Post Tagged with: "In The Pipeline"

Is Chemistry Incompatible with Web 2.0?

(This post is in response to the April 19 editorial in C&E News.  For the response to the May 10 editorial, click here)

A recent ChemJobber post notes that C&E News Editor-in-Chief Rudy Baum‘s editorials sometimes have a tendency to approach the controversial – and sometimes the purely political.  I wanted to discuss this weeks editorial which threatens to call into question much of my online existence (sorry, Mitch.  If Rudy’s right, I think you’re about to spontaneously e-implode).

In this week’s editorial, “The Limits of Web 2.0,” Baum decries the cliché “information wants to be free” for both its out-of-context usage (the full quote says information wants to be expensive because it is valuable and free because the cost of information dissemination is shrinking almost hourly – thus a struggle) and for its lunacy (information can’t wish for anything – it’s inanimate).  Rather, Baum says that it’s people who wish that information would be free.  I’d amend Baum’s correction slightly.  People really want information to be free and readily accessible.  I’d argue public libraries have long made most information “free,” if you were willing to do the legwork to get it.

But the bulk of Baum’s editorial promotes Jaron Lanier’s book You are Not a Gadget: A Manefesto, and summarizes Lanier’s main points, namely that the wisdom of crowds can be dangerous and science should be loath to adopt web 2.0 ideals.  Lanier points out that around the turn of century, a “torrent (a word hijacked by the web 2.0 crowd -ed.) of petty designs sometimes called web 2.0″ flooded the web.  And through the use of web 2.0, we apparently are losing sight of the trees for the forest, er, the taggers for the cloud.

Baum writes in his editorial (cross-posted for free on the web 2.0 CENtral Science blog, natch), “The essence of what Lanier is saying is that individuals are important and that we’re losing sight of that at our own peril in elevating the wisdom of the crowd to a higher plane than the creativity of a single person.”  That is, we are valuing the cloud more than the individuals, when the cloud can’t exist – and has no meaning – without the existence of the individuals.  Lanier notes that collective intelligence can be used well, but only when guided by individuals who can direct the course of the hive mind and help steer clear of common groupthink pitfalls.

But the most interesting quote comes near then end, when Baum quotes Lanier as saying that scientific communities “achieve quality through a cooperative process that includes checks and balances, and ultimately rests on a foundation of goodwill and ‘blind’ elitism.”  I’m not really sure what that means…

But to Lanier’s thesis that science ought to be wary of embracing web 2.0 and its ideals, I find it interesting that Baum writes his editorial at C&E News, the magazine of the ACS, whose flagship publication, the Journal of the American Chemical Society, has featured a JACSβ page for some time now.  The same C&E News whose blog has become so popular that it had to split off into several child blogs.  Where each post for each ACS article has links to share the article on one of several social networking sites.  Where scientists can now browse their favorite article on their iphones with ACSMobile.  While perhaps late to the party in some areas, the American Chemical Society has certainly ‘logged on’ to web 2.0 as a way to export content to the web-savvy scientist.

Plus, we have our own Mitch, a one man walking encapsulation of web 2.0.  His most successful application is, in my opinion, the chemical forums, which typically sees between 8,000 and 11,000 visitors per day.  This blog seems to be a big hit, and his ChemFeeds is a one-stop source for your aggregated list of your favorite journals’ graphical abstracts.  All this innovation on Mitch’s part earned him an interview with David Bradley (of ScienceBase) in his chemistry WebMagazine, Reactive Reports.

There’s also the Chemistry Reddit as another outlet of chemistry news and notes.

In the inaugural issue of Nature Chemistry, the Nature Publishing Group recounted how they have completely bought into web 2.0 as a means of science communication – each issue of Nature Chemistry even features a roundup of their favorite posts from the chemical blogosphere (which reminds me, to the left, Mitch has also created an aggregated rss feed of several popular chemistry blogs).

And, of course, web 2.0 in the sciences has been discussed in the blogs several times over the years.  We have over 3 pages of posts categorized Web 2.0, mostly Mitch’s posts on new web 2.0 platforms he’s developed.  Jean-Claude Bradley writes about web 2.0 in response to a very interesting post at Nascent, a blog from the folks at Nature.

So, all of these prove that web 2.0 has been talked about many times in the context of science.  Has it worked?  With the exception of blogs, sadly I’m inclined to say no.  At least not yet.  And even with blogs (with the possible exception of All Things Metathesis, and In the Pipeline, though Derek isn’t allowed to talk about his work b/c of intellectual property issues), not a lot of academic or industry leaders are prone to blogging.  It’s not like we’re reading Phil Baran’s blog and getting inside his head on a daily basis.

Sure, there is a subculture of people who are active on the web 2.0 scene, but it surely hasn’t taken off as a medium for all chemists to enjoy.  It theoretically should.  Chemists are always benefited from communal sharing of results and information.  But there are still (and probably always will be) people who seem reluctant to join the new technological paradigm.  I like the way Timo Hannay words it in his post on Nascent,

“But it’s not up to the doubters to ‘get it’, it is up to those of us who support these developments to demonstrate their value. And if we can’t then they don’t deserve to be adopted and we don’t deserve to be heard.”

Especially if there are people at the position of Editor-in-Chief for arguably the top chemistry magazine denouncing the web 2.0 movement, clearly it has a ways to go before it will be appreciated by all to the point where web 2.0 is ‘taken for granted,’ where we don’t even realize what we’re doing when we post results and opinions via web 2.0 technologies.

Let’s get moving!

tert-Butyllithium Claims Fellow Chemist at UCLA

butyllithium

Story is from UCLA Newsroom (Jan 19th):

A UCLA research assistant who was seriously burned in a laboratory fire last month has died of her injuries.

The 22-year-old woman, whose name has not been released, died on Jan. 16 at Grossman Burn Center in Sherman Oaks. She was transferred there after initial treatment for second- and third-degree burns at Ronald Reagan UCLA Medical Center.

The accident occurred Dec. 29 while the assistant was working with T-Butyl lithium, a highly flammable compound, in UCLA’s Molecular Sciences Building. The fire was extinguished by a colleague.

The fire is under investigation by UCLA’s Environment, Health and Safety department.

Link to article: Research assistant dies of injuries suffered in December lab fire

Update 1: More experimental details are coming out.

A 23 year old female research associate/laboratory technician intended to add an (unknown) aliquot of 1.6 M t-bu-Li (in pentane) to a round bottom flask, placed in a dry ice/acetone bath. She had been employed in the lab for about 3 months. The incident occurred on Dec. 29, during the UCLA holiday shutdown between Christmas and New Years. Researchers are granted permission to work during the shut down for “critical research needs.” There were two post doctoral researchers working in the lab and the adjacent lab, with limited English proficiency.

The principal investigator had trained the employee to slightly pressurize the bottle (an ~ 250 ml Aldrich Sure Seal container) with Argon and withdraw the desired aliquot using a 60 ml syringe, fitted with a 20 gauge needle. The PI likes to use these particular syringes because they have a tight seal. There is no evidence that the employee used this method. Speculation: she may have just tried to pull up the aliquot in the syringe. Somehow, the syringe plunger popped out or was pulled out of the syringe barrel, splashing the employee with t-bu-Li and pentane. The mixture caught fire, upon contact with air. She was wearing nitrile gloves, safety glasses and synthetic sweater. She was not wearing a lab coat. The fire ignited the gloves and the sweater.

Six feet from the fume hood was an emergency shower. When the employee’s gloves and clothing caught fire, she ran from the area away from the shower. One of the post-docs used his lab coat to smother the flames. 911 was called. UCLA Fire Dept. and emergency medical, Los Angeles City Fire, and Los Angeles County Haz Mat. The EMTs put the employee in the safety shower for gross decon and then transported her to the ER. She’s currently in the Grossman burn unit in Sherman Oaks with second degree burns on her arms and third degree burns on her hands, a total of about 40% of her body. There was very little damage to the lab. Bill has not interviewed the employee.

From: http://list.uvm.edu/cgi-bin/wa?A2=ind0901&L=DCHAS-L&P=13210

Update 2: From Daily Bruin (Jan 14th): Lab safety to be revised

Update 3: For those interested, the Chemistry Reddit is also tracking this story: A death in the science family. Be carefull with tert-butyl lithium!

Update 4: Proper Aldrich Sure-Seal technique can be found here: Handling air-sensitive reagents

Update 5: Name has been released from the Daily Bruin (Jan 21st): Assistant dies of fire injuries.

Update 6: Jyllian Kemsley from C&EN has picked up the story (Jan 22nd): Researcher Dies After Lab Fire

Update 7: Sheri Sangji facebook memorial for friends and family (Jan 22nd):
http://www.facebook.com/group.php?gid=116158190606

Update 8: Derek Lowe reminiscing on fires with tertiary butyllithium (Mar 2007): How Not to Do It

Update 9: Rebecca Trager also covering the story for RSC’s Chemistry World (Jan 23rd): UCLA lab assistant dies

Update 10: Derek Lowe mentions new fatality from trimethylsilyl diazomethane (Jan 23rd): The Real Hazards of the Lab

Update 11: Critiques of lab safety in Academia: Lab safety and chemical hygene in acadamia blows[TCB], A Death in the Lab[MCC]

Update 12: I was cleaning up some of the rabble-debate whether to release the PI name and accidentally deleted more comments then was my intention. Apologies to all commenteers effected. (Feb 19th)

Update 13: C&EN releases PI name. Insights: Learning From Mistakes (Subscription needed, Feb. 23rd)

Update 14: Los Angeles Times investigatory story on the accident. Deadly UCLA lab fire leaves haunting questions (Mar 1st)

Update 15: ChemJobber: What happened to Sheri Sangji? (Feb 27)

Update 16: LA Times: New details emerge in fatal UCLA lab fire (Apr 29)

Update 17: LA Times: State fines UCLA in fatal lab fire Fined $31,875 and Cal/OSHA will prepare an additional report to present to the Los Angeles County district attorney for consideration of criminal prosecution. (May 5th)

Update 18: ChemJobber: Patrick Harran, peeing in the jury pool? (May 5th)

Update 19: Statement of Patrick Harran

My students and I deeply mourn the death of our friend Sheri Sangji, and we realize our pain cannot possibly compare with the anguish felt by her family. She was an exceptionally gifted young woman with a bright future ahead, and her loss is truly tragic.

Since Sheri’s death, attention has focused on inspection and training records. These protocols are very important in developing and documenting a culture of safety, but in this case they are largely unrelated to the accident of Dec. 29, 2008. Sheri was an experienced chemist and published researcher who exuded confidence and had performed this experiment before in my lab. Sheri had previous experience handling pyrophorics, chemicals that burn upon exposure to air, even before she arrived at UCLA. Her most recent position prior to joining the group involved “scale-up process safety.” However, it seems evident, based on mistakes investigators tell us were made that day, I underestimated her understanding of the care necessary when working with such materials.

Sheri’s death resulted from a tragic accident. The California Division of Occupational Safety and Health has found no willful violations in its report. Throughout my career, I have strived to create a culture of safety. I am haunted by memories of this tragedy and wish that nothing like it happens again – in my lab or any other. In continuing our research, I go forward with a heavy heart in remembrance of Sheri and with a rededication to safety. I will also work tirelessly to achieve Chancellor Block’s goal of making UCLA the leader in safe laboratory practices.

(May ~5th)

Update 20: Chemical and Engineering News: UCLA Fined In Researcher’s Death (May 5th)

Update 21: Chemical and Engineering News: Negligence Caused UCLA Death (May 7th)

Update 22: Harry Elston’s Recipe for disaster editorial in the Journal of Chemical Health and Safety 2009, 16 (3), 3. (DOI: 10.1016/j.jchas.2009.03.011) (March 29th 2009)

Update 23: Science: Taken for Granted: The Burning Question of Laboratory Safety (May 1st 2009)

Update 24: ChemJobber: If I were working with tert-butyllithium… (May 10th 2009)

Update 25: The Sheri Sangji Petition: A tragic & preventable death (May 12th 2009)

Update 26: The California Fatality Assessment and Control Evaluation (CA/FACE): Worker Fatality Alert (May ~14th 2009)

Update 27: A Tribute to Sheri Sangji: www.sherisangji.com (May ~15th 2009)

Update 28: C&EN: UCLA Appeals Citations by Jyllian Kemsley (June 17th 2009)

Update 29: LA Times: Family of UCLA lab fire victim criticizes investigation (June 22nd 2009)

Update 30: LA Times: Cal/OSHA chief to oversee criminal investigation of fatal UCLA lab fire (June 30th 2009)

Update 32: An intensely detailed account of the experiment that caused Sangji her life. C&EN — Learning From UCLA (August 3rd 2009)

Update 33: ChemJobber and Chemical Space

Update 34: C&ENtral Science — Evaluating Safety (August 3rd 2009)

Update 35: C&ENtral Science — Personal Protection from Fire (August 4th 2009)

Update 36: C&ENtral Science reports their timeline of the accident and allegations of tampering — Tampering with Evidence? (August 5th 2009)

  • The fire occurred shortly before 3 PM on Dec. 29, 2008. Sheharbano (Sheri) Sangji was taken to the emergency room and Harran followed.
  • After Sangji and Harran left, Los Angeles County hazardous materials crews cleaned up the lab. (Recall that medical personnel had put Sangji under the safety shower. Showers are supposed to run at a minimum of 75.7 L/minute for 15 minutes, so there should have been about 1,100 L of water to test and mop up.)
  • Harran returned to the lab around 7 PM and was asked by fire officials to shut down the experiment to ensure the hood was safe.
  • Sometime after Harran shut down the experiment, UCLA deputy fire marshal Christopher Lutton took photographs of the lab and Sangji’s hood. Lutton also told Harran that the lab would be locked and investigated, although there’s no record of exactly what Lutton said.
  • At around 7:30 PM, Lutton left the lab and went down to his vehicle remove his gear, call the locksmith, and call one of his colleagues.
  • At about 8:30 PM, Lutton returned to the lab to find Harran and postdocs Weifeng Chen and Hui Ding in the lab. In a later interview with Gene Gorostiza, the UCLA police detective who investigated the scene tampering allegations, Ding said that he and Chen removed six empty flammable liquids containers from the lab and put them in the building’s trash. They also put other solvent containers into a lab storage cabinet.
  • Lutton ordered everyone out of the room and stayed on the scene until the locksmith arrived at 9:55 PM.
  • The locksmith finished changing the locks at 11:35 PM. At that point, the doors were locked and Lutton took possession of the only key, put up yellow barrier tape, and left.
  • Lutton returned to the lab the next morning to find that the restraining bolts in a side panel to one of the doors had been released, allowing the door to open freely. Lutton told Gorostiza that at that point he discovered that the room contents had been tampered with. A timeline of the incident included in UCLA fire marshal documents says that, comparing photos of the lab taken in the morning to the ones taken the previous evening, containers of flammable liquids were removed, other containers were moved into a walk-in fume hood, a cabinet door was left ajar, and some items in the fume hood where the fire had occurred had been moved around.

Update 37: C&ENtral Science — Promoting Safe Research Practices (August 6th 2009)

Update 38: C&ENtral Science — Some Thoughts on Lab Incidents (August 7th 2009)

Mitch (Our best thoughts, from everyone at Chemistry Blog, go to her family at this time)

By January 20, 2009 103 comments Uncategorized

A Word on Research Misconduct

Dig out your dictionary and look up the word “hyperbole” (I know, it might be a while since you’ve last had English class)—exaggerated statement or claims not intended to be taken seriously.  I tend to hyperbolize a bit when I replay an incident that happened at the bar or in class, which I attribute to the fact that I’m a terrible storyteller.  I think we all do it to a certain extent.  I know I’ve once said something to the effect of, “It was the greatest movie, ever…in the history of humans.”  A hyperbole at its finest.

While most common vernacular is riddled with hyperboles, I’d argue that the majority of intellectual study makes an effort to stay away from gross exaggerations (with history being the exception).  In particular, science is the observation and study of the physical world, and it leaves no room for hyperboles.  Just facts.  For example, if you mix an aqueous solution of silver nitrate with an aqueous solution of sodium chloride it is a fact that a precipitate will form.  There are no equivocations about scientific facts.  Though, science sometimes falls short when making assumptions that connect two or more facts into one coherent theory or proposal.  Still, these assumptions, en route to a new theory, are usually reasonable if not simplistic (i.e. Occam’s razor).

What about bad data?  Of course, there are ways to make our raw data more “natural” without exaggerating.  In the event that we have to plot data points, for example, as scientists we can exclude data that “doesn’t belong.”  We call these anomalies “outliers” and there is statistical rationale as to why a stray might be “bounced” from the data set without any bias to the result.  But even in these cases, the data point is often so far away from the others that including it might be a detriment to a fact about Mother Nature.

What irritates me to no extent is a term I refer to as “hyperbolized research.”  We have all seen these situations before: yields that are bumped a good 5 to 10 to 50%, data that is fit just right, patent procedures that are not reproducible.  Why are these practices tolerated?  Contemporary science is themed “publish or perish,” which essentially means that if you are not producing enough results (nevermind quality) you will soon be unemployed.  I recall hearing stories about early 20th century scientists who studied science without the proverbial gun to their respective heads and still made great findings.  A lot of these experiments were groundbreaking, marvelous and truly beautiful.

It’s no surprise that this issue of “publish or perish” rears its ugly head in science.  Society is incredibly fast-paced, and science is certainly trying to keep up.  But, it’s really hard to do so with a tiny, bankrupt research group (where most if not all members are teaching) versus a behemoth firm with hundreds of years of experience and millions of dollars of materials to use. 

So, what do groups do to keep pace (or at least appease the boss)?  “How did you do with that reaction you couldn’t get to work last week?”  “Um…I got 98% yield with 95% ee.”  “Great, let’s write up a manuscript and submit to JACS.”  I’ve heard stories of “big name” research groups who’s members purposely inflate their yields to keep “the man” happy.  In these cases, researchers keep two sets of lab notebooks: the real one (usually under lock and key with the actual experimental results) and the boss’ one (usually kept in the open, so the boss can see how his researcher got a 90% yield on chemistry that is next to impossible to reproduce).  The bottom line is that papers get published, lectures are given and proposals are funded—criminality is rewarded.  How is this right?  Furthermore, how is it fair to another researcher who needs to repeat the results?

Have we not learned anything from the Bell Lab incident?  For those not familiar, Hendrik Schön was a groundbreaking physicist working for Bell Labs in the late 1990’s.  He was purportedly on par to win a Nobel Prize with his creation of an “organic molecular transistor.”  The papers describing this work were met with criticism in the scientific community and at some point (c. 2001), Bell Labs launched an internal investigatory committee to examine Schön’s work.  Their final report ultimately alleged 24 accounts of misconduct that were essentially fit into three categories: “Substitution of data,” “unrealistic precision of data,” “Results that contradict known physics.”  In the end, he was ultimately stripped of his doctoral degree.  But think about the repercussions of not investigating Schön’s findings.  Had Schön’s work not been policed, potentially millions of dollars would’ve been invested into falsified research.  While I’m aware that Bell Labs was recently closed, without insinuating anything, it makes me wonder if this Schön incident had any weight in the lab’s termination.

Rex Dalton covered the aftermath of this incident along with several other examples of research misconduct (Nature 2002, 420, 728-729).  He ultimately offered up the following observation:

“Science may be self-correcting, but sometimes it is a painfully slow process.”

Perhaps he’s right.  Sure, several papers are going to be questioned in the future.  And of those papers, a few might be blatant lies.  How much time is it going to take to correct these mistakes?  According to Corey: “Occasionally, blatantly wrong science is published, and to the credit of synthetic chemistry, the corrections usually come quickly and cleanly.”  Case in point?  The hexacyclinol incident that was excellently covered by C&EN and by a couple of fellow bloggers: Derek Lowe and Paul Docherty.  In this case, there was a rapid turn around (possibly due to public interest).  However, this case might be the exception.  It could be years before a questionable project is proven incorrect.

I know…you want me to provide a solution.  Maybe there isn’t an immediate, reasonable answer.  But, alas, here’s what I’ve uncovered: there are a few wonderful articles in J. Chem. Ed. about scientific misconduct, which both hover around the LBNL and Bell Lab incidents (see: J. Chem. Ed. 2002, 79, 1391; ibid. 2005, 82, 1521).  The authors’ messages (albeit bluntly or implied) were that ethics and empathy should be at the forefront in the early years of scientific training.  Some people cannot discern between right and wrong and teachers should do their jobs by teaching students about the rights and responsibilities of being a scientist.  While I did not receive formal training on scientific misconduct, I was given a lambasting for bordering on plagiarism my freshman year of college.   I learned my lesson early—you and your lab partner need to keep separate lab notebooks.  Perhaps this experience has formed me into the scientist that I am today (I’m anal-retentive about my lab notebook). 

I guess there is a remaining question still looming.  What sparked this rant about “doing the right thing”?  I’ve been repeating experiments for the past couple of months that were reported to be exceptionally clean (requiring no chromatography) and high yielding.  Most of these reactions have tanked—miserably—even with exceptional preparation and precision.  So, I’m painstakingly re-optimizing experimental procedures so someone else doesn’t have to.  It’s taking a while—much longer than it reasonably should.  But, hey, “sometimes (correcting science) is a painfully slow process.” 

By October 6, 2008 6 comments Uncategorized

Diaza[12]annulene: Would You have Known Better?

The recent retraction of two papers regarding diaza[12]annulenes by Yamaguchi et al. and Shi et al. from separate groups have strengthened the argument for stronger peer review and more thorough literature review by authors. http://dx.doi.org/10.1002/anie.200704704

But anyone can be an armchair synthetic chemist and point fingers at what should have been done after the fact. The easiest finger to point, is presumably between 7 coauthors, 4 reviewers, 2 editors no one ran the appropriate literature searches to find that these reactions are known and yield products with exactly 1/2 the mass as those reported in the papers. But, now we come to the bitter truth in modern chemical research, we simply do not perform the thorough literature searches of yester’year. Some will say this is a problem, but assuming those 13 scientists are typical of scientists of today then it simply isn’t a fair commentary to make. So, I thought it would be more beneficial to reread the papers and see if I would have come to the same conclusions given the same series of data, as I’m oblivious to heterocyclic chemistry in general and the Zincke reaction in particular, and have a typically topical background like most chemistry graduate students (I’m a Nuclear Chemist after all).

First up the Yamaguchi paper: http://dx.doi.org/10.1021/ol061585q
The title is the One-Pot Synthesis of N-Substituted Diaza[12]annulenes. Just looking at the title, we should be expecting 1H,13C-NMR, definitely MS data, and likely a crystal structure since the molecule would have two cationic-like centers. Picture shown below.

As can be seen in the structure this monstrosity should have some serious pi-pi stacking possibilities, and isolating crystals shouldn’t have been too problematic, but none are isolated. An image of their NMR data for the structure above is below.

It would be at this point that the little voice in my head would be like, “hmm…. why do I have aromatic proton peaks? I should probably count those pesky buggers again. Yup, 12 delocalized electrons.” If one is postulating that this is antiaromatic, then one hallmark of antiaromatic hydrogens, located on the outside ring, are that they shift upfield (lower ppm) and lie to the right of 8 ppm and likely 7ppm. So, it would have been at that point where the paper would of confused me.

Second up the Shi paper: http://dx.doi.org/10.1002/anie.200702140
The title is the [12]Annulene Gemini Surfactants: Structure and Self-Assembly. So, we should be expecting yucky yellow oils, and with the word structure, perhaps even a crystal structure. The molecules examined are shown below.

Independently, they confirm the odd aromatic protons of Yamaguchi and they obtained a yellow powder, not necessarily an oil, but well within reasonable expectations. They did some calculations with Gaussian and discovered the results below.

The expected distorted structure is seen in II but lied 1.7 kcal/mol higher in energy than I. This is just odd, for a cyclic antiaromatic system we should expect to see 2nd order Jahn-Teller distortions shift the molecule away from planarity and this was not seen by calculations. This is where the authors and reviewers can be faulted, at that point some one should have suggested an experiment to see whether the NMR peaks would move upfield as a function of temperature. As scientists, we love making graphs, and that would have been a neat confirmation of both the structural predictions from calculations, and an easily verifiable hypothesis.

In summary, I don’t feel it is fair to fault the authors, reviewers, editors for not knowing every obscure heterocyclic named reaction. However, it is prudent upon all of us to ask the right questions about our research, to put-off deadlines if necessary, and to apply our full intellect and diligence to our experiments.

Some Armchair commentary here:

Mitch

By December 14, 2007 2 comments synthetic chemistry