Noncoding DNA and Junk DNA

Scientific American has published another short note on junk DNA [Jumping 'Junk' DNA May Fuel Mammalian Evolution]. RPM noticed that there was no reference to the actual study being quoted in the article so it wasn't possible to verify the accuracy of the reporting [Junk DNA in Scientific American]. I couldn't find it either when I looked last week but it has now appeared on the PNAS website [Thousands of human mobile element fragments undergo strong purifying selection near developmental genes]. RPM also complained about the over-use of the term "junk DNA" in the Scientific American Article. That's what I want to discuss.

The author of the Scientific American article, JR Minkle, has responded on the Scientific American website [The DNA Formerly Known as Junk]. Minkle is a science writer who has covered a lot of stories in many different fields. As far as I know Minkle has not written very much about biology before summarizing the work in the PNAS paper. There was a time when all the science in that journal was written by scientists who were experts in the field [The Demise of Scientific American]. Anyway, that's not the main point here. JR Minkle has listened to the critics and made a decision to avoid the term "junk DNA" from now on.

That's a bad decision. RPM never asked anyone to avoid the word "junk." He merely called for appropriate use. Ryan Gregory has serious doubts about the usefulness of the term as he explains in his excellent article A word about "junk DNA".. If you want to keep up with the discussion about junk DNA you need to read that article—but you don't need to agree with everything in it. :-)

Gregory has also commented on the Scientific American article by proposing a new term, Junctional DNA, to describe DNA that probably has a function but that function isn't known. According to him, this avoids the confusion between using "junk" DNA to describe DNA that we really know to be junk (pseudogenes) and DNA for which no function has been discovered so we assume it has none.

I think we don't need to go there. It's sufficient to remind people that lots of DNA outside of genes has a function and these functions have been known for decades. Thus, it is highly inappropriate to assume that all non-genic DNA is junk and no scientist should ever do this. Note that I'm avoiding the term "noncoding" DNA here. This is because to me the term "coding DNA" only refers to the coding region of a gene that encodes a protein. Thus, in my mind, there are many genes for RNAs that are not properly called coding regions so they would fall into the noncoding DNA category. Also, introns in eukaryotic genomes would be "noncoding DNA" as far as I'm concerned. I think that Ryan Gregory and others use the term "noncoding DNA" to refer to all DNA that's not part of a gene instead of all DNA that's not part of the coding region of a protein encoding gene. I'm not certain of this.

The importance of the term "junk DNA" is to highlight the fact that it has not evolved by natural selection. This is a point I made in one of my first blog postings way back in November [Bill Dembski Needs Help, Again] and again a few days later [The IDiots Don't Understand Junk DNA] [Two Kooks in a Pod].

This isn't original. Everyone knows that junk DNA poses a major threat to both Intelligent Design Creationism and adaptationism [Junk DNA Disproves Intelligent Design Creationism] [Evolution by Accident]. Read Gregory's article for the short concise version of this dispute. What it means is that junk DNA threatens the worldviews of both Dembski and Dawkins!

Science writers often get trapped into thinking like an adaptationist when it comes to junk DNA. Remember that according to the adaptationist worldview the existence of huge amounts of truly nonfunctional DNA in a genome must be a problem. It can't be explained if natural selection is a powerful driving force behind most of evolution. You can't propose that all minor changes in behavioral genes, for example, have been selected and then turn around and admit that 95% of the human genome is junk!

Adaptationists celebrate every discovery that some little bit of DNA has found a function. That's because in their heart of hearts they think that almost all of the junk DNA will eventually be found to have a function. This is one of the reasons why papers like the PNAS paper mentioned above get so much attention.

I want to keep the term "junk DNA" to refer to all functionless DNA. That includes DNA for which we have direct and indirect evidence of no function (pseudogenes, most of intron DNA, corrupted transposons etc.) and it also includes the rest of the DNA for which no function has currently been discovered and we think it's junk because it's not conserved (among other reasons). Junk DNA is not noncoding DNA and anyone who claims otherwise just doesn't know what they're talking about.

The term "junk DNA" forces people to think about the underlying causes of evolution. It makes them stop to appreciate the fact that modern organisms could have evolved with useless DNA in their genomes and the only way this could have happened is if there's a lot more to evolution than just natural selection and adaptation. It's a good term. It's an accurate term. It's a useful term. And it makes people think.

Undergraduate Research

 
My society has a long history of sponsoring undergraduate research and inviting undergraduates to present their work in a poster session at this meeting. I look forward to seeing these posters and meeting some of the undergraduates who did the work.

This is a contest. There's a prize for the best poster, I think it's several thousand dollars. Judges interview all the students who are dutifully standing by their posters. It's a lot of fun.

I took a photo of the poster session from a small balcony overlooking the giant exhibit area. This was the only session for today—all the rest start tommorrow. The reason for having the undergraduate posters first is so the prize can be awarded at a special presentation tomorrow at noon. As you can see in the photo, the poster session was well attended. By the time I got downstairs there were two or three people in front of every poster.

This was an impressive group of students. I had serious science discussions with about a dozen presenters. I don't think I could identify the winner because some of the topics were way outside my areas of knowledge but here are two posters that I liked very much.

Amit Gautam is an undergraduate at Johns Hopkins. He works with bacterial release factors. These are proteins that terminate protein synthesis and stimulate the release of the completed polypeptide chain from the translation complex (ribocsome). His particular release factor comes in two different conformations. You can see them just over his left shoulder. The compact version is what was seen when purified protein was crystallized. The elongated form was the conformation observed when the release factor was bound to the ribosome.

The extended form is almost certainly the active form since it spans the distance between the termination codon and the site where the completed polypeptide is bound to tRNA in the P site. The protein has to do this to function, that's why the compact form was a surprise when it was first discovered.

Amit reasoned that the release factor had to shift from the compact form in solution to the extended form when it attached to ribosomes. He also reasoned that if he could block that shift the release factor would not work.

Amit introduced two cysteine residues into the release factor at positions that were in close contact in the compact form but far apart in the extended form. He predicted that a disulfide bond would form when the release factor was folded into the compact form and this covalent bond would lock it into the compact form preventing, it from adopting the extended form when it bound to ribosomes. As predicted, the modified release factor formed a disulfide bridge and was unable to catalyze release.

Under reducing conditions the disulfide bridge is disrupted and the release factor regains full activity. This is a nice example of a prediction and an experiment that tests the prediction. It's a nice piece of work.

Beccy Joscwitz used the split ubiquitin yeast two hybrid system to look for proteins that interacted with a membrane protein in yeast [see Technology reveals 'lock and key' proteins behind diseases]. She's a very impressive student and seems to be right on top of the work. She knew most of the problems and she also knew when to ask questions. I think the judges were very impressed.

Beccy, like Amit, wants to be scientist. Any graduate school would be lucky to have them.

What Do Scientists Eat?

 
There are six societies at this meeting: American Association of Anatomists; The American Physiological Society, American Society for Biochemistry and Molecular Biology,American Society for Investigative Pathology; American Society for Nutrition; and American Society fpr Pharmacology and Experimental Therapeutics. The slogan for the conference is "Today's Research: Tomorrow's Health."

So, you might be wondering what this group would eat for lunch? I was, especially since I was practically starving by the time noon hour rolled around.

There's an excellent food court in the lower level of the Washington Convention Center. I love food courts. This one had seven stations.

1. Center Plate (sandwiches,salads, yogurt)
   
2. Cluck Universal Chicken (fried chicken)
   
3. Foggy Bottom (burgers, fries, hot dogs)
   
4. Hannam's Caribbean Cuisine (spicy Caribbean dishes)
   
5. Philadelphia (cheese steaks)
   
6. Tam's Asian Cuisine (chinese food)
   
7. Wolfgang Puck (pizza, salads)
   

What would 12,000 scientists working in health-related fields choose for lunch. The winner was obvious. There were three times as many people lined up at one of the stations. The most popular food was ....

Tam's Asian cuisine. There was nobody at the Center Plate—the station with the "healthiest" choices. Everyone was buying General Tso's Chicken .... mmmmmmm, good. Lots of calories. Lots of fat.

I don't know what they'll be buying tomorrow. Stay tuned.

Experimental Biology 2007: Registration

 
The Experimental Biology meetings are huge. There are thousand of people attending and one of the major road blocks at such meetings is getting registered and collecting all the material you need. It's a good idea to arrive early to avoid the rush and that's just what I did this morning.

Here's one corner of the registration area where there's a short lineup for late registration. Fortunately, I registered online several months ago so all I had to do was stand in line to pick up my badge. There were 12 lines and none of them had more than two people. This will change as the day wares on.

The next stop was to get a loot bag. Yes, that's right, you get loot bags at these parties just like when you were ten years old and you went to Erin's birthday party. My loot bag was a shoulder bag with advertising, three heavy books, and a bundle of other (mostly useless) stuff. Here's me with my registration badge around my neck holding two kilos worth of abstracts and programs.

The program is 560 pages. I haven't read it yet. The abstract books contain short, one-paragraph, summaries of all the talks and posters. There are 1444 pages of abstracts and each one has four or five abstracts. The print is very small. I haven't read them all yet.

These days all scientific meetings have a cyber cafe with wireless internet access and that's where I am right now. Back in the olden days when these meetings used to be in Atlantic City, there were other distractions but today there are dozens of people in here tapping away on their laptops. I can't waste any more time. I've got to start reading the program to see where I'm supposed to me. It's 9AM and things are starting to happen. There are about 20 things going on at any one time. I don't know how I'm going to begin.

In fairness, this isn't as overwhelming as it seems. I'm here mostly to attend the meetings sponsored by the American Society of Biochemistry and Molecular Biology (ASBMB). I just need to concentrate on what they're doing. I can pretty much ignore the sessions run by the other societies 'cause it's very unlikely that they will have something that interests me. Whew! That's a relief. That cuts the number of abstracts down to only 2500.

The exhibits are always a big attraction. I like the publishers row. That's where you find all the latest books on biochemistry, molecular biology, and genetics. It's fun talking to the reps from the publishers. I expect that the John Wiley & Sons booth will be getting a lot of attention. I'm sure there will be lots of people at the Pearson/Prentice Hall booth lining up to buy my book!

Which Gas Is Cheaper?

 
Show your calculations.

Road Trip!!!

 
Today we're driving to Washington. I'll blog from the Experimental Biology meeting when I get there.

Should Creationist Students Be Allowed into College?

 
Read all about it in the Stanford News [Kennedy lectures on challenges facing K-12 science education].

High school students who are taught creationism instead of evolutionary theory lack the critical thinking skills that are necessary for college, according to Stanford President Emeritus Donald Kennedy.

That sounds like something sensible although I'm not sure the correlation is a cause and effect relationship. Perhaps the lack of critical thinking skills and the teaching of creationism have a deeper cause?

I don't think that a student should be banned from college just because they're a creationist but I do think they need to demonstrate that they're ready for college. The ideal situation would be to have standardized entrance exams. The SAT's don't count.

Kennedy is currently serving as an expert witness for the University of California Regents, who are being sued by a group of Christian schools, students and parents for refusing to allow high school courses taught with creationist textbooks to fulfill the laboratory science requirement for UC admission. After reading several creationist biology texts, Kennedy said he found "few instances in which students are being introduced to science as a process—that is, the way in which scientists work or carry out experiments, or the way in which they analyze and interpret the results of their investigations."

Kennedy said that the textbooks use "ridicule and inappropriately drawn metaphors" concerning evolution to discourage students from formulating independent opinions. "Even with respect to the hypothesis that dominates them—namely, that biological complexity and organic diversity are the result of special creation—critical thinking is absent," he added.

I don't see why a college or university should be obliged to accept a creationist biology course as a legitimate science course.

[HatTip: RichardDawkins.net]

Project Steve

 
Project Steve just added it's 800th person named Steve. If you don't know what Project Steve is then hop on over to the NCSE website and find out [Project Steve: n > 800].

John Wiley & Sons Apologizes to Shelley Batts

 
Read about it at Retrospectacle [VICTORY! A Happy Resolution].

Riboflavin (Vitamin B2), FMN and FAD

 
Monday's Molecule was Flavin Adenine Dinucleotide or FAD [Monday's Molecule #23]. The flavin moiety is the three ring structure at the top of the figure. It's attached to a sugar called ribitol drawn in an open chain conformation. The ribitol, in turn, is attached to a single phosphate group at the other end.

The structure shown in black is called flavin mononucleotide or FMN. The blue structure is an AMP group so the complete FAD molecule (black + blue) called a dinucleotide. FMN and FAD are important coenzymes that carry electrons from one reaction to another. We've already encountered FAD last week when we described the pyruvate dehdrogenase reaction. In that reaction the FAD molecule picked up two electrons from the lipoamide swinging arm and passed them on to NAD⁺.

FMN and FAD are required for important reactions in all species. They are made from riboflavin (right). Riboflavin can be synthesized in bacteria, protists, fungi, plants and some animals but mammals have lost the ability to make it. Instead, we have to obtain riboflavin from our food and that's why it's a vitamin in humans (vitamin B₂). (It's not a "vitamin" in other species since they can make it themselves.)

Riboflavin deficiency is quite rare because we can usually get enough from the bacteria that inhabit our intestines. The most common cases of riboflavin deficiency are seen in chronic alcoholics who often show deficiencies in many other vitamins as well.

FMN and FAD are tightly bound to the enzymes that require them as cofactors. These enzymes often have a characteristic yellow color because of the flavin. One of the most famous enzymes in biochemistry is a flavoprotein called "Old Yellow Enzyme," which turned out to be an NADPH oxidase.

FMN and FAD are cofactors that can carry one or two electrons as shown below. This makes them similar to ubiquinone. There are many reactions that exchange electrons between FMN/FAD and ubiquinone in short electron transport chains. The passage of electrons from one cofactor/coenzyme to another is governed by well-defined chemical rules developed by chemists and biochemists at the beginning of the last century.

Who Owns the Data?

 
Shelley Batts was threatened with legal action for posting a figure and a table from a scientific paper [When Fair Use Isn't Fair]. This is an important issue that's only going to get worse on science blogs. My own feeling is that it's fair use to post stuff from papers in the scientific literature as long as it is properly attributed.

One of the advantages of the online journals is that they specifically allow this. Here's the official word from the PLoS website.

Everything we publish is freely available online throughout the world, for you to read, download, copy, distribute, and use (with attribution) any way you wish. No permission required.

If large corporations like John Wiley & Sons are going to threaten to sick lawyers on bloggers like Shelley then we'll just have to ignore everything that's published in their journals. That's what I'm going to do from now on.

[Hat Tip: Gene Expression]

Tangled Bank #78

 
Tangled Bank #78 has been posted at About: Archaeology. There's a brief list of articles on the framing debate in case anyone hasn't had enough. Don't be turned off. There's lot of good stuff as well. In addition, there's a link to one of my articles but y'all have read that already.

Unintelligent Design

 
A reader send this. Thanks, Mike.


 

Regulating Pyruvate Dehydrogenase

 
There are three basic ways to regulate the activity of an enzyme. The cell can control the synthesis of the enzyme by regulating the expression of the gene; the enzyme activity can be modified by binding small effector molecules that alter the structure of the enzyme (allosteric regulation); or the activity can be changed by covalent modification.

The activity of the pyruvate dehydrogenase complex (PDC) is controlled by the most common form of covalent modification, phosphorylation. There's an enzyme called pyruvate dehydrogenase kinase (PDH kinase, PDHK) that attaches phosphate groups to the E₁ subunit of PDC. The phosphorylated form of PDC is inactive. Another enzyme called PDH phosphatase (PDP) removes the phosphate groups making the enzyme active again.

THEME:
Pyruvate
Dehydrogenase
PDH kinase binds to the E₂ subunits, specifically the lipoamide swinging arm [The Structure of the Pyruvate Dehydrogenase Complex]. There are four different PDH kinases and two different PDH phosphatases expressed in different tissues. Thus, the kinases and phosphatases are regulated, in part, at the level of gene expression. It turns out that they are also allosteric enzymes.

Knoechel et al. (2006) have looked at the structure of PHD kinase 2 (PDHK2) and located the sites of binding of several molecules that control activity of the kinase. One of the most important allosteric inhibitors is pyruvate. When pyruvate binds to PDH kinase 2 it blocks the kinase (phosphorylation) activity by changing the shape of the protein. Since phosphorylation of PDC doesn't occur, the pyruvate dehydrogenase complex remains active. Previously phosphorylated PDC becomes active because the phosphate is removed by PDH phosphatase.


The regulation makes sense. As pyruvate accumulates inside the cell you want to activate the pyruvate dehydrogenase complex in order to convert the pyruvate to acetyl CoA. As pyruvate levels fall the PDH kinase will no longer be inhibited and PDC will be inactivated by phosphorylation.

It wasn't possible to crystallize PDH kinase in the presence of pyruvate but it was possible to solve the structure of the enzyme with a similar molecule bound at the active site. The molecule is dichloroacetate (DCA) a molecule that inhibits PDH kinase by binding to the pyruvate site. Unlike pyruvate, DCA inhibition is pretty much irreversible.

Cancer cells often have inactivated pyruvate dehydrogenase complex for reasons that aren't clear (but see references in the link below). Treatment of cancer cells with DCA reactivates the pyruvate dehydrogenase complex and this leads eventually to the death of the cancer cells— at least in some cases. Unfortunately, dichloroacetate (DCA) is toxic so using it to treat cancer is a case of the cure being almost as bad as the disease.

This has not prevented growth of an underground economy in DCA by people who are desperate to cure their cancers. The situation is a mess. Read blogs by Abel Pharmboy at Terra Sigillata and Orac at Respectful Insolence for lots more information. There's a nice summary of their posts at Perversion of Good Science.

Pharmaceutical companies are very interested in finding a non-toxic inhibitor of PDH kinase 2. In fact, the paper by Knoechel et al. is mostly work done at Pfizer Ltd, in the UK. Their goal is to characterize as many inhibitors as possible.

Knoechel, T.R., Tucker, A.D., Robinson, C.M., Phillips, C., Taylor, W., Bungay, P.J., Kasten, S.A., Roche, T.E., and Brown, D.G. (2006) Regulatory roles of the N-terminal domain based on crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands. Biochemistry 45:402-15. [doi: 10.1021/bi051402s]

Sequence Similarity and Intelligent Design Creationism

 
Logan Gage posted a message on Evolution News& Views where he discusses the interpretation of sequences similarity [What Exactly Does Genetic Similarity Demonstrate?].

As Francis Collins, head of the project which mapped the human genome, has written of DNA sequence similarities, “This evidence alone does not, of course, prove a common ancestor” because an intelligent cause can reuse successful design principles. We know this because we are intelligent agents ourselves, and we do this all the time. We take instructions we have written for one thing and use them for another. The similarity is not the result of a blind mechanism but rather the result of our intelligent activity.

This is an old argument. It ignores the fact that sequence similarities match the phylogenies determined independently from comparative morphology and the fossil record. This is the "twin nested hierachies" evidence for evolution and it's powerful evidence indeed. Furthermore, it ignores the fact that the differences in sequences correspond closely to what we expect from evolution by random genetic drift.

In order to sustain the argument that an intelligent designer is responsible for this data you pretty much have to argue that the designer (whoever that might be) went out of his way to deceive us into thinking it's due to evolution. But that's not why I'm commenting on this article.

Some design proponents think the evidence for common ancestry is good (e.g., Michael Behe), while others—citing the fossil record, especially The Cambrian Explosion—do not. But neither group thinks that sequence similarity alone proves either common ancestry or the Darwinian mechanism, as so many science writers of our day seem eager to assume.

I congratulate Logan Gage for acknowledging that there are disagreements within the Intelligent Design Creationist camp. That's not something we see very often. However, I think he may be distorting Behe's position a little bit. Perhaps he means to place all the emphasis on "similarity alone" but that seems to be a quibble. Here's what Behe says in Darwin's Black Box on pages 175-177. Judge for yourself whether Behe thinks sequence analysis provides strong support for common descent.

When methods were developed in the 1950s to determine the sequences of proteins, it became possible to compare the sequence of one protein with another. A question that was immediately asked was whether analogous proteins in different species, like human hemoglobin and horse hemoglobin, had the same amino acid sequence. [The question was asked because it was a prediction of evolution-LAM]. The answer was intriguing: horse and human hemoglobins were very similar but not identical. Their amino acids were the same in 129 out of 146 positions in one of the protein chains of hemoglobin, but different in the remaining positions. When the sequences of the hemoglobins of monkey, chicken, frog, and others became available, their sequences could be compared with human hemoglobin and with each other. Monkey hemoglobin had 5 differences with that of humans; chickens had 26 differences; and frogs had 46 differences. These similarities were highly suggestive. Many researchers concluded that similar sequences strongly supported descent from a common ancestor.

For the most part it was shown that analogous proteins from species that were already thought to be closely related (like man and chimp, or duck and chicken) were pretty similar in sequence, and proteins from species thought to be distantly related (such as skunk and skunk cabbage) were not that similar. In fact, for some proteins one could correlate the amount of sequence similarity with the estimated time since various species were thought to have last shared a common ancestor and the correlation was quite good. Emile Zuckerkandl and Linus Pauling then proposed the molecular clock theory, which says that the correlation is caused by proteins accumulating mutations over time. The molecular clock has been vigorously debated since it was proposed, and many issues surrounding it are still contended. Overall, however, it remains a viable possibility....

The three general topics of papers published in JME [the Journal of Molecular Evolution]—the origin of life, mathematical models of evolution, and sequence analysis—have included many intricate, difficult, and erudite studies. Does such valuable and interesting work contradict this book's message? Not at all. To say that Darwinian evolution cannot explain everything in nature is not to say that evolution, random mutation, and natural selection do not occur, they have been observed (at least in cases of microevolution) many different times. Like the sequence analysts, I believe the evidence strongly supports common descent. But the root question remains unanswered: What has caused complex systems to form? No one has ever explained in detailed, scientific fashion how mutation and natural selection could build the complex, intricate structures discussed in this book.

The reason for bringing this up is to show that Behe accepts common descent and sequence similarity is strong evidence of common descent. It would be nice if the Intelligent Design Creationists acknowledged this and discussed the sum total of the evidence and not just the sound bite version of sequence similarity.

[I'd like to make it clear that I do not support everything Behe says. It's become clear to me recently that I need to add disclaimers such as this whenever I make a complicated point.]