Archive for the ‘ChemBark 1.x’ Category

The 2010 Nobel Prize in Chemistry, Part I: Revisiting 2007

Sunday, August 22nd, 2010

ChemBark Medallion

In anticipation of the upcoming announcement (on October 6th) of this year’s Nobel Prize in chemistry, ChemBark oddsmakers will examine the competition in an unprecedented three-part series.  First up: a quick look back at our previous predictions.

We last posted odds for the Nobel Prize in chemistry in 2007.  At the time, our line had been extensively revised on the heels of structural biologist Roger Kornberg’s surprise win.  (Who saw that coming?  He wasn’t even a member of the ACS when he won.)

Here’s how the rundown looked back in 2007:

The Field (everything not listed below), 3-1
Molecular Studies of Gene Recognition, Ptashne, 15-1
Nuclear Hormone Signaling, Chambon/Evans/Jensen, 15-1
Fluorescent Probes/GFP, Tsien/Prasher/Shimomura, 15-1
Modern Surface Chemistry, Somorjai/Ertl/Whitesides/Nuzzo/+/–, 15-1
Transition-Metal-Catalyzed Cross-Couplings, Suzuki/Heck/Sonogashira/Tsuji/+/–, 17-1
Instrumentation/Techniques in Genomics, Venter/+, 19-1
Biological Membrane Vesicles, Rothman/Schekman/+, 19-1
Techniques in DNA Synthesis, Caruthers/Hood/+, 19-1
Molecular Structure of the Ribosome, Steitz/Moore/Yonath/+/–, 29-1
Telomeres & Telomerases, Blackburn/Greider/Szostak, 29-1
Application of Lasers to the Study of Chemical Reactions, Zare, 39-1
Bioinorganic Chemistry, Lippard/Holm/Gray/+/–, 39-1
Mechanistic Enzymology, Walsh/Knowles/Abeles, 49-1
Combinatorial Chemistry/DOS, Schreiber/+, 49-1
Pigments of Life, Battersby/+, 49-1
Global Warming, Thatcher/Gore, 99-1
Development of the Birth Control Pill, Djerassi, 99-1
Development of Chemical Biology, Schultz/Schreiber/+, 99-1
Molecular Modeling and Assorted Applications, Karplus/Houk/Schleyer/+/–, 99-1
Organic Synthesis, Evans/Danishefsky/Nicolaou/Ley/Trost/Stork/Wender/Kishi/+/–, 149-1
Fluorocarbons, Dupont/Curran/–, 199-1
Dendrimers, Frechet/Tomalia/+, 199-1
Application of NMR to Organic Chemistry, Roberts, 199-1
Understanding of Organic Stereochemistry, Mislow, 199-1
Mechanical Bonds and Applications, Sauvage/Stoddart/+, 199-1
Self-Assembly, Whitesides/Nuzzo/Stang/+/–, 199-1
Noble Gas Reactivity, Bartlett/+, 199-1
Tissue Engineering, Langer/+, 199-1
Contributions to Bioorganic Chemistry, Breslow/Eschenmoser/+, 199-1
Molecular Recognition, Dervan/+, 399-1
Development of Nanotechnology, Lieber/Whitesides/Alivisatos/Seeman/+/–, 399-1
Astrochemistry, Oka, 399-1
Zeolites, Flanigan, 399-1
Molecular Machines, Stoddart/Tour/+/–, 499-1
Studies in the Origin of Life, Miller/Orgel/+/–, 99999-1

Not too bad.  In 2007, Ertl won as a co-favorite listed at 15-1.  In 2008, the green fluorescent protein players also came in as favorites at 15-1.  The ribosome people, who were given odds of 29-1 in 2007, took home the prize last year.  Outside of chemistry, the telomerase people (listed here at 29-1 for chemistry) garnered the 2009 prize in medicine, and Gore (99-1) won the 2007 peace prize for his advocacy related to climate change.

In retrospect, we probably should have shortened the odds across the board for the favorites.  GFP and surface catalysis were obvious candidates that were sure to win, eventually; the uncertainty of just when they’d be recognized is what kept the odds long.

The list above will form the basis for our 2010 list, and oddsmakers at ChemBark’s international headquarters are already hard at work.  The field is wide open compared to past years, since a number of all-but-certain candidates have won and exited the queue.

Is this the year that the popular field of organic synthesis climbs back to Nobel glory?  Will another biologist “steal” the prize in chemistry?  What’s a materials chemist have to do to get some love?

Who knows?  Oh, right…we know, of course.  Yes.  We definitely know.  Stay tuned. 

Next post:  Part II — Criteria for Predicting Winners

The Blog is Dead; Long Live the Blog.

Friday, August 20th, 2010

I’m officially abandoning my attempts at effecting a meaningful resurrection of the data from the old blogs (both ChemBark 1.0 and my old personal blog).  The payoff is too small for the effort that seems required.  Instead, those data will have to be satisfied living within the confines of the Wayback Machine (http://www.archive.org).

I will also occasionally re-post some of the more interesting stuff from back in the day.  You’ll find these features in the category “ChemBark 1.x”.

This week’s lessons learned:

  • Don’t let stuff fester on the Internet
  • Update software regularly
  • Take blogging slightly more seriously
  • Maintain, maintain, maintain.  Backup, backup, backup.

 

The first trip into the archive appears below.

An Old Foray into the Corey Lab

Friday, August 20th, 2010

Perhaps the only legitimate traffic sent to the old blog was via the Wikipedia article for E.J. Corey.  Someone decided to link to my picture of the famous traffic light at the door to Corey’s office at Harvard.  Since this photo came down with the rest of the blog, I figured I’d get the pic back up in our first trip to the archives:

Photo of E.J. Corey's Office Door Traffic Light

That’s it, in all its glory.  When wishing to speak to Professor Corey, you would present yourself at his door and wait for a green light (i.e., enter) or red light (i.e., go away).  I’m not sure whether you knocked or pressed a button—I never mustered the pluck to talk with him.  I am told that anyone was welcome at his office and that everyone was expected to go through the same procedure.

In the comments on the original post, someone named “Pete” left this story:

With intent it was installed. Its effectiveness no doubt keeps it fucntioning although not ever seeing it “in use” during my 2+ years of observation whie taking the elevator from the 3rd floor to the basement to take an NMR. I am sure it is was it is living up to the reputation. The mildly interesting story I have on the matter is as follows.

Professor Kishi, a great scientist in his own right and a student of the great Professor Robert Woodward, wanting to chat with professor Corey pounded on the door to E.J.s in the presence of an able, albeit unsuspecting, student found himself standing in front of door with the “red light” signal. I should note that E..J.s office door, painted flat blue if I remember correctly but otherwise unremarkable, looks more like that of an entrance to a service box. The door is unusually flush with the wall with little to no threshold suggesting nothing of significance inhabits the other side, certainly not a Nobel Prize winner. Whether Kishi had specific knowledge that E.J. was in his office or whether he was interested in testing the innate behavior of a Harvard Graduate student is unknown but what followed was certainly consisent with Kishi using the situation to entertain himself. Kishi, perhaps being overly comfortable at identifying and taking advantage of opportunities to run experiments at the expense of others, went to work without hesitation. Kishi pounded on the door in the presence of the unsuspecting student. The light red light flashed. The student already feeling uncomfortable with what he had just observed responded to Kishi’s insolent question of “What is this?” with a quick retort of “That means don’t bother me know, I’m busy”. The student unable to move on at that moment was held in place by a more intense repetition of the action of Professor Kishi. The student was torn between escaping, informing Kishi of the impact of the transgression, and wanting to see what would follow. Again the red light flashed and this time with increased frequency. The student felt obligated to warned Kishi again that E.J. is busy and this means “not now”. Kishi, finding some sense of satisfation on the student’s apparent uneasiness of what had transpired in the past 20 to 30 seconds pounded even louder on the door. The student not understanding what was going on stood there frozen in fear and unable to move while Kishi stepped back against the wall and let the event he set into motion ensue. E.J., clearly upset that the red light was not sufficient in sending his caller away, opened the door ready to let someone, anyone, have it, so to speak. The student was there, feet glued to the floor, awaiting E.J.s onsluaght-a veritable deer in the head lights. Kishi, unable to contain himself began to laugh in his familiar way, wheezing while shaking his head sdie to side (think Precious the dog from Hong Kong Fouey). Immediately E.J. saw Kishi standing there, as well as the ashened faced student. Without hesitation E.J. dimissed the student and graciously invited Kishi into his office, himself realizing some gratification in that the student was shaken.

I’m a little conflicted as to what to think of the system.  On one hand, you have to admire the objectivity and fairness  of it.  Assuming Corey didn’t have a secret camera pointed at the entrance to his office, anyone could make it inside to chat with the Nobel laureate—it was just a matter of whether he was busy or not.  On the other hand, there is something degrading about having to obey a traffic signal in a hallway.  I don’t think you can make an argument that it saves any time, because Corey still has to stop whatever it is he’s doing inside to respond to the requests to enter.  (Again, I am making an assumption that he doesn’t flip a switch when he’s busy such that any requests to enter are automatically red lighted).

I prefer the system of my undergrad boss.  His office door was open 99% of the time he was inside, and if he was busy, he’d just say so and arrange to talk to you later.  Open doors provide one less psychological barrier to communication, and that’s definitely a good thing between advisors and students.

Here are some other pics taken on my jaunt through the Corey lab (way back in 2006):

Photo of E.J. Corey's Office Door and Traffic Light

E.J. Corey Lab Sign

E.J. Corey Lab Sign

E.J. Corey Lab Sign

E.J. Corey Lab Sign

E.J. Corey Lab Fridge

The Wayback Machine archive of the original post is here.

ChemBark Monthly!

Monday, November 12th, 2007

Happy Veterans’ Day, Gentlepersons.  Here are some items for your consumption:

– I recently registered for the Spring ACS National Meeting in New Orleans.  My talk will probably be the worst disaster to hit the city since…uhhh…nevermind.  In all seriousness, I look forward to the four days of wall-to-wall chemistry, since I really didn’t get the chance to consume that much in Boston.  It will also be interesting to see what’s going on with the reconstruction efforts following Katrina.  I assume that all of the debaucherous elements of the city will have been restored by April.  Is anyone else going?

–  The Crimson got to this story about a month late.  Someone’s moving to MIT…or not (?)  I really don’t get why there is any confusion here; the people being quoted are seemingly the ones who should know exactly what’s going on.

–  Later this week, Prof. Dr. E.J. Corey will sell and sign copies of his newest book in Harvard’s historic chemistry library.  I wonder if he’ll take personal requests.  “Professor Corey, could you please make this one out to ‘the greatest chemist of all time’?  Thanks.”

–  Retread has passed along the next installment of his Rip Van Winkle series, and I shall post it in short order.

Thanks for reading,
Rudy Paul

(more…)

The 2007 Nobel Prize in Chemistry, Part II

Tuesday, October 9th, 2007

Very early tomorrow morning, some lucky biologist will receive a call that he’s won the Nobel Prize in chemistry. Just kidding—it will probably be a medical doctor or a physicist.

When Roger Kornberg won the Nobel last year for transcription crystallography, a stink erupted not over whether his work was worthy of recognition, but whether it was chemistry.  But that’s old news. The big story this week is this year’s Nobel, and I know that the person who still reads this blog daily despite the fact that it’s never updated is interested in hearing revised odds for tomorrow’s winner.

I’m kind of torn about my final pick. On one hand, I’m thinking about adopting the same approach I used pre-2005 when I guessed that metathesis would win every year. My new perennial guess would be GFP/fluorescent probes, because I’m still of the opinion that these guys absolutely deserve to win it. It’s less a question of “if” and more a question of “when”—GFP and similar probes are ubiquitous in research nowadays.

On the other hand, given the stink made in the media over biology getting shoe-horned into the chemistry prize last year, I think the Swedes might feel some pressure to pick a pure chemist this year (Palladium couplings, anyone?). As Excimer points out, the stars might be aligned for the more physical achievements this time around due to the composition of the Nobel committee. That, plus the fact that the last two prizes have been organic and biological, means that this year’s prize stands a good chance of having some element of physical flavor, which GFP has none of.

So, in a nutshell, just about anyone could win the Nobel this year. My pick is GFP, but I expect to be surprised.

Now, back to the odds. I’ve revised them a little bit from earlier this year, thanks to reader input and personal changes of heart. Remember that these numbers address the question of who will win the Prize, not who should win it. As always, feel free to share your criticism in the comments. Also, my judgment is very probably impaired due to the fact that I’ve been inhaling a large quantity of thiols over the past several months.  Forgive me.

The Field
(everything not listed below), 3-1
Molecular Studies of Gene Recognition, Ptashne, 15-1
Nuclear Hormone Signaling, Chambon/Evans/Jensen, 15-1
Fluorescent Probes/GFP, Tsien/Prasher/Shimomura, 15-1
Modern Surface Chemistry, Somorjai/Ertl/Whitesides/Nuzzo/+/–, 15-1
Transition-Metal-Catalyzed Cross-Couplings, Suzuki/Heck/Sonogashira/Tsuji/+/–, 17-1
Instrumentation/Techniques in Genomics, Venter/+, 19-1
Biological Membrane Vesicles, Rothman/Schekman/+, 19-1
Techniques in DNA Synthesis, Caruthers/Hood/+, 19-1
Molecular Structure of the Ribosome, Steitz/Moore/Yonath/+/–, 29-1
Telomeres & Telomerases, Blackburn/Greider/Szostak, 29-1
Application of Lasers to the Study of Chemical Reactions, Zare, 39-1
Bioinorganic Chemistry, Lippard/Holm/Gray/+/–, 39-1
Mechanistic Enzymology, Walsh/Knowles/Abeles, 49-1
Combinatorial Chemistry/DOS, Schreiber/+, 49-1
Pigments of Life, Battersby/+, 49-1
Global Warming, Thatcher/Gore, 99-1
Development of the Birth Control Pill, Djerassi, 99-1
Development of Chemical Biology, Schultz/Schreiber/+, 99-1
Molecular Modeling and Assorted Applications, Karplus/Houk/Schleyer/+/–, 99-1
Contributions to Organic Synthesis, Evans/Danishefsky/Nicolaou/Ley/Trost/Stork/Wender/Kishi/Overman/+/–, 149-1
Fluorocarbons, Dupont/Curran/–, 199-1
Dendrimers, Frechet/Tomalia/+, 199-1
Application of NMR to Organic Chemistry, Roberts, 199-1
Understanding of Organic Stereochemistry, Mislow, 199-1
Mechanical Bonds and Applications, Sauvage/Stoddart/+, 199-1
Self-Assembly Whitesides/Nuzzo/Stang/+/–, 199-1
Nobel Gas Reactivity, Bartlett/+, 199-1
Tissue Engineering, Langer/+, 199-1
Contributions to Bioorganic Chemistry, Breslow/Eschenmoser/+, 199-1
Molecular Recognition, Dervan/+, 399-1
Development of Nanotechnology, Lieber/Whitesides/Alivisatos/Seeman/+/–, 399-1
Astrochemistry, Oka, 399-1
Zeolites, Flanigan, 399-1
Molecular Machines, Stoddart/Tour/+/–, 499-1
Studies in the Origin of Life, Miller/Orgel/+/–, 99999-1

Past Awards & the “Pre-Nobels”
Past Nobel Prizes in Chemistry
Lasker Award for Basic Research
Wolf Prize in Chemistry
Welch Award in Chemistry
Kyoto Prize
Von Hippel Award
Science Magazine’s Breakthroughs of the Year

Stories
The History of GFP
History of Pd-Catalyzed Cross-Coupling Reactions
History of Telomeres and Telomerases
A Really Biased History of the Global Warming Issue
History of Noble Gas Compounds

Buzz in the Blogosphere
ChemBark: 2007-1
Derek Lowe, In the Pipeline: 2005, 2006, 2007
Sceptical Chymist: 2006
Curious Wavefunction: 2006, 2007
Endless Frontier: 2006-1, 2006-2, 2006-3
Carbon-Based Curiosities: 2007
The Chem Blog: 2007

 

(more…)