Monday's Molecule #150

 

Today's molecule has a common name but this time I'll need the complete IUPAC name. There is considerable controversy over whether this molecule actually exists in most cells.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

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.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

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.

UPDATE: This one was more difficult than I expected. The molecule is oxalosuccinate or 1-oxopropane-1,2,3-tricarboxylate. I posted all the answers that used this IUPAC name or 1-oxopropane-1,2,3-tricarboxylic acid. This is clearly not the acid form of the molecule but that didn't make you ineligible to win the prize.

Oxalosuccinate is thought to be a transient intermediate in the reaction catalyzed by isocitrate dehydrogenase (citric acid cycle) but this is only a hypothesis—the intermediate has never been detected.

The molecule contains a chiral carbon atom (C3 of oxalosuccinate and C2 of oxopropane). I was expecting all answers to specifically identify the [2S] or [3S] stereoisomer, especially since we had recently discussed stereoisomers on this blog. "Cyau" was the only one to get this correct (on her second try) but she is not eligible because she didn't identify herself.

RaulFelix was the first person to name the molecule as 1-oxopropane-1,2,3-tricarboxylate and she would be the winner if I knew her real name. That means Vipulan Vigneswaran is this week's winner, beating out Joseph Somody by less that one minute.

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

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Don't Muzzle Our Doctrors

 
Last summer, the Ontario College of Physicians and Surgeons published a draft proposal on Non-Allopathic (Non-Conventional) Therapies in Medical Practice. It was horrible. As I noted at the time, "The document is flawed from the beginning because it gives credence and respectability to "alternative medicine," otherwise known as non-evidence based medicine or quackery" [Non-Allopathic (Non-Conventional) Therapies in Medical Practice].

Many groups took notice of the draft policy and criticized the Ontario College of Physicians Surgeons for their gutless response to a serious crisis in health. One of those groups was the Committee for the Advancement of Scientific Skepticism, a committee of Canada's Centre for Inquiry [Media Advisory: Ontario Doctors Given the Green Light to Promote Quackery]. The members of CASS worked hard to lobby for changes and they co-ordinated their activities with several other groups that are opposed to the weak-kneed position of the College.¹ The College conducted a survey of its members and discovered that 78% of them opposed the draft policy. About one third of the people who filled out the survey were directed to the site by CASS or its allies [Skeptical Activism Sends a Message to CPSO. Very impressive.

Those behind-the-scenes activities had an impact as more and more people voiced their criticism on the FeedBack Site.

All this lobbying convinced the Toronto Star newspaper that something serious was afoot and yesterday, Sunday Nov. 20, 2011, the newspaper published an editorial that sides with science [Don’t muzzle our doctors]. The paper deserves praise for getting it right and giving us hope that science will win in the end..

Patients walk into allergist Dr. David Fischer’s office almost every day expressing interest in trying “natural” therapies. These range from harmless diet changes to the truly bizarre, like applied kinesiology, says the Barrie physician. It’s an experience shared by other doctors. “We’re on the front line of dealing with ideas for which there is often a dearth of scientific evidence.”

Alternative medicine is booming even without much proof it works. A record 20,000 people are expected at Toronto’s Whole Life Expo at the downtown convention centre next weekend. Three-quarters of Canadians regularly use some form of natural health product, opening their wallets to spend at least $4.3 billion yearly. And the herbs and homeopathic tinctures they buy are just one facet of unconventional medicine — a thriving sector encompassing everything from acupuncture to zone therapy (supposedly stimulating the body’s organs through hand or foot massage).

Ontario’s College of Physicians and Surgeons is bending to the trend with a new policy inhibiting doctors’ criticism of unconventional therapies. In doing so it risks encouraging even broader use of dubious and potentially harmful treatments.

Make no mistake — blind trust in alternative cures can be dangerous. An unknown number of Canadians are opting out of science-based medicine to treat even deadly conditions, like cancer, with unproven “natural” approaches.

....

The field of allergy medicine, Fischer’s specialty, is especially prone to alternative approaches. Natural practitioners using applied kinesiology, for example, check for allergy by placing a food item in a patient’s mouth or in their hand. Then they pull down on the person’s free arm to assess its strength. If this “muscle testing” shows notable weakness, the patient is deemed to be allergic.

There is no good evidence that this method works, and no sound scientific reason why it should. Yet patients come in with an interest in that, says Fischer. “I’d like to be able to tell them it’s quackery.”

He may not be in a position to say so much longer under a new policy proposed by the college of physicians and surgeons. It states that doctors are obliged to give a patient their best professional opinion on an alternative treatment goal or decision, but physicians “must refrain from expressing personal, non-clinical judgments.”

....

There’s no denying alternative medicine is immensely popular. Patients are more independent than ever before, often researching their illness and trusting their own solutions. And a host of unconventional “natural” healers has risen capitalizing on that trust — offering unproven therapies with little validity and which, in some cases, are a menace.

The college shouldn’t seek to accommodate that trend or retreat to a neutral corner. Rather it should leave doctors free to punch hard against those peddling dubious cures and to challenge people’s comforting, but irrational, beliefs. Science-based medicine serves patients best. If doctors can’t vigorously defend it, who will?

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1. I'm a member of CASS but I had nothing to do with this campaign.

Blogiversary

 
I completely forgot about Sandwalk's blogiversary. It's a biggie!

My first post was on Nov. 4, 2006 [Welcome to my Sandwalk] so this makes Sandwalk five years old!

It was PZ Myers who got me started.¹ We were in England visiting Down House when he convinced me that starting a blog was better than posting messages on talk.origins. He took the picture of me on the upper-left-hand corner of this page Can you guess where we were? He also took the one in this post.

3811 posts later I'm still not sure whether to thank PZ or curse him.

On last year's blogiversary, none of the top five postings on Sandwalk were about science. This has now changed. As of today, four of the top five all-time postings are science postings.

The Genetics of Eye Color
Smart Crocodile Eaters?
Regulating Glycogen Metabolism
A Challenge to Theists and their Accommodationist Supporters
Carnival of Evolution #38

Sandwalk currently averages around 180,000 page views per month. This puts it at the low end of the middle group of science blogs. (Ranked number 36 this month.)

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1. He has a blog as well.

Medieval Teaching Methods

 
John Hawks posts a reference to an article in MacLeans magazine about undergraduate teaching. John supports a style of teaching that emphasizes "hands-on" experience over learning about theory [The Problem with Stem, A reason for practical genomic education].

Like many critics of education, John thinks that traditional lectures are old-fashioned and inefficient. I tend to agree with him on this point—we can do a much better job of education in a classroom setting. However, I part company with many critics who go overboard in rejecting traditional lecture formats as a way of communicating information. For example, I note that this style is readily accepted in many other contexts. John Hawks gave a talk last week n Madison that I would love to have attended [I would so go to this if I were in Madison]. There are all kinds of other public lectures that people pay good money to attend—we filled an auditorium when PZ Myers acme to town. Traditional lectures are very common at scientific meetings because nobody has figured out a better way to hear what an expert has to say.

The death of lectures has been greatly exaggerated.

Better Biochemistry: The Problem with Glycerol Phosphate and Citrate and What This Has to Do with Archaebacterial Membranes

Now that you've learned about Fischer Projections [Better Biochemistry: Fischer Projections] you're deady to tackle a more challenging problem. But first some background.

Glycerol phosphate is a major precursor in the synthesis of triacylglycerides and related compounds. These are the major lipid components of membranes. Here's a simplified pathway to show the importance of the glycerol backbone. ("R" stands for long-chain fatty acids.) I've deliberately avoided naming the glycerol-phosphate precursor because it requires a bit of thought.

Thinking Like a Theist

 

This figure is making the rounds with the title "When a theist starts a debate with an atheist." It's funny because it mocks the average theist who thinks that they have an overwhelming case for the existence of God. For some strange reason, theists don't think it's funny.

Brandon appears to be one of those theists. He's a Roman Catholic philosopher with a blog called Siris and he recently posted a rejoinder called When Atheists Try to Be Clever... .

Brandon noticed that the board has no kings. (Aren't those philosophers clever?) It also doesn't have any bishops but he doesn't mention that. In spite of the fact that the board is missing a few pieces, Brandon thinks that the standard rules of chess should apply ...

... it nonetheless ends up backfiring because ... it is logically and mathematically impossible, given any standard rules of chess, for either side to win this game. The rules of chess require an automatic draw if there is an impossibility of checkmate -- once it is established that no legal series of moves can reach checkmate, the game is over and both sides tie. A game with no kings has no possible checkmate, and so is an immediate draw. In trying to depict with a chessboard how much better their arguments are, a task in which they had perfect freedom to choose any possible chess set-up, they still managed to give themselves an unwinnable board. In other words, the atheist player doesn't know what he's getting into: the board is rigged so that the theist, with nothing but pawns, can guarantee a draw no matter how many queens the atheist has. Diabolically clever theist, getting atheist hopes up while making it impossible for them to win! That's on standard rules. And, of course, if the rules are supposed to be nonstandard, it is impossible to know what this board even means.

Looking at the board, you can can imagine that the contest will end when all the pawns have been wiped out and there are 15 queens left. At this point the theists will declare a draw because an imaginary, nonexistent, king has not been captured. Yep, that certainly sounds like an argument from a theist.

It also—for some strange reason— reminds me of The Black Knight. ("Right, we'll call it a draw.")

John Wilkins, who is also a philosopher, thought Brandon's "rejoinder" was clever enough to deserve a mention on his own blog [Agnostic versus atheist chess]. I guess you don't have to be a theist to believe in imaginary, nonexistent, chess pieces.

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Redundancy Explains Junk DNA, Redundancy Explains Junk DNA

 
From GilDogen, in a comment on: Jonathan Wells on Darwinism, Science, and Junk DNA.

Moran is particularly vicious concerning challenges presented by ID proponents. He’s a disturbed individual. (That’s not a personal attack, just an empirical observation, and I hope he gets over it somehow.)

Another factor in biology that should be considered is redundancy and backup systems, which are standard fare in human engineering. Redundant/backup systems ensure survival if one or more of the primary systems is disabled or compromised. In aviation, fly-by-wire systems (in which the pilot does not directly influence the aircraft’s control surfaces, but provides input to computer systems that execute the pilot’s commands) provide three or more redundant computers that process the pilot’s commands and vote about the outcome. If one computer disagrees, the majority wins.

I'll try really, really, hard not to be vicious or mocking in response to the redundancy argument. Instead, I'll just pose a few questions that occur to me.

1. Almost all IDiots intelligent design proponents accept microevolution. Why don't the unused redundant systems accumulate mutations and become junk?
2. Why would a truly intelligent, omnipotent, designer need to create redundant back-up systems?
3. When we look at genome sequences we don't see any evidence of redundant back-up systems for DNA replication, the citric acid cycle, or lipid metabolism (or anything else). Why?
4. Why are there so many genetic diseases if everything is backed-up?
5. I can see why I need two kidneys, but how come I've only got one heart?
6. Why didn't Wells mention redundancy in his book?
7. Where is the theory of redundancy published?

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When a theist starts a debate with an atheist ...

 
Also applies when a creationist starts a debate with a scientist ....

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[Photo Credit: imgur]
[Hat Tip: Friendly Atheist]

Jonathan Wells Talks About Sequence Conservation

Paul McBride (paulmc) tried to convince the readers on Uncommon Descent that there was evidence for junk DNA. One of the lines of evidence has to do with sequence conservation. If most of the genome sequences are not conserved between species this strongly suggests that they have no function, although it doesn't rule out a function that is independent of sequence.

Wells addresses this argument in: Jonathan Wells on Darwinism, Science, and Junk DNA. Before analyzing his response, it's worth reviewing what he wrote in The Myth of Junk DNA.

In chapter 5, Wells talks about sequence conservation as evidence of function—specifically the fact that the sequences of some potential pseudogenes are more conserved that would be expected if they were really pseudogenes [Junk & Jonathan: Part 8—Chapter 5]. That's an important argument and, if true, it would point to a function. The irony is that Wells doesn't believe in common descent so, from his perspective, these are not conserved sequences due to negative natural selection. Nevertheless, he is happy to use evolutionary arguments whenever it suits him.

Monday's Molecule #149

 

Today's molecule is one member of a large class. Give me the complete, unambiguous, name of this molecule to win a free lunch. Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

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.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

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!)

Name the molecule shown in the figure. Remember that your name has to be unambiguous. The best way to do this is to use the full IUPAC name but usually there are traditional names that will do. In this case there's a trivial name and that will suffice.

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

UPDATE: Several people got this one right. The molecule is prostaglandin H2. The winner is Thomas Ferraro. The undergraduate winner is "Vip" = Vipulan Vigneswaran.

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

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Better Biochemistry: Fischer Projections

Biochemistry is a three-dimensional subject but most of us aren't comfortable thinking in three dimensions. For example, we often have difficulty envisaging how a three-dimensional substrate binds to a three-dimensional enzyme.

The problem is exacerbated because we usually teach in two dimensions for simplicity—especially in textbooks.¹ There are certain rules that have to be followed when displaying a three-dimensional object on a two-dimensional page. This is especially true for metabolites where the stereochemistry is crucial. One of these rules is called the Fischer projection.²

Most students (and faculty) don't understand the relationship between a two-dimensional Fischer projection and the three-dimensional molecule it's supposed to represent. This is unfortunate because it means they don't really understand the three-dimensional conformation of metabolites.

Let's look at a simple three-carbon compound—glyceraldehyde. There are two different versions of glyceraldehyde: D-glyceraldehyde and L-glyceraldehyde. The two different molecules cannot be superimposed, that's why you know that they are different molecules. Enzymes can tell the difference; that's why D-glyceraldehyde is a common metabolite and L-glyceraldehyde is rarely found in cells.

Jonathan Wells Talks About Genetic Load

Most people don't understand the positive evidence for junk DNA—this includes most scientists. Paulmc tried to convince the readers on Uncommon Descent that they had been misinformed about junk DNA. The fact that our genome has huge amounts of junk DNA is not just an argument from ignorance—an argument that most IDiots are familiar with—because there are several good reasons for concluding that most DNA has to be junk.

Wells addressed those arguments in: Jonathan Wells on Darwinism, Science, and Junk DNA.

Jonathan Wells Sends His Regrets

Paulmc visited Uncommon Descent in order to defend junk DNA [Here’s Jonathan Wells on destroying Darwinism – and responding to attacks on his character and motives]. Now Wells has responded to several of paulmc's points [Jonathan Wells on Darwinism, Science, and Junk DNA].

We'll get to those issues in another post but right now I want to take note of something Wells said at the end of his article.

Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.

I can understand why Wells might decline to post a comment on Sandwalk. Many of us know what it's like to try and argue with the readers of the intelligent design blogs. Wells would meet the same reception here that we get over there.

But that doesn't preclude Wells from posting on Uncommon Descent or Evolution News & Views. If he really believes that my review of his book is an example of "confused thinking and malicious misrepresentations of my work"¹ then why not back up such a statement with a thoughtful response on a friendly blog? Evolution News & Views would be ideal since comments are banned.

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1. Wells has accused other scientists of misrepresentation. It's a common theme in The Myth of Junk DNA and in Icons of Evolution. I quoted this passage in Junk & Jonathan: Part 13—Chapter 10.

Coyne and Avise are professors of genetics at major universities, so they cannot claim ignorance of the genomic evidence without thereby admitting negligence or incompetence. In fact, one of Coyne's colleagues at the University of Chicago is James Shapiro, co-author of the 2005 article cited in Chapter 6 that listed over 80 known functions for non-protein-coding repetitive DNA. [The other author is Richard (von) Sternberg ... LAM] But if Coyne and Avise were not ignorant of the evidence, then they misrepresented it—and they continue to do so. Like Dawkins, Shermer and Kitcher they have forfeited any claim they might have to be speaking for science.

I can understand why Wells is reluctant to defend such statements. It's because they are indefensible.

A New View of Evolution

There have been lots of new books about evolution in the past decade or so. I tend to divide them into three categories:

1. The Standard View: These are books that basically support the Modern Synthesis with some small tweaks here and there. They do not advocate major shifts in the way we look at evolution. Books by Richard Dawkins (The Greatest Show on Earth: The Evidence for Evolution), Jerry Coyne (Why Evolution Is True), Sean B. Carroll (Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom, The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution), and Ken Miller (Only a Theory) fall into this category.
2. The New View: Some books make the case for a new way of looking at evolution. I'll call it the "New View." Many of Stephen Jay Gould's books fall into this category (The Structure of Evolutionary Theory). He refers to it as extending the modern synthesis. Most of the "extension" is based on a pluralist, rather than an adaptationist approach but other modifications are important. Two recent books by Michael Lynch (Origins of Genome Architecture) and Eugene Koonin (The Logic of Chance: The Nature and Origin of Biological Evolution) fall into this category. It's a view that I share.
3. The Radical View: Some books advocate a more-or-less complete overthrow of the Modern Synthesis, replacing it with the author's pet theory. Examples are: Marc Kirschner, and John Gerhart (The Plausibility of Life: Resolving Darwin's Dilemma), James Shapiro (Evolution: A View from the 21st Century), Lynn Margulis and Dorion Sagan (Acquiring Genomes: A Theory Of the Origin Of Species), Massimo Pigliucci and Gerd B. Müllerand (editors) (Evolution - the Extended Synthesis), many others.

The Problem with STEM

The new buzzword in science education is STEM: science, technology, engineering, and math. In America, there are dozens of studies on how to improve STEM education at all levels—including universities. Leading scientists have signed on.

Here's the problem. "Science" is NOT the same as "technology" and not the same as "engineering." There's a big difference between learning science and learning how to build things. The purpose of a degree in technology and engineering is obvious—it's job training. The purpose of a science education is quite different—it's supposed to teach you how to think critically.

But that distinction seems to have been lost on politicians, the general public, the media, and—most disappointingly—my fellow scientists. A recent article in The New York Times illustrates the extent of the problem [Why Science Majors Change Their Minds].