Archive for the ‘Web Resources’ Category

Odd Web Material

Tuesday, May 21st, 2013

Thursday’s post on lab manuals brought my attention to this nice cheat sheet from the Zakarian Group at UCSB on how to collect an NMR spectrum. I am a big fan of cheat sheets—they let you focus on the big picture when you’re getting trained on an instrument instead of focusing on recording every simple command. That said, the Zakarian NMR guide is weird. It inexplicably ends with the statement:


I guess the line is some sort of inside joke in the lab, but why on Earth would you post it to a professional Web site? It reminded a labmate of the incident where racially insensitive material was posted on Clifford Kubiak’s site, for which he later issued a public apology.

If you enjoy these sorts of jokes, keep your boss out of trouble by not posting them to your lab’s Web site.

UPDATE (5/21, 5 pm): The line quoted above has been removed from the NMR guide. More info in the comments…

Lab Manuals

Thursday, May 16th, 2013

ChemBark's Orby the InsectI’m always interested to come across instructional documents on chemistry professors’ Web sites. These documents can be great resources, because they often contain very practical advice about safety, direction on how to maintain instruments, and guidance on experimental technique from experts in the field. Taking the time to commit this information to writing also helps prevent “institutional” loss of memory when senior members of the lab graduate without having properly trained the next generation of students.

Unfortunately, you don’t come across that many lab manuals online. Perhaps this is because some of them are distributed in hard copy only. Perhaps, some professors don’t want to explicitly write procedures and safety guidelines in fear they might be used against them in court. My guess, however, is that most people can’t find the time to sit down and write out this information—or they don’t see the value in doing so.

Jim Tour’s “Guidelines for Research” is among my favorite documents. He gets very specific about some of the advice he doles out. For instance, all nitrogen bubblers left on overnight should have a flow rate of one bubble per second or less. Tour provides guidance on how he likes notebooks to be kept, and he also provides expectations about work ethic and vacations. Finally, there is the passage on personal hygiene:

Personal Hygiene: Although not customary in all countries, Americans generally bathe at least several times per week. As a result, many Americans are offended by the infrequent bathing habits of others (whether Americans or internationals). Thus, you may be leaving a negative impression of yourself without ever knowing it. Unfortunately, bad impressions are often difficult to overcome. Likewise, be sure to use an underarm deodorant since most Americans find body odor to be most offensive. I have seen people causing themselves to be ostracized by others simply because of poor personal hygiene habits.

It might seem trifling or overbearing to provide advice on this level, but the info is correct and I wish more people heeded Tour’s advice.

While the idea of writing a manual all at once seems daunting, I think that doing it in pieces seems quite reasonable. In fact, I think you can assemble some really good tidbits of advice from material that is already posted online. These documents are almost like official memoranda to members of professors’ labs. For instance:

The famous “How to Write a Scientific Paper” article in Advanced Materials had its beginnings as a type-written memo from George Whitesides to his lab.

There’s also Ken Suslick’s cool presentation on how to give a talk.

And I like how some professors provide specific instructions on how to ask them for letters of recommendation.

Anyway, before I go writing similar stuff in the future, I wanted to know if you all had come across any great lab manuals or memos. Leave them in the comments, and I’ll compile a list below.

Lab Manuals

Jim Tour’s “Guidelines for Research
Melanie Sanford’s “Group Welcome Kit
Dave Collum’s site
Bart Bartlett’s “Standard Operating Procedures
Turro Group’s site
Watson Group Manual
Tolman Lab’s “Standard Operating Procedures
Armen Zakarian’s site


Professor Baran Enters the Blogosphere

Tuesday, March 5th, 2013

First they ignore you,
then they laugh at you,
then they fight you,
then they join you,
then everybody wins.

Mahatma Gandhi posted that piece of advice on his blog shortly before his death in 1948, and it still holds true today.

After admitting that chemistry faculty typically roll their eyes at blogs and that he personally doesn’t have time for them, Phil Baran—or, more precisely, the Baran Lab at Scripps—has established the newest chemistry blog on the Internet. Baran and his lab are at the top of the game of organic synthesis, so this is a major development for academic chemistry. Their participation can do nothing but lend legitimacy to an activity that has been robustly and repeatedly poo-pooed by the respected Old School of our field.

The establishment of the Baran Lab’s blog fell out of the ongoing post-publication review of IBX-promoted benzylic oxidation at Blog Syn, a relatively new site that focuses on checking synthetic procedures in the vein of Organic Syntheses. Post-publication peer review is something familiar to the chemical blogopshere. Previous examples include the questioning of the science in the “Arsenic Life” paper, the exposure of duplication by Breslow in the “Space Dinosaur” saga, and the experimental investigation into the oxidation-by-NaH paper in JACS. Blog Syn takes post-publication review of synthetic procedures to the next level by coordinating replication of the procedures among a group of bloggers who compile and compare their results for all to see and discuss.

Last month, Blog Syn decided to examine a method for IBX-promoted benzylic oxidation published as part of Baran’s graduate work in K.C. Nicolaou’s lab. What started as a straightforward effort to test the (questioned) reproducibility of the reaction quickly evolved into a vigorous and thoughtful discussion of both the merits of anonymous bloggers’ questioning peer-reviewed research and of the reaction itself. Baran and the first author of the paper have participated actively in the generation of data and its analysis, and the most recent development appears to be improved mechanistic insight as to how the reaction might work.

Those interested in this specific reaction can check out the discussion for themselves, but all chemists can appreciate the value that blogs and other Web 2.0 venues offer in terms of advancing scientific knowledge and enriching our understanding of chemistry. While blogs may often engage in journalism that is a little rough at the edges, the ease of online publishing has helped to provide open venues for meaningful discussion, to give voice to important ideas, and to democratize power in a field where many grumble that power is overly centralized. What Blog Syn has started is a great service to the field of organic chemistry, and I look forward to the wealth of material that the Baran Lab can bring to the table in its own addition to the blogosphere.

Great stuff!

Edit to add: This great post by Rich Apodaca at Depth First places Blog Syn in historical context among similar experiment-based efforts in the chemical blogosphere. The post also offers an interesting analysis of the role that blogger anonymity plays.

Edit: Another (similar) great analysis and comment thread in this post by DrFreddy at C&EN‘s blog.

Chemical Citizen of 2006: Wikipedia User “V8rik”

Wednesday, December 27th, 2006

The Chemmy Award for Citizen of Year goes to:

User “V8rik” for his contributions to the chemical content of Wikipedia

I have no idea who this guy is, but he spends an insane amount of time adding chemistry articles to everyone’s favorite online encyclopedia. Just look at his contributions list. Chances are that if you’ve searched for anything chemical on Wikipedia, he’s had something to do with the article.

Cycloadditions? Yup. Ylides? Yup. The Ugi Reaction? That too. The guy is amazing.

This year, I finally made the leap and starting editing Wikipedia. It takes a while to get a hang of the Wiki code, and the style guidelines are even less fun to deal with. Finally, after you’ve learned the code and the style, what you write is forever subject to being changed by any random person on the Internet. So not only are Wikipedia users not paid for their contributions, they have zero editorial control over what they’ve written.

That’s what makes V8rik’s contributions all the more amazing. Sadly, he’ll probably never find out that he’s been awarded a Chemmy, but if he does, he has my sincere appreciation for his hard work. The world of chemistry could use more people like V8rik.

Next post: Top Chemical News Story of 2006


The Laws of the Universe

Friday, December 15th, 2006

I’ve recently discovered the fantastic Web site of Ken Suslick, a Professor of Chemistry at UIUC. His stories about serving as an expert witness during a patent lawsuit and as a consultant for a Hollywood movie are good reads, and his seminar on seminars is right on the mark. Some money advice:

“Your job is to convince and inform, NOT to archive.”

“Don’t get cute [with formatting and animations].”

“Don’t go more than 50 minutes”

Finally, his collection of “Laws of the Universe” is pretty good. My favorites:

Ninety Rules of Project Schedules: The first ninety percent of the take takes ten percent of the time, and the last ten percent takes the other ninety percent.

The Roman Rule: The one who says it cannot be done should never interrupt the one who is doing.

Westheimer’s Rule:
To estimate the time it takes to do a task: estimate the time you think it should take, multiply by 2, and change the unit of measure to the next highest unit. Thus we allocate 2 days for a one-hour task.

So true. Westheimer still roams the halls around here and often attends seminars, including the annual lecture for the Westheimer Medal. In an introduction to the last such lecture, a second Westheimer’s Rule was mentioned: “Two weeks in the lab will save you two hours in the library.”

It never ceases to amaze me how often people waste time trying to reinvent the wheel. Thank goodness for SciFinder.