The worst thing about Washington is ....

 
There's no Tim Horton's.

Everybody drinks Starbucks coffee. I don't like Starbucks and even if I did I have no idea how to order one. They seem to speak a different language. Whatever happened to "small," "medium,"and "large?"

Incidentally, the price of coffee is like the price of hotel rooms. It's outrageous but that doesn't seem to stop anyone from buying.

Everybody Should Have One of These

 
One of the most popular exhibits was the Leica booth. They set up a number of their most popular microscopes including the one shown in the photo. People gathered around drooling.

I wondered whether I could buy one so I asked the price, "three-fifty" was the answer. That's not bad. For only $350 dollars (US funds?) I'm thinking of getting one to put in my basement. Since I'm driving I don't have to worry about carrying it on a plane.

Herbert Tabor/Journal of Biological Chemistry Lectureship

 
One of the big events for ASBMB is the Herbert Tabor JBC lecture. It was held Saturday night in one of the large ballrooms. There were about one thousand people attending.

The first lecture was by Tony Hunter from The Salk Institute in California (USA). He spoke about mammalian kinases and phosphorylases with an emphasis on tyrosine kinases, which he discovered back in 1979. Tyrosine kinases are enzymes that attach phosphate groups to tyrosine residues in proteins. They are important because the phosphorylation and dephosphorylation of enzymes regulates their activity. Many of the genes that cause cancer (oncogenes) encode tyrosine kinases.

Hunter is trying to find out how many different proteins kinases there are in humans. The latest count suggests about 900 different enzymes. This is a remarkable number when you think about it. It means that 3-4% of all genes in our genome are kinases.

The second award winner was Tony Pawson from the Samuel Lunenfeld Research Institute and the University of Toronto (Ontario, Canada). I've heard Tony speak many times so I wasn't quite as attentive during his lecture. Tony discovered a number of proteins domains, notably the SH2 domain, that interact with tyrosine kinases and their target proteins. The work of the two Tony's is complementary and that's why they received this joint award.

UPDATE: I forgot to mention that there was a reception after the talks. Lots of delicious munchies and an open bar. I had a beer (or two). Most biochemists drink wine or fruit juice. It was not a wild bunch.

Monday's Molecule #24

 
Name this molecule. We need the exact name, preferably the correct one.

As usual, there's a connection between Monday's molecule and this Wednesday's Nobel Laureate. This one is dead easy. The prize (free lunch) goes to the person who correctly identifies both the molecule and the Nobel Laureate. (Previous free lunch winners are ineligible for one month from the time they first won.)

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Experimental Biology: Posters & Exhibits

 
Poster sessions and exhibits are a big part of any scientific meeting but at big meetings such as this one the number of posters and the number of exhibitors is so huge that they can only be accommodated in a very large convention center. The photos show the main exhibit hall in the process of being set up for posters and exhibits and what it looks like when people start viewing the posters and visiting the exhibits.

Happy Birthday Jane!

 


My daughter was born on this day in Geneva Switzerland some significant number of years ago. It was one of the best days of my life.

Happy Birthday Jane.

I think I'll Skip This One!

 
There's so much going on at the Experimental Biology meeting you just can't hope to see everything. You have to be ruthless in making decisions about what to attend and what to skip. Sometimes there are important talks going on at the same time and you just can't decide.

In addition to the formal talks there are lots of the things on the notice boards that look exciting. On the other hand, there are lots of things that don't.

Today I have to set aside time for the poster sessions because that's where I get a lot of ideas for my textbook (and for blogging). I also want to visit the displays in Publishers' Row and in the scientific equipment/supplies areas. I won't have time for church or fellowship meetings.

Washington Convention Center

 
The Washington Convention Center is a wonderful facility. It covers four city blocks in downtown Washington just north of Massachusetts Ave. between 7th and 9th. It's about a fifteen minute walk due north of the Capitol where the Congress is housed. The neighborhoods on the South, North, East, and West sides of the building are good examples of the diversity of a typical American city.

The inside of the building is huge and the facilities are as good as, or better than any I've seen in other cities.

I love Washington. Whenever I'm here I think it's the best city in the United States. If only they could fix the parking problem ....

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]