Where has all the (-)-sparteine gone?

*Welcome Pipeline readers!  No really, if you have a dusty bottle of sparteine, we’ll probably take it

Our lab uses a lot of (-)-sparteine in enantioselective aldol additions, so we tend to buy large bottles which last us a while.  As such, we haven’t had to order (-)-sparteine in a while.  But our bottle is getting low (read: there are a few hundred microliters left), and it’s time to order more.

But it’s all gone.

All of it.

No one sells (-)-sparteine anymore.  Acros.  Fisher.  Alfa Aesar.  VWI.  Strem.  TCI.  I’m sure I’m missing some, since I don’t actually do the ordering.  Our ordering guy called Aldrich specifically, and was able to order three 10 mL bottles (probably the last available in the world).

Well, today we get a letter from Sigma-Aldrich telling us… they’re canceling our order.  They’re not selling it anymore either.

What is going on, here?  Anyone know why the major (-)-sparteine shortage?  Is this all of a sudden or has this been happening gradually?  Is this related to the acetonitrile pinch, or is this something different?  Anyone got any black market (-)-sparteine they want to, er, not sell to us?

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Science as Art

Princeton University’s Art of Science contest has produced a gallery of pretty spectacular images of science in action.

This is the fourth Art of Science competition hosted by Princeton University. The 2010 competition drew more than 115 submissions from 20 departments. The exhibit includes work by undergraduates, faculty, research staff, graduate students, and alumni.

The 45 works chosen for the 2010 Art of Science exhibition represent this year’s theme of “energy” which we interpret in the broadest sense. These extraordinary images are not art for art’s sake. Rather, they were produced during the course of scientific research. Entries were chosen for their aesthetic excellence as well as scientific or technical interest.

Interestingly, first second and third prize were determined according to the golden ratio, with first prize earning $250, second prize earning $154.51, and third prize earning $95.49.

Be sure to check out all the images, many of them are quite striking.  Clicking on the images gives a caption explaining what you’re looking at.

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How Can Science Embrace Web 2.0: A Response to Rudy Baum

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

First, I want to thank Rudy Baum, editor-in-chief of C&E News, for taking the time to respond to my commentary.  I know he probably has other issues he’d rather talk about on his editorial page, and I appreciate the engagement in this dialogue.

I’d like to continue the dialogue here and I hope to keep this conversation going – at least informally – for a long time.

Mr. Baum and I seem to agree that Web 2.0 is a part of science now; however, we may disagree on the merits of SciW2.0.  If you don’t believe SciW2.0 has arrived, consider that the fact that you are even privy to this conversation.  Not only do I have a W2.0 platform upon which I can comment on C&E News editorials, but within days the comments were populated with a who’s who of SciW2.0 leaders offering their opinions and helping shape the conversation.  And the conversation became so loud that it prompted an editor-in-chief to write an entire editorial in response to, essentially, a nobody in the chemistry world (let’s face it.  I certainly don’t count myself in the elite of chemistry, blind or not).  That all of these things can happen within a month – and without any face-to-face meetings between any of the players – proves the establishment of SciW2.0 as a communication tool.

Now, before we continue, I want to re-link to this blog post on Nature‘s Nascent blog.  In my opinion, this post is a must read for anyone who wants to engage this discussion.  It is a nice overview of SciW2.0, its strengths and especially its weaknesses.  Why there’s resistance to SciW2.0, why academic and industry leaders aren’t all buying in, and why he’s committed to making SciW2.0 successful.  It really is mandatory, and I’ll wait for you to click over and read it now.

(lounge music break)

While severely cautioning people about SciW2.0 (but not denouncing), Baum seems to want to walk a fine line.  It’s dangerous, it’s not a panacea, he reads blogs, he’s not an opponent of all W2.0, he agrees with author Jaron Lanier when he warns scientists not to adopt W2.0 ideals, and he finds proponents of W2.0 overenthusiastic.  Perhaps he is just cautioning scientists against ‘irrational exuberance’ when it comes to buying in to SciW2.0.  And those warnings would be well heeded (although I doubt we’re anywhere near the irrationally exuberant days of SciW2.0).  My question for Baum is: if he doesn’t think SciW2.0 is a panacea, does he think the current model for scientific communication (peer-reviewed journals) is a utopia?  And if not, what would he suggest happen differently?

As to his comment about the panacea of W2.0 and how it ‘changes everything’ as he says W2.0 proponents adamantly claim, I suspect he’s referring to Don Tapscott’s and Anthony Williams’ book Wikinomic: How Mass Collaboration Changes Everything.  I haven’t read it, so I can’t comment on it.  But I would imagine, as is true in other areas of life, when people mention ‘everything,’ they rarely mean things like cutting edge academic and scientific research.  Rather, I imagine people mean ‘everyday things,’ usually for everyday people.  I’ll link here to notes by Will Richardson on W2.0 and how it’s changing politics, government, journalism, and business, and how it is starting to change education.  So while it seems to be changing certain industries, I’ll admit that it’s not changing everything.  In fact, I don’t think any of the commenters on the other post thought so, either.  Pop science is not the same as pop culture and does not think the same way.  Comments made in one arena are not necessarily transferable to the other arena.

But rather than getting into a hair-splitting contest over who used what words and who meant what, I propose to move the conversation forward in a different direction.  My open question: What should SciW2.0 look like, and how will we know it’s successful?

W2.0 is ultimately a communication tool.  It harnesses the power and dexterity of the internet and allows people to communicate with each other in ways never before possible and on timescales never before possible.  In certain circles (politics, pop culture), if you’re not actively following the W2.0 scene, you’re way behind and have nothing to bring to the table.  Not so in SciW2.0.  If you’re following SciW2.0, you’re reading about and reacting to people’s analysis of things that happened in the past.  Missing a week or two won’t put you behind, because by and large you’ve already read the same papers and seen the same announcements.

I doubt that SciW2.0 will become an instant data/paper communicating tool for hard science anytime soon the way it has in other aspects of life.  I agree with the reasoning by Timo Hannay in the Nascent link:

[E]ven if the direct financial cost of sharing this information is low, the cost in terms of scooped findings, rejected papers and grant applications, and perhaps even diminished reputation could be very high. … It’s sad, but most scientists don’t publish in order to share results with their peers, they do so in order to secure grant funding and promotions. We know this because when we provide ways of sharing information that do not affect their likelihood of getting funding or promotions – such as preprint servers for biologists – most don’t use them.

There will always be a place for reactionary SciW2.0.  Communities of people talking about science and sharing ideas and information cannot hurt anyone.  But because there’s rarely breaking news coverage on SciW2.0 (see Totally Synthetic’s sodium hydride oxidation post for an example of breaking news coverage), the majority of chemists don’t seem to find the need to tune in regularly.

Before we’ll get large numbers of people on board, in my opinion, might we need to make SciW2.0 less reactionary and more innovative?   I think we’ve started seeing bits and pieces of that scattered throughout, and that might be how we make it more appealing to the science community at large.  I mentioned in the comments previously that ACS had their NanoTube contest, which asked users to upload original videos explaining ‘What is Nano’ in an clear and entertaining way.  Perhaps this is the way science utilizes W2.0 in a productive manner.  Demystifying aspects of science to make it accessible to anyone curious about science, but perhaps without the training.

But, as the Nascent link alludes to, other types of crowd sourcing have not been as successful.  Nature‘s open peer-review system posted a small number of ‘opt in’ papers online and asked the crowd to review and comment on them before being accepted to the journal.  The open peer-review process happened concurrently with the ‘typical’ closed, anonymous peer-review process.  As noted if you listen to the audio version of the talk, it added no apparent value, but a lot more work for the Nature folks, so they abandoned the experiment.  I suspect it was just ahead of its time.

We may look to the results of a current crowd sourcing experiment to see if the time is right yet.  The Haystack, one of CENtral Science’s child blogs, reports on the expansion of the Pool for Open Innovation against Neglected Tropical Diseases.  In this experiment, scientists dump patented information into an open pool, and different users around the world are able to access the data to try to make progress on treatments for neglected diseases.  It will be interesting to watch that story unfold over the next few years.

I guess I don’t really know what SciW2.0 needs to look like to be successful. … But I bet I know a way to get some of the brightest minds in the field together to think about it communally!   I’d love to hear from people what their ideas are for the future of SciW2.0 and how to make it more commonplace in the field.

Finally, I’d like to say to Baum (and everyone else reading), if you haven’t read Who Moved My Cheese?, then pick it up from the library on the way home tonight and read it.  It will take maybe an hour, and it can be read in the easy chair after dinner while watching 24 if you’d like.  The cheese is moving, Rudy, I just don’t know where to, yet.

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A Few of My Favorite (Chemistry) Things

To carry on with Chemjobber’s Favorite Things list (thanks, btw.  Now I can’t get that silly Dove commercial out of my head), here’s my list of some of my favorite things about chemistry

1. Clickable Sharpies
2. Vanillin TLC stain
3. Pericyclic reactions
4. Dump-and-Stir reactions
5. A set of nested beakers (my set goes from 600 mL down to 10 mL)
6. Review articles
7. PhD comics
8. Short paths (with or without the cow receiver)
9. Playing with liquid nitrogen
10. Dry ice bowling (a lab Olympic event, where you roll a piece of dry ice down our long hallway to see whose goes the farthest)

(Update)

See Also:

• Chemjobber (the original!)
• The Haystack
• Newscripts
• The Sceptical Chymist (+ bonus in comments)
• ScienceBase
• Carbon Based Curiosities
• Chemistry World
• It’s the Rheo Thing
• Jon Edwards
• Endless Possibilities
• Chemist Geek
• The Safety Zone
• Chem-bla-ics
• Chemical Space
• Chemvoice Blog
• scheikundejongens

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Calvin and Hobbes on Chemistry

Ok, so maybe they were originally talking about his math homework… but the joke’s still funny

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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!

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Indiana University Biochemistry Major Commits Suicide with Hydrogen Sulfide

Almost exactly one month ago, I posted on a recent duo of suicides in my area by hydrogen sulfide (MSDS) – a toxic gas generated by mixing together certain easy-to-obtain household chemicals.

Today, I saw a story out of my home state of Indiana that a 21 year old junior biochemistry major from Indiana Univeristy has taken his life using this same hydrogen sulfide method.  Gregory Willoughby apparently worked as an undergraduate research assistant in the Cognitive Neuroimaging Laboratory in the Department of Psychological and Brain Sciences.

In this instance, Gregory Willoughby barricaded himself in the closet of his dorm room on or about April 4.  He left notes on the closet door warning first responders that hydrogen sulfide gas was present.  Several days later, his suitemate began notifying physical plant of a strange odor in the area, and it took several visits by various facilities management groups over several days before they decided to enter Willoughby’s room.  Police had to break down the door as it was barricaded from the inside by tape and furniture.  By this time, the gas had thoroughly dissipated and no first responders complained of injuries as a result of residual hydrogen sulfide.

I’ve talked about the dangers of hydrogen sulfide before.  Perhaps its most dangerous symptom is olfactory fatigue.  Low concentrations of hydrogen sulfide smell like rotten eggs.  Prolonged exposure leads to olfactory fatigue – you lose the ability to detect the odor of hydrogen sulfide.  You no longer smell rotten eggs, so you think the threat has passed.  Instead, you are still inhaling potentially lethal levels of the toxic gas.  High concentrations of hydrogen sulfide can lead to instantaneous unconsciousness and near immediate death.

Hydrogen sulfide suicide is also potentially dangerous to first responders and innocent bystanders.  In several instances in several countries, first responders have been hospitalized for hydrogen sulfide inhalation after trying to rescue victims who do not leave notes warning the first responders of the danger.  Additionally, one story notes a Japanese teen who used hydrogen sulfide in an apartment building and sickened almost 100 other residents as the gas spread throughout the complex.  It is very fortunate that did not happen here, given the close living quarters of the typical college dorm.

I talked last time about the thin line between responsible and irresponsible use of chemicals found both around the house and especially in the chemistry lab.  We don’t – and probably won’t – know if this student made use of his chemistry knowledge in making his final decisions.  All we can do at this point is remind readers – chemists and non-chemists alike – to take seriously the responsibility inherent in handling chemicals.  It’s all too easy for bad things to happen (unintentional as well as intentional) when playing with chemicals.

Again, I want to take this opportunity to encourage anyone struggling with thoughts of suicide – especially anyone who came to this page today for that reason – to call 911, your local emergency response number, or any of the numerous national and local suicide hotlines available.  Do it now.  I will also post the same disclaimer as last time: the comments of this post will be closely monitored.  Anyone attempting to post recipes for the generation of hydrogen sulfide gas will have their comments removed immediately.

Previous at Chemistry-Blog:

• Hydrogen Sulfide Suicide
• Suicides in Chemistry

Helpful information for first responders and health care providers:

• Very detailed CDC bulletin on hydrogen sulfide with sections for on-site medical care as well as information for long-term care
• St. Louis University bulletin on the dangers of and treatment for hydrogen sulfide inhalation
• Shelby County (KY) EMS presentation on hydrogen sulfide

Stories about the IU suicide:

• Initial Indiana Daily Student (IU newspaper) story on the death
• IDS follow up on victim
• WTHR (NBC Indianapolis) story with news video.
• WTHR follow up on victim
• Bloomington, IN, Herald Times on autopsy report
• Indianapolis Star story

Update (4/15):

New news stories:

• Indiana Daily Student article about the life of Willoughby.  Undergraduate research with apparent plans to pursue a Ph.D. in chemistry, Wells Scholar, accomplished cellist (in a quartet called “Stringin’ Scientist”, approved for study abroad for summer 2010
• WRTV (ABC Indianapolis) story on the risk to first responders
• WISH (CBS Indianapolis) TV news segment on the incident
• Terra Sigillata (of ScienceBlogs) coverage

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You are my density … I mean Destiny*

(for other entries in the Chemistry in Space series, click here)

Chemistry in space has been greatly aided by the addition of the Destiny Laboratory Module (see also: here for overview, and here for images) to the International Space Station.  Destiny was delivered by the Space Shuttle Atlantis during STS-98 in February 2001.  It is the first permanent operating orbital research station since Skylab was vacated in February 1974.  Destiny is a cylinder measuring 28 feet long and 14 feet wide.  Inside, there are 24 ‘racks’ (6 on each side) measuring 73 inches by 42 inches.  The racks can be configured for storage, life support systems, or – more importantly – science experiments (check out the interactive on this page).   13 racks are available for science, while 11 are used for other purposes.

One rack bay remains open and houses the highlight of the module: a 20 inch optically perfect window made of telescope-quality glass – the largest produced for use in space.  It allows the use of high quality video and still cameras primarily for capturing images of Earth in detail not before possible.  One rack bay houses the Minus Eighty Degree Laboratory Freezer for ISS (MELFI).  It has 4 dewars of 75 liters which can hold samples of various sizes and shapes and keep them at variable controlled temperatures.  Currently, temperatures of -80 degC, -24 degC and +4 degC are in operation on the ISS.

The purpose of Destiny is to provide space for scientific research, including experiments in the physical sciences.  Experiments are designed and built into the shape of one rack, which is ported into space and installed in Destiny.  Racks can be built to be controlled by astronauts aboard the ISS or remotely by scientists on Earth.  Destiny is joined by Columbus and Kibo as the main research ‘wing’ of the ISS.  Columbus is the science laboratory contributed by the European Space Agency and Kibo is the science laboratory contributed by the Japanese space agency JAXA.  Kibo also includes a ‘terrace’ where experiment payloads are fully exposed to the space environment.

Check back for stories of experiments conducted in the microgravity of space aboard the ISS.  There’s some pretty awesome research being undertaken.

*Bonus points if you can tell me what movie that’s from

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Hydrogen Sulfide Suicide

I woke up this morning to Breaking News on my local morning news.  Police responded to a suspicious vehicle call around 10pm, where they found a woman slumped over in her car.  Police opened the door, whereupon they discovered a bucket with chemicals on the front seat.  The officer was overcome with the fumes and treated at the hospital for burning in his throat.  His condition is as yet unknown (update: he was released).

The regional hazmat team evacuated the surrounding neighborhood while they attempted to remove the woman from the car.  The woman did not survive.

The police are not releasing details of the chemical used, but it appears to be related to a similar suicide on the other side of town in February.  In that case, the victim left notes all over the car saying, “Do not open!!! poison gas!!! hydrogen sulfide.”  Another note, in part, read “hazmat team needed.”  When hazmat crews opened the car in that case, they measured levels of hydrogen sulfide more than 3 times the lethal limit.

Hydrogen sulfide (HS) (MSDS) is a colorless, highly flammable gas.  Humans can detect hydrogen sulfide at low concentrations, where it smells like rotten eggs.  Higher levels (~40 ppm) can irritate mucous membranes and cause headache, fatigue, dizziness, and even memory loss and bronchitis on repeated exposure.  At concentrations 50-400 ppm, can produce cough, dyspnea, hemoptysis, cyanosis, agitation, vertigo, confusion, nausea and vomiting, tremulousness, cardiac arrhythmias, hypertension, and, possibly, loss of consciousness.  According to one source, “just 2-3 breaths of HS at >700 ppm can cause immediate death.”  Most notably, prolonged exposure quickly leads to “olfactory fatigue” whereupon you can no longer smell hydrogen sulfide and can no longer detect its presence.

The mode of action is as follows: “The major route of toxicity for HS is by inhalation. At lower doses, local irritant effects predominate. At higher exposures, cellular respiration may cease as HS forms a complex bond to the iron ion in mitochondrial cytochrome oxidase, arresting aerobic metabolism in an effect similar to cyanide toxicity and affecting all organs, particularly the nervous system.”

It’s no secret that chemicals can be used for nefarious purposes.  Perhaps the most familiar is death by cyanide poisoning, with perhaps the most infamous case being the suicide of graduate student Jason Altom at Harvard in 1998.  Atropine, adrenaline, carbon monoxide, chloroform, and even the bizarre UK case of assassination by polonium.  The educated chemist has only a thin line to cross when reaching across the chemical shelf.  A good dose of respect with a large side of humility is in order as we remember the power of the knowledge we have attained.

Suicide by hydrogen sulfide was new to me.  But a wave of this type of chemical suicide swept Japan beginning in 2008.  A USA Today article written in July 2008 noted over 500 deaths so far that year from hydrogen sulfide.  One teen, who released the gas in her apartment, sickened more than 80 people throughout the complex as the gas spread from unit to unit.  Isolated cases have appeared throughout the United States in the past few years, including these two around me in the last 3 weeks.

Fortunately, emergency management teams have produced a number of documents to aid emergency responders.  The CDC, St. Louis University, and Shelby County (KY) EMS have good information for first responders.

Previous Chemistry Blog post on suicides in chemistry.

On behalf of the Chemistry Blog community, anyone struggling with thoughts of suicide – especially anyone who came to this page today for that reason – is urged to call 911, your local emergency response number, or any of the numerous national and local suicide hotlines available.  The comments of this post will be closely monitored.  Anyone attempting to post recipes for the generation of hydrogen sulfide gas will have their comments removed immediately.

Update: Chemjobber sends along an article from The Atlantic magazine talking in sometimes raw emotion about the suicide mentality that seems to be problematic in parts of Japan.

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