The Core Genome

Hundreds of genomes have been sequenced. It should be relatively easy to search all these genomes to identify those genes that are found in every single species. This small class of genes should represent the core genome—the genes that were probably present in the first living cell.

Turns out it's not that easy. For one thing, you have to remove parasitic bacteria from your set of genomes because these species could easily be getting by without some essential genes that are supplied by their hosts. Next you have to make sure you have a huge variety of different species that cover all possible forms of life. In practice, this means that you need about 300 different genomes, mostly bacteria.

I'm reading The Logic of Chance: The Nature and Origin of Biological Evolution, by Eugene Koonin. This is just one of many books that are critical of the most popular views of evolution. Most of these books are written by kooks or religious nutters but some of them are valid scientific critiques of modern evolutionary theory. Koonin's book is one of those and I agree with most of what he has to say. One of his topics is genome evolution.

As Koonin describes it, the first genome comparisons looked at Haemophilus influenzae and Mycoplasma genitalium, two species of bacteria that aren't distantly related. There were about 240 orthologous genes found in both species.¹ The first surprise was that this core set was missing some very important members that should have been there.

Some essential metabolic reactions must have been catalyzed by enzymes in the very first cells but the Haemophilus enzyme isn't present in Mycoplasma and vice versa. It took a bit of digging but eventually the problem was solved with the discovery of different enzymes that carried out the same reaction. The genes for these enzymes are completely unrelated.

As more and and more genomes were sequenced, the size of the core genome set shrunk until today it comprises fewer than 100 genes. Most of these genes are genes for the three ribosomal RNAs, about 30 tRNAs, and a few other essential RNA molecules. There are only about 33 protein-encoding genes in the universal core set. They include genes for the three large RNA polymerase subunits and 30 proteins required for translation (mostly ribosomal proteins).

DNA polymerase isn't in the core set because some species of bacteria have unusual DNA polymerases that replicate DNA just fine but are unrelated to the enzymes found in most cells. There are multiple, unrelated, versions of the aminoacyl tRNA synthetases—the enzyme that attaches an amino acid to its cognate tRNA. Some species have one version and other species have the second version. Some species have both. In any case, no single synthetase gene is found in every species so it's not part of the core set.

Koonin refers to this observation as non-orthologous gene displacement (NOGD). He envisages a scenario where a cell with gene X takes up a copy of a non-orthologous gene (gene Y) that catalzyes the same reaction. Over time the newly acquired gene displaces the original version. In this way a non-orthologous version (e.g. gene Y) could have arisen after the formation of the first cell and spread to a variety of different species by horizontal gene transfer. The scenario doesn't rule out the possibility that the two non-orthologous versions could have arisen independently in two separate origins of life but this seems less likely.

Let's look at a couple of examples. Biochemistry textbook writers have known for decades that there are different versions of some common metabolic genes ² The aldolase enzyme in gluconeogenesis & glucolysis is a classic. Some species have the class I enzyme/gene while others have the class II enzyme/gene. Some species have both.

This is an example of convergent evolution. The enzymes have different mechanisms and, as you can see from the figure, completely different structures. It doesn't seem to matter if a species has a class I enzyme or a class II enzyme since both enzymes are very good at catalyzing the fusion of two three-carbon molecules into a six-carbon fructose molecule or cleaving the six-carbon molecule in the reverse reaction.

The pyruvate dehydrogenase complex (PDC) is a huge enzyme that catalyzes an important metabolic reaction making acetyl-CoA—the substrate for the citric acid cycle. It seemed likely that every single species would have the genes for all of the PDC subunits but many species of bacteria were missing the entire complex. They have a different enzyme, pyruvate:ferredoxin oxidoreducatase that catalyzes a similar reaction. The enzymes have completely different mechanisms and are unrelated.

In this case, we have reason to believe that the enzyme requiring ferredoxin is more primitive and the more common pyruvate dehydrogenase complex evolved later. The PDC genes displaced the gene for pyruvate:ferredoxin oxidoreductase in many, but not all, species. That's why the genes for neither enzyme are part of the core set.

We don't know whether the existing core set of 100 genes truly represents genes that were present in the first living cell or whether they completely displaced the original versions. The fact that many of these genes are part of large operons might have made it easier for them to be transferred by horizontal gene transfer. (The selfish operon model.)

The bottom line is that attempts to reconstruct the genome of the first cell have failed because of NOGD and we now have to incorporate that concept into our way of thinking about early evolution. The good news is that the evolution of completely new genes seems to be much easier than we first imagined. We even have examples of three or four completely different enzymes carrying out the same reaction.³

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1. Koonin refers to conserved genes as Clusters of Orthologous Genes or COGs. It actually counts conserved domains rather than entire genes but the differences aren't great so I'll just refer to them as genes.

2. That is, those textbook writers that emphasize comparative biochemistry or an evolutionary approach to biochemistry. Some textbooks just cover human (mammalian) biochemistry so they won't even mention whether bacteria do biochemistry.

3. I'm not sure how the Intelligent Design Creationists explain these observations. Maybe there were several different designers who each came up with their ideal solution to the problem? Maybe there was only one designer who just got a kick out of making different versions of the same enzyme activity but got bored at only two or three?

Atheist Calls Religious People 'Idiots' On British Debate Show

 
Good for her. Kate Smurthwaite tells it like it is! It's fun to watch the theists try to defend themselves. Note that none of them tries to offer a rational explanation for their belief in heaven.

Kate's statement is undoubtedly something that the accommodationists would complain about. They probably thing it's counter-productive to point out that believing in heaven makes about as much sense as believing in the tooth fairy.

They probably think it's perfectly respectable to say that all aborted babies are in heaven. In most other contexts, people making statements like that would be candidates for the loony bin and nobody would be criticized for saying so. But if you say stupid things in the name of religion you need to be protected from criticism. According to theists, it has to be "rude" to criticize faith because otherwise it might be subjected to the same scrutiny that we reserve for belief in homeopathy, UFO abductions, and 9/11 conspiracy theories.

Society will undoubtedly fall apart if we criticize religious faith, right? I think we're about to find out.

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[Hat Tip: Friendly Atheist]

Read Kate Smurthwaite's blog: CRUELLA_BLOG

The "Intelligent Design" Version of Creationism

The IDiots are at it again. Over the past few months there's been an noticeable increase in the number of whining complaints about the way Intelligent Design Creationism is being treated in the popular press and on science blogs.

Here's the latest from David Klinghoffer on the Discovery Institute website: Here There Be Dragons: The Journalists' War on Science. Kinghoffer thinks that his movement is being treated unfairly by journalists. Let's see why.

If there's one thing we've learned from repeated uniform experience it is that on one scientific issue, the most contentious there is -- evolution -- it's treated as taboo for writers to inform themselves properly, to know the facts and evidence behind the scientific challenge to Darwinian theory.

Hmmm ... here's an Intelligent Design Creationist complaining that his critics haven't taken the time to "inform themselves properly" about a 100-year old version of evolutionary theory that's been modified and extended so that modern evolutionary theory no longer qualifies as "Darwinian theory." I don't know a single IDiot who has the gumption to refer to modern evolutionary theory by its proper description. I'm not even sure there's a single IDiot who understands modern evolutionary theory. That includes David Klinghoffer [see, The IDiots Respond].

Can you say "hypocrisy"?

Detecting God's Signature

Stephen Meyer has two main objectives. He wants to prove that Intelligent Design Creationism is the best explanation for the origin of information in the cell and he wants to prove that Intelligent Design Creationism is genuine science.

Let's look at the form of argument he uses in Signature in the Cell: DNA and the Evidence for Intelligent Design. This is from Chapter 17 where he's trying to refute the accusation that Intelligent Design Creationism is nothing more than an argument from ignorance.

... the argument made in this book ... takes the following form:

Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.
Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information.
Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for information in the cell.

Or, to put it more formally, the case for intelligent design made here has the form:

Premise One: Causes A through X do not produce evidence E.
Premise Two: Cause Y can produce E.
Conclusion: Y explains E better that A through X.

In addition to a premise about how material causes lack demonstrated causal adequacy, the argument for intelligent design as the best explanation also affirms the demonstrated causal adequacy of an alternative cause, namely, intelligence. This argument does not omit a premise providing positive evidence or reasons for preferring an alternative cause or proposition. Instead, it specifically includes such a premise. Therefore, it does not commit the informal fallacy or arguing from ignorance. It's really as simple as that.

Scientist are often accused of picking on the most idiotic of the IDiots and avoiding the really big guns who have all the best arguments for Intelligent Design Creationism.¹ See A Reason to Doubt the Real, Rather than Pretended, Confidence of Darwin Advocates, where David Klinghoffer asks,

How about answering the arguments of a real scientist who advocates intelligent design on scientific rather than Bible-thumping grounds -- a Douglas Axe or Ann Gauger, for example? How about a thoughtful critique of The Myth of Junk DNA or Signature in the Cell? A response to serious science bloggers like ENV's Casey Luskin or Jonathan M.?

So, here's my response to the very best that the IDiots can offer.

Premise One

Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.

On the surface this looks like a purely scientific statement. I'm sure that most creationists accept it at face value since the leaders of the movement have been saying for years that evolution can't account for specified complexity or irreducible complexity.

Stephen Meyer is a philosopher but he's confident that his knowledge of biology is sufficient to establish the truth of this claim. He says on page 341 ...

Undirected materialistic causes have not demonstrated the capacity to generate significant amounts of specified information.

This is an important point since the logic of his argument depends on establishing that specified complexity can never arise from natural (materialistic) causes. You might think that a large part of this book would be devoted to backing up his premise. You would be wrong. Turns out, the real premise isn't exactly how it appears above.

Dennis Venema has written a critical review of Signature in the Cell and one of his criticisms is that there are many excellent examples of new information evolving by entirely materialistic mechansims that not violate the laws of physics and chemistry [Seeking a Signature]. We're all familiar with the examples of gene duplication and divergence but he might just as well have used dozens of other examples where specified complexity evolved. The wings of birds are for flying but they evolved from legs and fins. The irreducibly complex citric acid cycle evolved from simpler pathways.

These examples establish beyond a shadow of a doubt that there are perfectly reasonable, materialistic explanations for the evolution of specified complexity. That seems to negate Premise One.

Hang on. Meyer responds to the Venema criticism by pointing out that he was not referring to the origin just any specified information. He was only referring to the kind of specified information that appeared when life first formed. It's an origin of life problem.

The balance of [Venema's] review is spent refuting an argument that Signature in the Cell does not make and, thus, the evidence he cites is irrelevant to the main argument of the book; in short, Venema "refutes" a straw man. ... I happen to think -- but do not argue in Signature in the Cell -- that there are significant grounds for doubting that mutation and selection can add enough new information to account for various macroevolutionary innovations. Nevertheless, the book that Venema was reviewing, Signature in the Cell, does not address the issue of biological evolution, nor does it challenge whether mutation and selection can add new information to DNA. That is simply not what the book is about. Instead, it argues that no undirected chemical process has demonstrated the capacity to produce the information necessary to generate life in the first place. The book addresses the subject of chemical evolution and the origin of life, not biological evolution and its subsequent diversification. To imply otherwise, as Venema does, is simply to critique a straw man. [Stephen Meyer Resonds]

Meyer is correct. The book is about the origin of life and the problem of getting information into DNA 3.5 billion years ago, before there were cells, and before evolution. Meyer isn't always clear about this distinction but the argument that he frames above is about the origin of life.

Here's how he should have expressed Premise One ...

After decades of research, biologists have good explanations of how specified information can arise by evolution but they do not have a good explanation of how life began 3.5 billion years ago.

Premise Two

Intelligent causes have demonstrated the power to produce large amounts of specified information.

He's referring, of course, to the fact that bees make beehives and beavers make dams. There are hundreds of examples where animals produce complex structures full of specified information. That's what he means by "intelligent causes." All of this creation obeys the laws of physics and chemistry, therefore the explanation is entirely materialistic.

Don't forget that the argument is not about the creation of specified information throughout the history of life. It's about the ultimate origin of the information. Animals can create complex structures just as living cells can create new genes. What Meyer really wants to know is where do animals get this ability? Where did the information to create more information come from?

Animals evolved from more primitive ancestors. It's quite reasonable to postulate that all animals evolved from a common ancestor that had very rudimentary intelligence and that intelligence evolved from primitive neurons. Thus, the ability of intelligent animals to create complex structures—like pocket watches—ultimately traces back to the origin of life.

We can re-word Premise Two ...

Intelligent animals can produce large amounts of specified information by purely materialistic means. The ability to do this depends on the evolution of animals from the first living cells that arose 3.5 billion years ago.

Conclusion

Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.

This conclusion does not follow from either of the corrected premises.

Here's a better conclusion.

All of the information we see in biology, including the ability of beavers to make dams, can be traced back to the information present in the first cells. We don't currently have a good explanation for how DNA and cells arose.

It's difficult to see how you can squeeze a supernatural intelligent designer into this conclusion. Whenever we have good explanations for the origin of specified complexity, those explanations involve materialistic actions and not actions that require violation of the known laws of physics and chemistry. Beavers do not wave a wand to poof their dams into existance and bees don't get their beehives by praying for them

Therefore, it seems quite reasonable to assume that all examples of biological information arise by natural means, including the very earliest examples of DNA in the first cell.

(I don't address information theory, which takes up a significant part of the book for some unknown reason. See Jeffrey Shallit's take-down on Stephen Meyer in: More on Signature in the Cell.)

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1. Atheists have the same problem. We're always going after the most stupid theists and avoiding the really sophisticated arguments for the existence of God. You'll find a list of those arguments at: A Challenge to Theists and their Accommodationist Supporters.

Is Creationism Anti-Science?

 

It's very hard to define science—it's the demarcation problem and, in spite of what you've been told, philosophers don't agree on how to define science.

A lot of the activities of Intelligent Design Creationists qualify as science, as far as I'm concerned. That's why I spend so much time arguing against their attacks on evolution. Many of the IDiots accept common descent. Their attacks on other aspects of evolution aren't much different than similar attacks from legitimate, non-theistic scientists (e.g. objecting to junk DNA, questioning the Cambrian explosion, challenging strict Darwinism). It counts as "science" but it's very bad science and it's wrong.

All IDiots are anti-evolution but some go farther than others. If you are a Young Earth Creationist who believes that the universe was created less than 10,000 years ago, then you are not just anti-evolution, you are anti-physics, anti-chemistry, anti-geology, anti-astronomy, and anti-biology. I think it's fair to say that Young Earth Creationists are anti-science. This includes most (all?) of the Republican Presidential candidates in the United States and more than half the citizens of that country.

The only way YECs can possibly justify their strange beliefs is to assume that all the experts in all those fields are completely wrong about the fundamental concepts in their discipline. How could they possibly trust anything else those scientists have to say about their areas of expertise?

Let me introduce you to a "new voice" in the Intelligent Design Creationist world. Here's what Evolution News & Views says about him [A New Voice in the Debate Over Evolution and Intelligent Design].

There is literally a new voice in the debate over evolution and intelligent design. If you're a regular listener to the Center for Science & Culture's very popular and thrice weekly podcast, ID The Future, you have probably come to recognize familiar personalities, like ENV's Casey Luskin. (If you're not yet a listener, then you should be.) Now you will be hearing more often from radio broadcaster David Boze of Seattle's KTTH.

I assume David Boze is a heavy-weight and it's okay to criticize him.

Listen to the Discovery Institute podcast where Boze defends Young Earth Creationism against the charge that it's anti-science ["Anti-Science": Unpacking a Vague & Distorted Label]. (You can click on the embedded copy below.) Note the sleight of hand where he lumps together the Young Earth Creationists with all other IDiots. His point is that just because you're opposed to "atheistic Darwinian evolution" does not mean you're anti-science.

Perhaps not. But if you believe in the literal truth of the Bible then you are definitely anti-science. You are a genuine idiot. Does David Boze do a good job of defending Republican Presidential candidates against the charge of being anti-science? Will a YEC President harm the reputation of the United States? You be the judge.

Personally, I don't think the new kid on the block is much of a threat. Is this the best they can do?

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Ravel's Bolero at the Copenhagen Central Train Station

 
I love these things!

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An Interview with Maarten Boudry

 

As most of you know already, I've been a big fan of Maarten Boudry ever since I first met him in Toronto a few years ago. Last year I visited him in Gent and he bought me a beer (or three). Maarten's thesis (Here be dragons) has been published on the internet. If you haven't read it by now, you're in for a treat.

Now you can hear him in person in an interview on Think Atheist: Episode 31 Dr. Maarten Boudry OCT 23, 2011.

It almost makes you want to be a philosopher.

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Stephen Meyer Talks About Junk DNA

Stephen C. Meyer has a Ph.D. degree (1991) in the History and Philosophy of Science from Cambridge University in the UK. He is currently Program Director of the Center for Science and Culture at the Discovery Institute in Seattle, Washington, USA.

Meyer's book, Signature in the Cell: DNA and the Evidence for Intelligent Design, is an attempt to present Intelligent Design Creationism as genuine science. I'll have more to say about this later but for now I want to concentrate on one particular aspect of his case.

Mayer claims that one requirement of a genuine scientific theory is the ability to make falsifiable predictions. Does Intelligent Design Creationism make such predictions? Yes, one of the predictions is that genomes will not contain very much junk DNA. It will be instructive to see how Intelligent Design Creationists handle this issue, especialy since I've just finished a thorough review of The Myth of Junk DNA by Jonathan Wells.

Here's what Meyer says about junk DNA.

The Myth of Junk DNA by Jonathan Wells

This is the final installment of my review of The Myth of Junk DNA by Jonathan Wells (Discovery Institute Press, 2011). The other posts are listed at the bottom of this summary and in the theme posting "Genomes & Junk DNA."

Most of the IDiots at the Discovery Institute feel threatened by the existence of large amounts of junk DNA in some eukaryotic genomes, including our own. That's why they are determined to refute this idea by showing that most putative junk DNA actually has a function. Jonathan Wells feels confident enough about his reading of the scientific literature to announce that junk DNA is a "myth" and he's written a book to promote this idea.

Wells never defines "junk DNA" correctly. The correct definition of "junk" is DNA that has no known function. Wells pretends that the original definition of junk DNA was "noncoding" DNA. Thus, all those bits of noncoding DNA that have a function are evidence that refutes the notion of junk DNA.

The truth is that no knowledgeable scientist ever suggested that regulatory regions, origins of replication, centromeres, telomeres, genes that produce functional RNA molecules, and chromatin organizing regions were ever classified as junk DNA. They all knew that there was lots of noncoding DNA that had a well-defined function. Right from the beginning of his book, Wells is attacking a strawman and misleading his readers.

Monday's Molecule #146

 

Give me the complete, unambiguous, name of the molecule to win a free lunch with me.¹ Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins.

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.

UPDAYE: The winner is DK.

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1. Or with Johnny Depp or Angelina Jolie, depending on who's available on a given day.

Pray for Peterborough

 
Tomorrow the city council of Peterborough, Ontario will open their meeting with The Lord's Prayer [Agenda].

Saying Christian prayers at public meetings was declared illegal following an Ontario Court of Appeals ruling in 1999. The city council of Peterborough is announcing in advance that it will be performing an illegal act tomorrow at 6:30 PM. I assume the police will be there to arrest the mayor and council members (not).

Veronica will be there.

What's the point of having council members recite a Christian prayer before their meeting? Probably half the council members are not practicing Christians. What's the point of making the audience sit through the Lord's prayer? Many of them are at the meeting to make a presentation. What message does it send if they are not Christian?

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[Photo Credit: Saying prayers at a Durham council meeting [Praying before City Council Meetings]]

Daniel Belden and the Deerfield Massacre

William Beldon (1609-1655) was born in Heptonstall Parish, Yorkshire, England. He settled in Wethersfield in the Colony of Connecticut in 1641. (Wethersfield is just south of Hartford.)

William Beldon married Thomasine Sherwood (1615-1655) and they had the following children.

1. Samuel Beldon (1647-1737)
2. Daniel Belden (Belding) (1648-1732)
3. John Belden (1650-1713)
4. Susannah Beldon (1651-1706)
5. Mary Beldon (1653-1724)
6. Nathaniel Beldon (1654- )

I descend from John Belden (1650-1713) and his wife Ruth (Hale) Hayes (1646-1700). But this is a story about his brother, Daniel Beldon (sometimes known as Daniel Belding).

More than a Blog?

Mainstream scientists and mainstream journals are still trying to figure out what blogging is all about. They aren't alone. Science journalists are also puzzled. Even the bloggers are confused.

The latest contribution from the mainstream has just been published in the journal EMBO Reports: More than a blog. It discusses, among other things, the effect blogging had on the Wolfe-Simon et al. (2010) paper claiming that a strain of bacteria could incorporate arsenic into its DNA in place of phosphorus.

The author of the EMBO Reports article is Howard Wolinsky, an American journalist. I want to address one part of his article. Wolinsky writes,

This incident, like a handful before it and probably more to come, has raised the profile of science blogging and the freedom that the Internet offers to express an opinion and reach a broad audience. Yet it also raises questions about the validity of unfettered opinion and personal bias, and the ability to publish online with little editorial oversight and few checks and balances.

It's true that there's no editorial oversight on science blogs. It's not quite true that there are no checks and balances since most science bloggers read and comment on each other's posts and bad science bloggers are easily exposed (e.g. creationist sites).

But that's not what I want to comment about. Wolinsky's implies that the world of traditional science communication is free of personal bias and regulated by checks and balances. That's not true. The incident he's referring to is the "arsenic affair" and it a good idea to keep in mind what happened last December.

First, most of the fuss arose over the press release where the lead author made claims that were not in the Science paper and were not supported by evidence. Up until the advent of science blogging there were no serious checks and balances on press releases save for the occasional journalist who sometimes expressed a bit of skepticism. Science blogs are actually serving as checks and balances on press releases and irresponsible science journalism. That needs to be stated more often.

Second, it's simply not true that papers published in the scientific literature undergo rigorous editorial/peer review that is subject to checks and balances. It's simply not true that papers in the scientific literature are free of "unfettered opinion and personal bias." We've all known about this for decades. Science bloggers are now bringing that knowledge to the general public and (among other things) exposing bad papers to the critical analysis they should have received before being accepted for publication. There's general agreement that the Wolfe-Simon et al. (2010) paper was not subjected to rigorous peer review before it was published online. Thanks to the bloggers, publication of the print version of the paper was delayed for months and when it appeared it was accompanied by several letters of criticism. That never would have happened without science bloggers.

Science bloggers are providing the checks and balances that have gone missing in the so-called "peer-reviewed" scientific literature. The bloggers are becoming the "peers" that review the papers when the system breaks down.

While it is true that science bloggers may have an agenda and aren't subjected to rigorous peer review before publication, this should not be treated as a new phenomenon that's peculiar to blogs. If you're going to raise these issues in an article about blogging then you should also raise them with respect to the traditional scientific literature.

Third, science journalists are partly responsible for the increased role that science bloggers are playing in exposing bad science. Traditionally it was supposed to be science journalists who acted as a check on bad science and bad press releases. Recent incidents have shown us that we can no longer count on science journalists to act as skeptical reviewers. The "arsenic affair" is a good example (Carl Zimmer is a notable exception).

Today it's more likely that science journalists will follow the lead of science bloggers rather than do the required homework on their own. Many science journalists just publish paraphrased versions of press releases leaving it up to the science bloggers to expose the flaws in the press releases, and in the published paper.

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[HatTip: Jarry Coyne: An EMBO report on science blogging]

Junk & Jonathan: Part 13—Chapter 10

This is part 13 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the links in Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

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The title of Chapter 10 is "From Junk DNA to a New Understanding of the Genome." It's a very misleading title since the bulk of the chapter is an attempt to refute the arguments of various evolutionary biologists.

In this chapter, we return to the arguments based on junk DNA that we encountered in Chapter 2. Richard Dawkins, Kenneth Miller, Michael Shermer, Francis Collins, Philip Kitcher, Jerry Coyne and John Avise all claimed that most of our DNA is nonfunctional junk, and that this provides evidence for Darwinian evolution and against intelligent design (ID).

Wells' statement is very misleading. He's confusing the argument about conserved pseudogenes with a claim that most of our genome is junk. Several of these authors have pointed out that the presence of similar pseudogenes at the same location in the genomes of different species (e.g. humans and chimps) is powerful evidence of descent from a common ancestor. They also point out that the IDiots have a hard time explaining such observations [Creationist Logic]. (In fact, no IDiot has ever offered a satisfactory explanation.)

Better Biochemistry: Near-Equilibrium Reactions

This is part of a series on important concepts in biochemistry. I'm concentrating on those concepts that may be widely understood and/or not well described in most textbooks. Naturally, I think we do a pretty good job in our book!

Biochemical reactions are characterized by a Gibbs free energy change that describes the amount of energy produced or consumed in the reaction. In order to compare different reactions, chemists have developed a standard Gibbs free energy change that can be used to describe all reactions. The standard Gibbs free energy change in biochemical reactions is the energy produced or consumed when all the reactions and products are at a concentration of 1M, the temperature is 25°C (298 K), the pressure is 1 atm, the pH is 7.0, and the concentration of water is 55M.

Here's an example from the gluconeogenesis/glycolysis pathway (see below). It's the reaction catalyzed by aldolase where a six-carbon molecule (fructose) is cleaved to produce two three-carbon molecules. The reaction shown here is the one in the glycolysis pathway that breaks down glucose.

The standard Gibbs free energy change for this reaction is ...

ΔG'°_reaction = +28 kJ mol^-1
In a chemistry course you might learn that this reaction is NOT spontaneous because the standard Gibbs free energy change is positive. In other words, you need to supply energy—as indicated by the plus sign in the standard Gibbs free energy change—in order to make the reaction go from left to right. The reaction will be "spontaneous" in the opposite direction where ΔG'°_reaction = -28 kJ mol^-1.

The concept of "spontaneous" and "not spontaneous" based on the standard Gibbs free energy change makes no sense in a biochemical context. The aldolase reaction, for example is part of the gluconeogenesis pathway where the two three-carbon molecles are joined to produce fructose-1,6-bisphosphate. This eventually leads to the production of glucose.

The adolase reaction is also part of the glycolysis pathway that runs in the opposite direction (as shown above). Cells can easily switch from making glucose to degrading it. How can this happen if the free energy change is +28 kJ mol^-1.¹

It isn't. The actual Gibbs free energy change inside the cell is very different than the standard Gibbs free energy change. This reaction rapidly reaches equilibrium inside the cell. Under those conditions the rates of the forward and reverse reactions are equal and ΔG = 0.

In the case of the aldolase reaction, the concentrations of the reactants and products at equilibrium will not be equal as the standard Gibbs free energy change requires. Instead, the concentration of fructose-1,6-bisphosphate will be much higher than the concentrations of glyceraldehyde-3-phosphate and dihydroxyacetone phosphate.

In biochemical terms we say that this is a "near-equilibrium" reaction. Most metabolic reactions are near-equilibrium reaction with ΔG = 0 (or close to it).

This is an important concept in biochemistry. You can't understand pathways and flux if you don't know that most of the reactions are near-equilibrium reactions where ΔG = 0.Sup>1 You also can't understand regulated reactions, where ΔG is not zero, unless you've grasped the fundamentals. (Regulated reactions are called "metabolically irreversible reactions.")

Many textbooks do a poor job of explaining near-equilibrium reactions and their importance in metabolic pathways. Some still use standard Gibbs free energy changes as a measure of direction. Fortunately, the teaching of this concept has improved enormously over the past 15 years.³ The bad news is that if you took your last biochemistry course before 1995 you may be hopelessly out-of-date!

Here's an example of bad teaching from a 2003 textbook!

Although the cleavage of fructose-1,6-bisphosphate is frequently unfavorable (ΔG'° = +23.8 kJ/mol), the reaction proceeds because the products are rapidly removed.

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1. You also have to understand the concept of steady-state—the concentrations of intermediates in a pathway don't change very much.
2. Some textbooks use +24 kJ mol^-1.
3. The best textbooks had it right long before that.