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].

The New Scientific Version of Intelligent Design Is Compatible with Junk DNA

 

Over on Uncommon Descent we've been discussing junk DNA [Here’s Jonathan Wells on destroying Darwinism – and responding to attacks on his character and motives]. One of the IDiots (Joseph) has proposed a modification of the existing scientific theory of intelligent design. The new version now accounts for junk DNA.

You might think this is just his personal take on intelligent design but I asked everyone else to comment if they objected to his ideas. After more than 24 hours, nobody raised any objection so I assume Joseph's ideas are acceptable to the other IDiots.

The new version goes like this .....

1. You can have junk DNA because physical constraints and design compromises prevented a perfect design.
2. Due to genetic entropy the originally designed genomes might have degenerated.
3. Junk DNA could have been put in the genome by the intelligent designer as preparation for future creations.
4. Some of the junk DNA is redundant functional DNA that's present in case a gene breaks down.

This new version of intelligent design is not in conflict with the presence of large amounts of junk in our genome.

The evolution side should know about this new development just in case we're ever accused of not keeping up with the latest advances in Intelligent Design Creationism.

UPDATE: Some readers are a little confused by this article. Of course there's no "new" version of Intelligent Design Creationism. Joseph's speculations are completely at odds with the views of the leading IDiots like Dembski, Myers, Wells, Behe etc. Most of the "leading lights" think there's a serious problem with junk DNA. According to them, ID predicts that most of our genome will be functional.

The point of my article is that the IDiots never criticize or correct their friends no matter how stupid they get. That's why you won't see any proponents of intelligent design posting comments below that question Joseph's statements.

BTW, Joseph, or Joe G, is a field service engineer. Please refrain from making unflattering comments about The Salem Conjecture. (That's my job.)

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The Wreck of the Edmund Fitgerald

 
Twenty-nine men died on November 10, 1975 when the S.S. Edmund Fitgerald sank in a storm on Lake Superior.

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Ahem!

 
David Klinghoffer is at it again: How Ignorance Insulates the New Atheists

First, that's because the key argument against belief in God lies, as it always did, in the attempted critique of the design argument. New Atheists like Richard Dawkins recognize this, and so does Coyne. Otherwise why would he name his blog, a venue overwhelmingly devoted to religion bashing, "Why Evolution Is True"? Yet the New Atheists have uniformly kept themselves just as ignorant of modern expressions of the design argument as they have of adult religious beliefs. When Dawkins goes after Darwin-doubters, he ignores -- will not debate, will not grapple with in print, probably doesn't even read -- proponents of intelligent design, a credible scientific alternative to and critique of Darwinian evolution. So too with Coyne. When Dawkins or PZ Myers or the rest does critique a Darwin doubter, it's always some hapless creationist, apprehended unarmed in the Internet wasteland and presenting a nice easy target. Like a schoolyard bully, they will pick on the little kids, but never on an opponent their own size.

Aside from David Kinghoffer, I don't usually pick on hapless creationists. I'm more than happy to pick on the very best that Intelligent Design Creationism has to offer. Problem is, they don't listen to me.

Is that because the IDiots prefer to attack the small fry rather than stand up to someone their own size (or larger)?

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Carl Sagan Day

 

Happy Carl Sagan Day.

In every such society there is a cherished world of myth and metaphor which co-exists with the workaday world. Efforts to reconcile the two are made, and any rough edges at the joints are tend to be off-limits and ignored. We compartmentalize. Some scientists do this too, effortlessly stepping between the skeptical world of science and the credulous world of belief without skipping a beat. Of course, the greater the mismatch between these two worlds, the more difficult it is to be comfortable, with untroubled conscience, with both.

In a life short and uncertain, it seems heartless to do anything that might deprive people of the consolation of faith when science cannot remedy their anguish. Those who cannot bear the burden of science are free to ignore its precepts. But we cannot have science in bits and pieces, applying it where we feel safe and ignoring it where we feel threatened—again, because we are not wise enough to do so. Except by sealing the brain off into separate compartments, how is it possible to fly in airplanes, listen to the radio or take antibiotics while holding that the Earth is around 10,000 years old or that all Sagittarians are gregarious and affable?

Carl Sagan, The Demon-Haunted World (1995) P. 297.

Visit Bad Astronomy: On the birthday of Carl Sagan to hear Carl Sagan read his famous essay "The Pale Blue Dot."

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I would so go to this if I were in Madison

 
Upcoming lecture in Madison¹

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1. Coincidentally, Ms Sandwalk and I were just talking—less than 15 minutes ago— about how long it would take to drive to Madison from Toronto. I think we could do it in 12 hours.

Haught vs Coyne: The Q&A

Here's an excellent summary of the Q&A from the debate. It's from Eric MacDonald at Choice in Dying: Q&A: Haught on God: Bitter, Impolite and Wrong.

He has a blow-by-blow account of the questions and answers following the debate but I especially like this ....

The assumption that science decided to leave out questions of god, meaning, purpose and value is a caricature of the history of science, and Haught, who claims to be making a serious attempt to show the compatibility of science and religion, must know this. If he doesn’t, and he really thinks that science made such a decision — how does “science” do this, by the way? — then his misunderstanding of the relation of science and religion is total.

When Haught turns around, then, and castigates Jerry by saying that everything that he said was a caricature, that every quotation that Jerry took from Haught’s work was taken out of context, and that instead of reading carefully and thoughtfully Jerry got his idea of god and theology from creationist websites, this was undoubtedly the most aggressive and impolite move of the whole debate. Listen to what he says:

Remember that John Haught is a Roman Catholic theologian. As far as I know he has never dissociated himself from the main teachings of the Roman Catholic Church. If he doesn't believe in any of the stuff that Jerry mentioned then isn't it up to him (Haught) to clarify what he does believe in?

Does he believe in the resurrection? Does he believe that humans have souls? Does he believe in miracles? Does he believe that God answers prayers? Does he believe the Nicene Creed? Are all these things compatible with science?

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How to Explain Creationism to People Who Don't Think Critically

 

Uncommon Descent isn't really the very best that Intelligent Design Creationism has to offer and Denyse O'Leary isn't in the same league as William Dembski and David Klinghoffer.

Nevertheless, from time to time Denyse comes up with a good example of IDiot thinking. A few days ago she asked the following question: How do you get ideas about design in nature across to people who are not learning critical thinking?.

That's easy. You write books like The Myth of Junk DNA, The Edge of Evolution, and Signature in the Cell. Non-critical-thinkers just love that sort of stuff.

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Two Kinds of Atheists

 

Let me remind you that Evolution News & Views is the Discovery Institute website. When it comes to defending Intelligent Design Creationism, this is as good as it gets.

Let me also remind you that David Klinghoffer is a Senior Fellow at the Discovery Institute. When you see an article by a Senior Fellow on the Discovery Institute website, you just know it's got to be good.

That's why I was so excited to see The Two Types of Atheists on Nov. 3, 2011.

I meant to say that broadly there are two types of people who call themselves atheists but only one really deserves the dignity of the term. The first category -- the peasant, clod, village atheist, am ha'aretz -- is the person like Jerry Coyne with a cartoon version in his head of some one religion or all religions. He rejects the cartoon, figuring that as far as faith goes in general, he's got it all figured out and it's all nonsense. This type of person typifies the New Atheist movement. He has very little of interest to say.

There's a second much rarer type, however, the person who has not only investigated at least one serious faith seriously but also experienced it, known believers, ideally was a believer himself at some adult stage of life. This person, in rejecting God, merits a real hearing.

Aren't you glad that you can get the best of the best by just reading David Klinghoffer on Evolution News & Views?

It amuses me to think of David Klinghoffer as an atheist in training.

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Professor or Hobo?

 

Can you tell the difference between a Professor and a hobo? Joseph Somody has posted a quiz. Check it out: Professor or Hobo?.

Joseph is the undergraduate winner of Monday's Molecule #147. I'll be having lunch with him on Wednesday. If you have any other pictures of professors or hobos, you could post a link in the comments and I'll be sure to pass them long. (Joseph will probably read them anyway.)

I'm thinking we could do a similar quiz for students—something along the lines of "university student or not?" There are plenty of pictures on facebook that professors could use.

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Monday's Molecule #148

 

Today, as a special treat, you get to identify three (3) different molecules. Give me the complete, unambiguous, names of these molecules 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 molecules shown in the figure. Remember that your names have 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 are trivial names for all of the molecules but make sure you have the stereochemistry correct.

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

UPDATE: Oh, oh. There's only one correct answer—congratulations Jason Oakley. I posted another answer that's almost correct (should be L-sorbose). All the rest of you need to review your understanding of Fischer projections. Here's a hint: Name This Molecule #1.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody

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