lot of kooks who can speak well and exude enthusiasm. How many times have you listened to a TED talk in your area of expertise and wondered how the heck that person got on the stage?

TED talks are just big soundbites and soundbites are not good ways to explain complicated, and potentially revolutionary, ideas.

The NAFTA Superhighway

I just heard about the NAFTA Superhighway. It's going to be as wide as four football fields. Is that Canadian football fields, Mexican football fields, or American football fields?

I can't wait 'till it's finished.

The good news is that I should be able to drive from Toronto to Texas in less than 24 hours.

The bad news is that Texans will be able to drive to Toronto in less than 24 hours.

I hope they have Tim Hortons at the rest stops.


What Does "pH" Mean?

The term "pH" is used to measure acidity. Strong acids, like hydrochloric acid or sulfuric acid, have very a very low pH while weaker acids, like acetic acid (vinegar), have pH readings that are higher. A "neutral pH" is 7.0, this is close to the pH value of the cytoplasm in living cells.

Higher pH values are "alkaline" rather that acidic. The highest pH value is usually shown as 14 and the lowest pH value is shown as 0.

Acidity is a function of the concentration of hydrogen ions (H+), or protons. The strength of alkaline solutions is measured by the concentration of hydroxide ions (OH-).

There's a reciprocal relationship between the concentrations of these two ions because we're dealing with aqueous solutions (water). Water molecules dissociate into H+ and OH- ions so in pure water there will always be equal concentrations of both ions.

The extent of this dissociation determines the concentration of these ions in pure water. We express the extent of dissociation using a term called the equilibrium constant (Keq) that is defined as the concentration of the products of a reaction over the concentration of the reactant(s).

For the dissociation of water, the actual equation is ...

Intelligent Design Creationists Attempt to (re)Define Junk DNA

Paul McBride is causing quite a stir among the creationists. His review of Science & Human Origins was so devastating that they couldn't ignore it.

Jonathan McLatchie (Jonathan M) is the latest creationist to attempt a defense of the home team. He concentrates on defending the Intelligent Design Creationist position on junk DNA [A Response to Paul McBride on Junk DNA].

On this topic (junk DNA), the IDiots make a lot of errors. One of them is to deliberately conflate "junk DNA" and "noncoding DNA" so that when they come up with evidence for function in noncoding DNA they can tout this as evidence against junk DNA. This error is so pervasive in the IDiot literature that Paul McBride even predicted that Casey Luskin would make this mistake in the book.

On this Day in 1945

Today is the day that the Mars rover Curiosity landed. A remarkable American technological achievement. There have been many other technological achievements in the past century and it's wise to remember them

[reposted from August 6, 2009 (slightly modified)]

At 8:15 AM on August 6, 1945 an atomic bomb was detonated over Hiroshima, Japan. Approximately 78,000 civilians were killed on that day. Six months later the death toll had risen to about 140,000 people.

There are many arguments in favor of dropping the bomb, just as there are many arguments against it. What's clear is that in the context of 2012 we are not in a good position to judge the actions of countries that had been at war for many years.

The most important lesson of Hiroshima is that war is hell and many innocent people die. It's all very well to enter into a war with the best of intentions—as the Japanese did on December 7, 1941—but it's foolish to pretend that when you start a war there won't be any suffering. When you do that, you can really say that the victims of Hiroshima will have died in vain.

The killing and maiming of civilians is an inevitable outcome of war, no matter how hard you might try to restrict your targets to military objectives. Before going to war you need to take the consequences into account and decide whether the cost is worth it.

One of the many mistakes in Iraq was the naive assumption that it would be a clean war with few casualties and no long-term consequences for the Iraqi people. Yet today, the numbers of innocent lives lost in Iraq is comparable to the numbers lost in Hiroshima and Nagasaki. And what is the benefit for Iraq that outweighs the cost in human lives? Is it "freedom" and "democracy"?

Hiroshima was not a glorious victory. It was ugly, heartbreaking, and avoidable. War is not an end in itself, it is the failure of peace. War is not an instrument of your foreign policy—it is an admission that you don't have a foreign policy.


[The top photograph shows the mushroom cloud over Hiroshima on the morning of August 6, 1945 (Photo from Encyclopedia Britanica: Hiroshima: mushroom cloud over Hiroshima, 1945. [Photograph]. Retrieved August 7, 2007, from Encyclopædia Britannica Online.

The bottom image is taken from a Japanese postcard (Horoshima and Nagassaki 1945). It shows victims of the attack on Hiroshima.]

Sunday, August 05, 2012

Dr. Greg Wells Writes about Athletes and Telomeres

Dr. Greg Wells is a professor in the Faculty of Kinesiology and Physical Education at the University of Toronto. He's the author of Superbodies and he's one of the people commenting on biochemistry on Olympic broadcasts in Canada (see Muscles and the Lactic Acid Myth). It's somewhat unusual to promote yourself as "Dr. Wells" with a Ph.D. in physiology but that's his right.

Here's what he says on his blog,
Greg Wells, Ph.D. is a scientist and physiologist who specializes in health and performance in extreme conditions. Most recently, Dr. Wells was the host of the Gemini-Award winning “Superbodies” segments for Canada’s national Olympic broadcast and the on-camera sport science and sport medicine analyst for the CTV Broadcast Consortium, ABC News and ABC’s 20/20 during the 2010 Vancouver Olympics. Dr. Wells’ on-camera analysis will be a part of CTV’s 2012 Olympic broadcast in London.
Here's one of the "Superbodies" clips that are being shown on Canadian television. Most of them are quite interesting and informative even if Greg Wells does talk about lactic acid from time to time.

I was checking out his blog and found this interesting article: Olympic Science Blog: The science of exercise and ageing.
It is well established that training helps to improve pretty much every organ system in the body including the muscles, blood, brain, nervous system, skin, heart among others. Check out the book "Spark" to read about how exercise can help the brain! But new research shows that exercise can protect our genes as well!

In a recent study, researchers examined the DNA of young and old athletes and healthy control non-smokers for a total of four study groups. As expected, the researchers were able to demonstrate that the athletes had a slower resting heart rate, lower blood pressure and body mass index, and a more favorable cholesterol profile. But the surprising finding was that the rate of accumulated damage to the DNA was much less in the older athletes (average age: 51) than the older healthy non-athletes. In fact, the DNA of the older athletes was “younger” than the younger non-athlete participants. Researchers measured the ends of the chromosomes that contain our DNA. The ends of the chromosomes are called telomeres, and can be thought of as being similar to the caps on the end of your shoelaces (they’re called aglets in case you’re wondering) that prevent the laces from fraying. The scientists who discovered telomeres and how they work won the Nobel Prize in Physiology and Medicine in 2009. Telomeres control the number of times that a chromosome can divide when replicating itself as happens through our lifetime. Cells naturally grow, divide to replicate themselves and then die off. Gradually through this replication process, telomeres shorten and when they become “critically short” the cell dies. On the whole body level this may lead to ageing and a shortened lifespan. Scientists have shown that exercise activates an enzyme called telomerase that protects telomeres and chromosomes and that this has an anti-ageing effect, especially on the cardiovascular system.

World class athletes are training smarter, eating better, and recovering more effectively than ever before. The combination of these factors is helping athletes to have longer and more successful careers. So while you're watching our athletes compete in London and marveling at their performances, think about getting out and doing some exercise yourself! You'll be helping your body - right down to your DNA!
There's a lot wrong with this claim. First, it's not clear that there's a cause-and-effect relationship between telomore length and aging in spite of what some people claim. In fact, the correlation between age and telomere length is barely significant in most studies.

Second, it seems very unlikely that Lamarck was correct and it seems very unlikely that exercise has an effect on expression of the gene for telomerase.

Third, do you suppose it could be possible that when you get older and your health deteriorates for various reasons (disease, aging, accident) you tend not to continue to be an athlete? Thus, the only old athletes you measure are those that are still in good health?

Fourth, what's the evidence that telomere length has more of an effect on the cardiovascular system than on other parts of your body?


Casey Luskin Wants Us to Categorize Evolution Critics

Casey Luskin has posted an email message that he recently sent to someone who inquired about Intelligent Design Creationism. It describes his view of the debate between Intelligent Design Creationists and scientists [Personal Attacks Against ID Proponents Say More About the Attackers than the Abused].
With that, please let me give you a little introduction to how this debate works. Evolutionists regularly accuse their critics of being "dishonest" and "deceiving." It's a primary tactic they use to respond to criticism and intimidate critics into silence. You're not allowed to dissent from their view and be (a) informed, and (b) honest. Many of them can't fathom the possibility that a person on the other side of the debate could be both.

Here's a fact you might ponder: Virtually every single major person who has criticized the Darwinian viewpoint has faced personal attacks on his or her character. It happens to everyone, myself included. So one of two things are true: Either (1) virtually every single critic of Darwinism (of which there are many) is "dishonest" and "deceiving," or (2) evolutionists habitually respond to scientific challenges with personal attacks.
There's more than two choices here. Let's list the possibilities. Most creationist critics of evolution are ....
  1. Uninformed and honest
  2. Uniformed and dishonest
  3. Informed and honest
  4. Informed and dishonest
There are creationist critics of evolution who fit into all categories but category #3 is the least populated. I think Michael Denton and Michael Behe qualify. They seem to have a pretty good knowledge of evolutionary biology and they seem to be sincere in their criticism

Category #4 is tricky. There are some creationist critics of evolution who should be informed but they still say some very silly things. This leads me to suspect that they are being dishonest. Jonathan Wells is a good example.

Categories #1 and #2 contain the vast majority of creationist critics of evolution. They really don't know what they're talking about but it doesn't prevent them from talking. I think most of them are honest IDiots—Casey Luskin is an example and so is Phillip Johnson. Some of them are uniformed and dishonest, that's where I would place Bill Dembski and David Berlinski.

Casey Luskin is wrong when he claims that we accuse all creationist critics of evolution of being dishonest and deceitful. Mostly we just accuse them of being uninformed but acting as if they were.1 That's probably due to stupidity and not malevolence.

I've left out a huge number of creationists, including the theistic evolutionists who fall mostly into category #3: informed, honest, but wrong.

Where do the rest of them fit in?


1. Being uninformed is perfectly okay. Most of us are uniformed about a lot of things. You aren't stupid or an idiot just because you don't know something. You become an IDiot when you don't recognize how little you know about a subject but still feel qualified to tell the experts that they are wrong.

Understanding Phylogenetic Trees

A few months ago I posted an exam question from my course on evolution [Exam Question #1]. It was designed to test student's understanding of phylogenetic trees—a serious problem in evolutionary biology. That post generated quite a few comments.

Take a look at this figure from a 2008 issue of Nature. Do you see the problems?

If not, read David Morrison's guest post on Scientipoia: Ambiguity on Phylogenies. He patiently explains all the common misconceptions about phylogenetic trees and references all the important articles in the scientific and pedagogical literature. Once you read his article you will never look at trees the same way again.

You will also be astonished at how bad the scientific literature has become when it comes to explaining phylogenies based on these trees. You would think that evolutionary biologists would have long ago stopped thinking about directions in evolution but it's surprising how often the great chain of being creeps into modern scientific papers.


[Hat Tip: Mike the Mad Biologist]

Saturday, August 04, 2012

Muscles and the Lactic Acid Myth

If you've been watching the Olympics, you've heard the story many times from coaches, athletes, and even team doctors. They all tell you that the performance of endurance athletes is limited by the buildup of lactic acid in their muscles and this is what causes the pain and limits their ability to win a gold medal.

It's the acid that does it and that acid is caused by synthesis of lactic acid taking place during anaerobic exercise, or so the story goes. That happens under extreme conditions when the energy needed by working muscles exceeds the ability to produce it by normal aerobic oxidation. It all sounds so logical ... and so biochemical.

It's all a myth. Lactic acid has nothing to do with acidosis (the buildup of acid in the muscles). In fact, it's not even clear that acidosis is the problem, but let's deal with that another time.

Assuming that acid buildup in muscles is what causes the pain of the long distance runner, where does that acid comes from? In order to answer that question we need a brief lesson on acids.

Friday, August 03, 2012

The Paradox of Stasis?

The word "stasis" entered our consciousness when Gould and Eldredge promoted the concept of punctuated equilibria (see Darwin on Gradualism ). Their observations of the fossil record showed that the morphology of many species remains unchanged for millions of years. Change occurs during speciation by cladogenesis when the new daughter species fixes morphological change, thereby allowing us to recognize it as a different species.

Stasis is an important observation. Here's how Gould describes it in The Structure of Evolutionary Theory (p. 759).
Abrupt appearance may record an absence of information but stasis is data. Eldredge and I became so frustrated by the failure of may colleagues to grasp this evident point—though a quarter century of subsequent debate has finally propelled our claim to general acceptance (while much about punctuated equilibrium remains controversial)—that we ureged the incorporation of this little phrase as a mantra or motto. Say it ten times before breakfast every day for a week, and the argument will surely seep in by osmosis: "stasis is data; stasis is data ..."
Okay, we get it.

What causes stasis? There are many possible explanations. One of the most common is stabilizing selection or the idea that a species is so well-adapted to its environment that any change will be detrimental. According to this view, evolution only occurs when the environment changes.

On the Evolution of New Enzymes: Completely Different Enzymes Can Catalyze Similar Reactions

It's often quite difficult to imagine how a new enzyme activity could have evolved "from scratch." After all, aren't enzymes highly complex proteins with very specific folds? What's the probability of stringing together just the right amino acids by chance in order to get a new enzyme?

In many cases, new enzymes evolve from primitive enzymes that catalyzed similar reactions [see The Evolution of Enzymes from Promiscuous Precursors]. It's quite easy to see how this could happen by gene duplication and there are tons of examples.

But what about the first primitive enzymes themselves? Presumably, they evolved all on their own. When scientists think of this problem, they usually think in terms of evolving a specific modern enzyme. This looks like a long shot, similar to the probability that a specific person will win the lottery tomorrow. What they don't realize is that this is an unnecessarily restrictive scenario.

Advice to New Creationist Students

We're getting close to the beginning of the semester in the northern hemisphere. That means a lot of high school students will be experiencing university for the first time.

In many cases, students will have graduated from high school with only a rudimentary knowledge of some important topics. This isn't necessarily a bad thing as long as they realize that they still have lots to learn. It becomes a bad thing when they think they know the subject but what they know is wrong.

Universities are places that challenge your beliefs and force you to think. New students should embrace this challenge and look forward to giving up misconceptions and ideas that can't stand up to critical analysis. The last thing you want to do as a new student is to begin university with the idea that your high school ideas are always right.

Which brings us to creationism. A large number of students enter university with little or no knowledge of evolution but they are convinced that it's wrong. They will soon encounter teachers who try to convince them that evolution is true. How should students react to this challenge?

David Klinghoffer1 proposes one solution on the Intelligent Design Creationist blog Evolution News & Views. Here's his advice [A Piece of Unsolicited Advice to Students].
The practical question is nearly self-answering. You should be very, very circumspect about even hinting at your views to people who will end up giving you grades. But beyond that fairly obvious and uninteresting advice, I wanted to add that you should, in your own mind, strive to give respect to your Darwinist teachers no matter how firmly convinced you are that they are wrong.

If I were a professor and had a student who walked into my class intending to inform me that my fundamental views on the subject of my professional training were in error, I can well imagine thinking the kid deserved a good smack. Unfair? Yes, but true. Overturning scientific theories is not the job of an undergraduate student. A student's job is to learn what his teacher has to teach him, so that perhaps later when the student is intellectually ripened, he can lead or participate in a revolution. It's not at all that you need a PhD to hold a dissenting view, but age, thought and experience count for a lot.

At an emotional and personal level, I can sympathize with the Darwinist prof who resents his openly Darwin-doubting student. What arrogance, it must seem, to imagine that what I spent decades mastering, you a little pipsqueak think you're ready to discard half-way into the semester. Imagine yourself in your teacher's place. To him, this is about you, in your ignorance and arrogance or at best innocence, sitting in judgment of the system to which he's devoted his professional life.
In other words, hide your views because your professor might punish you. Recognize that your professor thinks he/she knows more than you do but be confident that they're wrong. Realize that when you encounter professors in class they probably don't understand their subject even though they've devoted their lives to studying it. They might be a bit angry if you exposed them so keep you mouth shut.

Above all, resist the temptation to learn and to question your beliefs. You already know the right answer. University is not the a place for learning.

Here's my advice. It you don't want to learn then don't go to university. If your belief in creationism is really strong then don't ever take a biology class—it might turn you into an atheist and your parents will be very upset. If you need the grade, then take the class, but be prepared to fail. It takes courage to openly stand up for what you believe, especially if there might be consequences. But it's the Christian thing to do.

Most professors love it when students challenge their ideas in class. We prefer those kind of students even if they are wrong. You will never fail a course because of your ideas and beliefs as long as they don't conflict directly with scientific facts. If you believe that the Earth is 6000 years old then you will not pass a geology course or a biology, unless you lie. If you dispute the existence of junk DNA then you could get an excellent grade as long as you get your facts correct.


1. I don't think Klinghoffer has ever been to university. None of the creationist websites mention any university degrees.

Wednesday, August 01, 2012

Our genome is degenerating, but wait, someone is coming to help us

According to plant geneticist, John Sanford, the human race is degenerating rapidly. It's one of the trade secrets of biology. Every population geneticists knows that it's true.

Sanford has even written a book about this trade secret: Genetic Entropy and the Mystery of the Genome

Now if humans are degenerating at the rate of 1% or so per year then this must mean that they were perfect only a short time ago—like maybe 6000 years?

Are humans doomed just as described in scripture? Yes. Is there any hope for us? Our only hope is Christ.

Interesting. Sanford doesn't exactly say exactly what Christ will do to fix all the mutations in our genome. Will He invert better DNA repair enzymes? What's taking Him so long? And why weren't we better designed to begin with?



[Hat Tip: Uncommon Descent]

Carnival of Evolution #50

This month marks the 50th edition of Carnival of Evolution. The latest version is hosted on Teaching Biology. Read it at: Carnival of Evolution 50: The Teaching Edition
Welcome to the 50th edition of the Carnival of Evolution! In keeping with the name of the blog, this edition will have an educational theme to it. The posts are categorised into modules. Each module has an introduction by me about why it’s important to learn about it, and each post has a short blurb by me on the post’s content and, if appropriate, personal comments. I include a further reading list with links to relevant books and review papers for further discussion/background information. Most of these papers are behind draconian paywalls. If you don’t have institutional access, my e-mail can be found here. Just saying.
I've got seven posts from Sandwalk on the list. That's a record for me and it means one of two things: (a) my posts are getting more interesting, or (b) they were hard up for posts this month.

The next Carnival of Evolution (August) will be hosted by The Stochastic Scientist. If you want to volunteer to host others, contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before. Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution.

Why Should an Atheist Care About the Problem of Evil?

I am an atheist. What does that mean? It means that I have never seen any evidence that supernatural beings exist. I don't think the devil exists, I don't think that Zeus exists, or Thor, or Gitche Manitou. I don't believe that the god of the Bible exists.

There are thousands of gods that I don't believe in. Some of them have imaginary reputations of cruelty, some of them are supposed to be kind, and some of them are indifferent. It doesn't matter to me because the one thing they all have in common is that they don't exist.

I'm told that some people believe in gods who are supposed to be kind. Those people have trouble understanding why the world is evil. It's a problem that has spawned an entire discipline called theodicy. Bully for them. It's their problem, not mine. I don't accept their premise.

For reasons that seem incomprehensible to me, there are some atheists who really like to talk about the problem of evil as though it were a real problem. Jason Rosenhouse is one of them. You can read his latest at: The Only Reasonable Reply to the Problem of Evil. Jerry Coyne is another. See his post from yesterday at: More Sophisticated Theology: The world’s worst theodicy.


They Like Me, They Really Like Me!

Well, maybe not all the IDiots really like me but David Klinghoffer is sure a big fan [You Go, Larry Moran!]
Just think. Imagine you're one of those undecided fence-sitters on the Darwin question that he thinks he's appealing to. Or say you're a journalist, reflexively pro-Darwin but one who's never had an occasion to follow the controversy in the past. Now something's come up in the news that touches on evolution and you figure you'll sample the arguments on both sides with a view to writing on it.

You stumble upon the blog, named in honor of Charles Darwin's famous "Sandwalk," of a University of Toronto biochemist and man of mature years who writes this way, over and over and over. He will, for example, reproduce a photo of an Internet Darwin critic with the words "I'm an IDiot" superimposed. This same biochemistry professor and Darwin advocate writes blog posts trying to defend and recommend this approach, including his favorite term "IDiot," to others. Are you impressed? That's a self-answering question.

Of course it would be different if Moran were not a guy who teaches in a relevant scientific field at a university you've heard of. If he were just another one of those pseudonyms that populate comment boxes around the Internet, and who dish out their own vicious/viscous stuff, no one would care. Much as it's distasteful to read Moran's blog (as I very rarely do), there's reason to be grateful for its existence.

Now watch, he's going to trawl the Internet for a picture of me and write "I'm an IDiot" on it and post that.

If I were purely strategic, I would say: Give us more, Larry Moran! Pour it on. Please!
Happy to oblige.

Tuesday, July 31, 2012

Carbon Dioxide Fixation in the Dark Ocean

Cells require both a source of energy and a source of building blocks for synthesis of organic (carbon-containing) molecules. Some of the most interesting species are those that only need inorganic molecules to survive. They can make all their carbon compounds from carbon dioxide (CO2) by "fixing" it into more complex molecules like sugars.

These species are called "autotrophs'" The most familiar are the plants. As most of you know, plants can grow quite successfully in a glass of water (with minerals). Animals are the most obvious example of "heterotrophs," species that need to be supplied with complex organic molecules in order to survive. We can't survive on water alone. We need to get sugars and a host of other compounds from eating other (mostly dead) species.

Oscar Miller (1925 - 2012)

Oscar Miller died last January. Steven McKnight, Ann Beyer, and Joseph Gall (2012) wrote up a nice tribute to their former mentor.
Those of us so fortunate as to have worked under his guidance learned how to think freely, yet rigorously, and how to dream big and gamble on new adventures. We learned from Oscar how to free ourselves from convention, yet abide by the principles of science as crafted by its most honorable pillars. We remember two pieces of advice given by Oscar: “Don't believe everything you read in the scientific literature” and “There are a thousand Ph.D. thesis projects in a mound of dung.” The latter brings to mind the famous phrase of Vannevar Bush that science is an “endless frontier.” Oscar Miller was comfortable on the frontier of the unknown; he taught us that it is only on the frontier that discoveries of significance can be made. Our community of science will miss Oscar, as will all his dear friends and family. A good man has passed.
Most of you have never heard of Oscar Miller but you've seen his work. He invented a technique for looking at genes in the electron microscope. The beauty of his technique, called "chromatin spreads" is that it shows genes in action. They are captured in the act of being transcribed and you can see the RNA being produced.

His photographs are in all the textbooks. The example shown here is ribosomal RNA genes being transcribed in the nucleolus. The "Christmas tree" structures are due to multiple transcription complexes transcribing the same gene. (Ribosomal RNA genes are very active.) The newly synthesized RNA is splayed out on either side of the DNA being transcribed. It would look like a cone inside the cell but it appears two dimensional here because it has been spread out on an electron microscope grid.

The initial transcripts are quite short but as the transcription complexes progress along the gene they get longer and longer giving rise to the Christmas tree structure. You can learn a lot from looking at these fantastic pictures. Notice that there are multiple ribosomal RNA genes arranged in tandom along the genome with relatively short spacers between them. These photos were taken before cloning and sequencing were invented so it was our among our first clues about gene organization in eukaryotes.

There's not much actual data from the 1960s that's still shown in modern textbooks. Remember Oscar Miller the next time you see his work.


McKnight, S., Beyer, A., and Gall, J. (2012) Retrospective. Oscar Miller (1925-2012). Science 335:1457. [DOI: 10.1126/science.1220681

Monday, July 30, 2012

Monday's Molecule #179

Last week we discovered two chemically similar reactions that were catalyzed by related enzymes of the same gene family [Monday's Molecule #178]. Today's molecule is a lot more important than any of the four molecules from last week although you won't find it in most biochemistry textbooks. (Surprise! It's in my book.)

What is this molecule (IUBMB name) and why is it important?

Post your answer as a comment. I'll hold off releasing any comments 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 with a very famous person, or me.

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 comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is 2-carboxy-3-ketoarabinitol 1,5-bisphosphate, an intermediate in the reaction catalyzed by rubisco (ribulose 1,5-bisphosphate carbozylase-oxygenase). This is the main enzyme responsible for carbon dioxide fixation in plants and one of the most enzymes on the planet.

This week's winners are Bill Chaney and Raul A. Félix de Sousa.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia
July 23: Raul A. Félix de Sousa
July 30: Bill Chaney and Raul A. Félix de Sousa