fun to look in a microscope

October 26, 2007 at 3:03 am | | cool results, everyday science

Sometimes it’s just entertaining to look into a microscope. I like this pic I took the other day:

It looks like a tiny sun. But it’s just a fluorophore solution that has dried up and left some large aggregates (which emit at a longer wavelength—the green is the normal emission—maybe Excimer will like this, at CBC’s new website).

You can also see a bleached region in the middle of the green from the peak of the laser excitation region, and a swath of bleached dye where I moved the stage up and down before the picture. You might even make out some single molecules in the center. Quite impressive for a simple digital camera!

This was actually before I aligned the beam for real experiments, so all the ring patterns are actually interference due to poor alignment. I just thought that the misalignment made it pretty, so I took a color picture.

bad chemicals

October 24, 2007 at 8:58 am | | crazy figure contest, literature, nerd

OK, I know this is old news (Paul already blogged about it), but I just received my very own hard copy in my mailbox, so I have to post it:

I just love this! I want to use it next time I teach gen chem. I know chemistry can be hard. Look, even OUP and ACS get it wrong sometimes. And I mean really wrong.

What I don’t understand is how did they do this?!? Which chemical-drawing program let’s you make a hydrogen join the ring of benzene? Or have oxygen form four bonds? Or… They must have had little red squares all over their screen!


October 19, 2007 at 2:51 pm | | everyday science, literature, science community

Initialisms and acronyms pervade science. I mean, they’re pervasive everywhere, but scientists use them a lot. And each field and subfield and subsubfield has its own set of acronyms.

I can be sorta a snob when it comes to grammar and acronyms; I like sentences that I can understand. So I decided to set down some guidelines for making a good acronym. Now these are neither exhaustive nor necessary: I’m sure I forgot some rules and I know that some good acronyms fail some of the rules. I just wanted to get something down on epaper; maybe y’all can help me flesh out the list.

Guidelines for Introducing a New Acronym in a Paper (GINAP)

  1. First off, for new compounds, basically anything goes as long as the acronym is simpler than the IUPAC name.
    Of course, you should check whether the chemical or a similar structure has already published with an acronym. If it hasn’t, then just choose the major letters and make an acronym so you can refer to it throughout the paper and other papers. For instance, 6-propionyl-2-dimethylaminonaphthalene (PRODAN) is a great acronym; it has the added bonus that once can pronounce the word. It could also have been PPDMAN: not as sexy but it would accomplish the purpose.
  2. Ask yourself, Does this method/system/etc. need a new acronym? Does it deserve one?
    Not all new ideas necessitate a new word. Not all ideas you publish will be new. For these reasons, it’s important to question how important it is to introduce a new acronym in the first place. If your method is a slight variation on a common practice, or a common practice applied to a new system, maybe you don’t need a new acronym. Moreover, if you can describe what you are doing with a few words (or in a few sentences one time in the methods section), then there’s another reason not to come up with a new acronym. This guideline has two goals: (a) to avoid further obfuscating the terminology in your field and (b) to avoid taking credit for a whole method if you only contributed a minor part. For instance, polarized radiation imaging of single-molecules (PRISM) would be a fun acronym, but people have been doing that for decades without naming it.
  3. Don’t try to be too cute
    Acronyms are best justified by making sentences more clear. So come up with an acronym that makes sense, not one that is catchy.
  4. Make the acronym descriptive and meaningful
    If an informed person knows what each letter of the acronym stands for, they should understand the method (or system or instrument or whatever). For instance, TEM stands for transmission electron microscopy; a reasonable scientist could understand that this refers to a microscopy technique that involves transmitting electrons through a sample. But what does mean cleverly harnessing the absorption of single molecules (CHASM) mean? (OK, I made that one up.)
  5. Make the acronym unambiguous
    I think that each letter should be unambiguous: if a letter could easily stand for two opposites, then clarify by adding another letter. For instance, “I” could stand for “inter-” or “intramolecular,” so for excited-state proton transfers, ESIPT could be ESInterPT or ESIntraPT. Another example is Förster resonant energy transfer (FRET): because the ambiguity with the “F,” the first word is often referred to as “fluorescence,” which is wrong. (My favorite exception to this rule is laser. Laser is one of the best acronyms ever, but the “s” could easily stand for “stimulated” or “spontaneous,” the two types of emission. If you know how a laser works, it’s obvious that it’s amplification by stimulated emission, but the acronym doesn’t necessarily help someone who doesn’t know.)
  6. Be consistent
    Be consistent in which letters you use. For instance, GINAP above uses each capitalized letter when in title case (it skips the prepositions and articles). PRODAN isn’t consistent because “pro” comes from “propionyl.” FlAsH (Fluorescein Arsenical Hairpin binder) is not consistent, but the capitalization indicates that.

OK, what else did I forget? Or what are your favorite acronyms? Does anybody know of a good list of bad scientific acronyms out there? (NMR acronyms don’t count because they’re all bad. COSY. Pffft!)

hot gum!

October 17, 2007 at 4:36 pm | | help me, open thread, science and the public, science@home

Who wants to help me?

Here’s an email my PI received. First of all, it’s pretty cute that some high-school student is emailing professors at Stanford for some help. Secondly, it’s even cuter that the profs actually read the email!


My name is [redacted] and I’m a highschool student who is currently doing an Honors Chemistry project. My idea that I’m experimenting with is that I’m going to try to determine if there is a temperature change or a chemical change that affects the feeling of the mouth when gum is chewed. I was actually doing quite well with my ideas, but now I’m kind of stuck, so I was wondering if somebody in the chemistry department could e-mail me back or possibly help me.

My idea that I was going with is that I wanted to first start out and (using a mouth thermometer) get a starting temperature of a person’s mouth before chewing gum. Then, I wanted to pick a brand of gum in both mint and cinnamon flavors and seperately measure if there is an increasing or decreasing temperature change. My hypothesis is that there will not be a significant change at all, so that’s where the chemistry part comes in. I wanted to then somehow test saliva samples or something with the different chemicals of gum to determine which ingredient creates the “feeling” that the mouth is hot or cold. Except I really have no idea how to go about doing that.

Do you think someone could give me some ideas within the next day or so and let me know/point me in the right direction on how I should go about doing this experiment? That would be amazing, thank you!

My first thought was to look at two flavors of the same brand of gum, find the ingredients that are different, buy those (food-grade) chemicals, and taste them! But most gums just list “natural and artificial flavoring” in the ingredients, so that wouldn’t work. Separating the different ingredients in the gum is a possibility, but probably too difficult.

Another option is to guess the flavors the manufacturers used for cinnamon and mint (an educated guess, but doing some research about flavorings). I bet they use menthol for the mint. I don’t know what they use for the spicy cinnamon, but I know that capsaicin is the chemical that makes chili peppers taste “hot” (by interfering with the pain receptors in your mouth). You could use capsaicin and menthol on saliva samples and measure changes in the temperature or whatever. These would be good estimates of the chemicals they use as flavoring in gum.

Other thoughts? Would there be a very simple way of separating the flavor ingredient without a column or TLC plates? Maybe a paper towel? Or maybe the student could just dissolve the gum in warm water and use the solution of all the ingredients.

But I don’t know what they would measure in the saliva sample (gross!) that could relate to taste.

Alice in Neurologyland

October 15, 2007 at 10:02 am | | literature, science and the public

I came across a delightful article about the neurology of Alice in Wonderland (via boingboing, if you must know). If you’re a fan of Jabberwocky, the article is a fun read.

Mad Hatter’s Tea Party

My favorite quote:

Sadly this hypothesis is not amenable to empirical investigation since Humpty Dumpty apparently suffered irreversible traumatic injuries in falling from a wall, thereby confounding any further assessment.

citizen kane wins the peace prize!

October 12, 2007 at 8:59 am | | news, science and the public

I shouldn’t post twice in the same day, but look, Citizen Kane won the 2007 Nobel Peace Prize:

I’m surprised that Gore won, mostly because his was the only name I actually heard floated.

I can’t believe the Nobel Committee overlooked George Walker Bush for yet another year! How can they ignore the wonderful work he’s done reshaping the Middle East and torturing Germans? Maybe Bush still has a chance for an Ig Nobel Peace Prize, like Teller in 1991.

ACS insider?

October 12, 2007 at 8:36 am | | news, open thread, science community

Did everyone get this email?

Subject: Time to Reform the American Chemical Society
From: Madeleine Jacobs <>
Date: Thu, 11 Oct 2007 17:24:22 -0700 (PDT)
To: [redacted]


I’ve been an ACS employee for many, many years, but I’ve grown concerned with the direction of the organization. I’m sending this email to alert you that ACS has grown increasingly corporate in its structure and focus. Management is much more concerned with getting bonuses and growing their salaries rather than doing what is best for membership. For instance, Madeleine Jacobs is now pulling in almost $1 million in salary and bonuses… That’s almost 3X what Alan Leshner makes over at AAAS, and almost double what Drew Gilpin Faust makes to lead Harvard.

I think Madeleine is smart, but I’m not quite sure if she’s in the same category as Dr. Faust. She doesn’t even have a PhD!

What really concerns me is a move by ACS management to undermine the open-access movement. Rudy Baum has been leading the fight with several humorous editorials—one in which he referred to open-access in the pages of C&EN as “socialized science.” ACS has also spent hundreds of thousands of dollars in membership money to hire a company to lobby against open-access.

What troubles me the most is when ACS management decided to hire Dezenhall Resources to fight open-access. Nature got hold of some internal ACS emails written by Brian Crawford that discussed how Dezenhall could help us undermine open-access. Dezenhall later created a group called Partnership for Research Integrity in Science and Medicine (PRISM), which has this silly argument that open-access means “no more peer-review.”

If you’re wondering why ACS is fighting this, it’s because people like Rudy Baum, Brian Crawford and other ACS managers receive bonuses based on how much money the publishing division generates. Hurt the publishing revenue; you hurt their bonuses.

I’m hoping that sending out this email will get people to force ACS executives to become more transparent in how they act and spend membership money. Not to mention their crazy need for fatter salaries.

It’s time for some change. If you want to check out the sources for this information, there is a wiki site that has all the articles and documents outlining what I’ve just written.

You can find it here:

Those of us inside ACS know that it’s time for things to change. But management won’t alter their behavior. The money is just too good.

ACS Insider

Strange. Did this “ACS insider” send the email to all ACS members?

What do people think about this? I’m not surprised that ACS is working to fight the open-access movement, because it threatens their business (or their business model). Whether it’s appropriate for ACS to spend member fees to fight that fight is a different matter, I suppose.

I do agree that exorbitant pay rates for the top executives is a problem, and an indicator of larger issues within the organization.

All in all, it’s hard for me to care that much: My student membership fees are relatively small and I don’t have to pay for journals (although I know they are expensive for the library). And the ACS conference is well run.

What do other people think?

Let’s Be Fair to Dow

October 9, 2007 at 1:30 pm | | news, science and the public, science community

[Editor’s note: This is a follow-up of a previous post. Apparently, Charles disagrees with me. -Sam]

Let’s be fair to Dow here.

The Bhopal pesticide plant explosion was a horrible incident by all accounts! The disaster caused around 8,000 immediate deaths. 12,000 deaths have been linked to the disaster, and another 100,000 or so people suffer lingering health risks.

To start with, let’s see what Union Carbide has tried to do to rectify the situation:

  1. The day of the explosion (December 4th, 1984), Union Carbide sent material aid and medical experts to Bhopal to assist with treatment.
  2. Carbide donated an immediate $2 million into the Indian Prime Minister’s disaster relief fund within 1 week after the incident (December 11th, 1984).
  3. 3 months after the incident (February 1985), Carbide established the “Employee’s Bhopal Relief Fund” which raised more than $5 million for immediate relief.
  4. 5 months after the incident (April 1985), Carbide paid for Indian medical experts to take part in training of treatment techniques.
  5. Less than 3 years after the incident (August 1987), made an additional $4.6 million for humanitarian relief.
  6. In 1989, Carbide settled with the Indian Government in the Indian court system for $470 million. The settlement was paid in full almost immediately. In the settlement it was agreed that the state government of Madya Pradesh would take full responsibility for the site cleanup.
  7. In April 1992, Carbide sold 50.9% of it’s shares of UCIL (Union Carbide of India Limited – the subsidiary responsible for the incident) to fund a $90 million trust fund for the establishment of a Bhopal hospital treating heart, lung, and eye ailments. As of 2001, when the hospital opened it’s doors, the trust had amounted an estimated $100 million.
  8. In addition, Carbide provided $2.2 million to Arizona State University to establish a vocational-technical training center in Bhopal (which was later closed) and $5 million to the Indian Red Cross.
  9. Carbide developed the “Responsible Care” system with other members of the chemical community to “help prevent such an event [as Bhopal] in the future by improving community awareness, emergency preparedness, and process safety standards.”

So, over the course of the 20 years between the incident and the purchase of Union Carbide by Dow Chemical, Union Carbide had spent almost $600 million towards the cleanup and relief efforts.

Now, let’s compare the 1989 $470 million dollar settlement ($686.2 million in 2007 dollars) against other U.S. settlements by chemical companies:

The largest Superfund site in the U.S. today is the Hudson River, in which over 500 tons of polychlorinated biphenyls (PCBs) have been dumped over the course of 80 years (most by GE in the last 30 years). The estimated cost is $500 million. GE has formed an agreement with the EPA to pay a total of $7.62 million and donate scientists and manpower to the initial sampling and cleanup effort. Unknown population affected over 80 year period. PCB’s have been linked to cancer, although GE denies that there are increased cancer risks in the area.

The 2nd largest settlement in Superfund history, and the largest settlement involving a chemical company, was the Sikes Disposal Pits near Crosby, an illegal toxic waste dump used by a variety of petrochemical companies, which has affected an estimated 10,000 people. 30 chemical companies were sued successfully for an estimated $120 million in cleanup costs.

The Love Canal incident in 1953, which prompted the creation of Superfund, occurred when the Hooker Chemical Company covered area over a toxic dump with dirt and sold it the city of Love Canal for $1 an acre. Numerous houses and a school were built on the site. Unknown numbers of people were affected, but over 221 families were evacuated by 1981. People from the area suffered larger than average rates of birth defects and miscarriages. The government finally sued and won around $129 million for cleanup costs in 1995.

Of course, the scale of the disaster in the Bhopal case makes these other cases pale in comparison. That’s why criminal charges are proceeding against 6 UCIL members (including the former Chairman of UCIL, the Managing Director, the Vice-President Functioning in charge, the Works Manager, and the Production Manager). That’s also why the parent company of Union Carbide paid out so much both to the Indian Government (which it HAS to work through for environmental cleanup) and directly to the victims (around 20% of the money Carbide spent went to medical training, immediate humanitarian aid, and the establishment of hospitals and medical trust funds).

And also, granted, much of the money (specifically the $470 million) did not reach the victims families and was not spent on cleanup, but that’s due to the incompetence and/or corruption of the Indian government. In April 2005, the Indian Supreme Court ruled the government had to release remaining settlement funds to the victims and their families. After taking into account accrued interest, the remaining settlement amount is estimated at $330 million (See NYT article cited below). It is certainly NOT Union Carbide or Dow’s fault that the Indian government and sat on the money instead of using it for cleanup or victims reparations. Remember, part of the $470 million settlement was that the local government be responsible for cleanup (presumably using part of the settlement for cleanup).

Now, Union Carbide can’t take what happened back – I’m sure they would like to if they could. No one wants to be responsible for up to 20,000 deaths. But they can’t, so they spent more on the cleanup efforts than any other single U.S. corporation for a chemical spill or dumping in the short history of corporate environmental responsibility. Not only more, but almost 5 times more (6-7 times more in current dollars).

So where is the justification, legal or moral, for the Indian Government to sue Dow, who was NOT responsible for the incident, for $22 million when they are sitting on $330 million from the initial settlement? Why should Dow pay for the cleanup when Union Carbide already paid for the cleanup as part of it’s 1989 settlement, and paid more than any other single U.S. corporation in history (that I could find) for a chemical spill!

If Dow were to accept any responsibility, it would set a very dangerous precedent. Can you imagine a world where a company is sued by a government and settles: the case is closed. That company is acquired 15 years later. The government now sues the new corporation even though the previous acquisition has already fulfilled its legal and financial obligations. That’s legally and morally irresponsible, especially considering the goverment in question has 70% of the intial settlement still on-hand.

Bhopal Sources:

Wikipedia Article on Bhopal with Citations

Union Carbide Bhopal Information Center

New York Times Article from 2004: “Bhopal Victims Not Fully Paid, Rights Group Says.”

Other Sources:

EPA: Hudson River Superfund Site

EPA: Sikes Disposal Pits Superfund Site

DOJ: Fiscal Year 2001 Accomplishments (Including Sikes Disposal Pits Settlement)

EPA: Love Canal History

DOJ: Press Release on Love Canal Settlement

the inhuman element

October 3, 2007 at 11:03 am | | lab safety, news, science and the public

Is anyone else sick of Dow’s Human Element campaign? I know I’m not the first to note the irony. Dow bought Union Carbide and now refuses to take responsibility for the cleanup and liability of a terrible chemical accident in Bhopal many years earlier.I know that it is a complex issue—legally, politically, and ethically—but Dow is a little disingenuous to claim that they care so much about humankind. If Dow were human-conscious, the problem might become simple: Union Carbide shirked on its responsibility to clean up a disastrous chemical spill; Dow bought Union Carbide; along with the benefits of owning Union Carbide come the responsibility of correcting a financial and moral wrong. Instead, Dow only points out that it didn’t own the plant when the accident occurred. But that ignores that fact that today Dow is still benefiting from Union Carbide’s escaping responsibility.I say that Dow just pay for the cleanup (which other companies are willing to help with). Maybe even pay some liability settlements to the poor people harmed by the spill and contaminated lands. Then Dow can show ads like the following with a clear conscience.

[google -5925107796437659727 nolink]

To learn more, you can read a book by a PhD chemist from Union Carbide: The Black Box of Bhopal. I haven’t read it. I’m nowhere near an expert on this topic. Maybe I’m way off in my opinions: It’s just a gut reaction at this point. Other viewpoints?

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