7/19/2007

Because Organic Chemistry Doesn't Smell Bad Enough

Someone published an Org. Lett. paper on analyzing rotting fish guts. Yeah.

So let's say you're a hungry shark. You want some fish, and you want to make sure it's delicious and fresh and whatnot. How does a hungry shark go about quantifying the following analysis?


I mean, to a shark, it's all good, probably. Dead and rotting? Dory? A hungry shark will eat them all. But those rotting fishies can have some nasty toxic amines in them like putrescine or histamine that can accumulate before you can smell them. So what's a shark to do?

Basically, nothing. The shark's totally fucked in this case.* ** But lucky for us humans, a new technique for detecting nasty amines has been developed using some functionalized polythiophenes. Using a polythiophene that has been functionalized with a carboxylic acid, the Lavigne group has shown in the latest Org. Lett. ASAP that the UV/Vis absorbance profiles of poly(thiophene)s changes when amines form aggregrates with them.

Since every amine is a little different either in size, binding character, or both, the poly(thiophene) aggregates that form will vary from amine to amine. In other words, one amine will aggregate poly(thiophene) such that the polymer molecules are closer to one another, while another amine will space them out more. This "multidimensional response," as the authors call it, changes the solution absorbance profile of the polymer, which can be qualified for each amine. After testing the profiles of different amines, they did a blind test with 97% accuracy, regardless of the complexity of the matrix.


But the best part of the paper was the "proof of concept," or, as I like to call it, "the PI suckered some poor grad student to blend rotting fish guts with trichloroacetic acid." Seriously. They took "fish matrix," which was canned tuna doped with a known amount of histamine (a common biogenic amine found in rotten tuna). They blended it in trichloroacetic acid, centrifuged and added the polymer, then measured the absorbance. Then they repeated it, over and over again. (And you thought you had to do shitty work for your PhD.) Turns out their little polymer makes for a pretty handy amine detector, able to quantify the amount of histamine in your rotten tuna.

It's not without its limitations (what if you have more than one amine? you're screwed; it'd be nice if you could just make a freshness sticker like they do with other meats), but still a neat idea that utilizes familiar chemistry in a really freaking stinky way. Someone give that fish guts guy/gal a medal.

*EDIT: Or not.

**Okay, more relevant example that'll appeal to the retro gaming crowd. Let's say you're playing Final Fantasy III (VI in Japan or if you're a prick) and the world just ended. And you're Celes, and you just woke up a year later on an island with Cid, who's basically your adopted father. And he's really sick after taking care of you for so long. You have to get fish for him to eat, but if he eats bad fish, he gets worse and dies and Celes attempts suicide (depressing!). What do you do? WHAT DO YOU DO? (The real answer is just catch the fast fish, but what if you couldn't tell?)

15 comments:

Mitch said...

Would histamine really be bad for sharks? It is a common enough metabolite, I would assume a shark's gut wouldn't have a problem with it.

Mitch

Excimer said...

I don't really know what's good and bad for sharks. I tried anthropomorphizing our theoretical shark enough to the point where the shark is... human society? I imagine that sharks prefer live fish over dead fish and so large quantities of amines that build up after fish death might be toxic. Dammit mitch, I'm a doctor, not a... fish... doctor... (where are the biologists when you need them?)

msg said...

Sharks eat anything. I once saw one eat a person

mevans said...

Man, the FF6 reference...you guys just proved your blogitude superiority...

mevans said...

That whole sequence was uncharacteristically boring for that game though, I must say.

Ashutosh said...

are you implying that a hungry shark would have no way to distinguish between healthy fish and fish that could potentially be toxic for it? i find that a little surprising to say the least...i think it would be worth checking out, because animals usually can make out good food from bad.

Excimer said...

sharks have pretty good noses, but most sharks i know don't have UV/Vis equipment. The paper claims that the detection is more sensitive than mammalian olfactory senses, but says nothing about sharks. I'm not really implying that sharks don't have any way to detect bad food from good. I'm really more implying that trying to be cute has no effect on chemists. Don't worry, it won't happen again. :-\

taitauwai said...

Why did you put Dory? Where's Nemo? You don't like Nemo? :<

Ψ*Ψ said...

Maybe the best thing about being in the lab here away from happy-carbon-land is that I haven't smelled any amines. That'll change as soon as I get back home and get to Sonogashira something to death. Yay! (Not yay for amines, though. Ick.)

Excimer said...

Whatever, triethylamine doesn't smell THAT bad. Diethylamine, the alkyldiamines and (my least favorite) pyridine are way, way worse. I can at last have triethylamine on my bench without gagging.

T, I like Nemo... I just couldn't find a good pic of him. And I loved Dory. Wait, that's a whale! I speak whale!

I wish there was more love for the FF6 reference. Come on, there HAVE to be more chemistry/RPG nerds out there. Come out, come out wherever you are...

Ψ*Ψ said...

Yes, yes, outed. I'm a Final fiend too, I just never got around to playing that one.
Part of me likes the Zelda games more anyway.

Chemgeek said...

I bought my kids two goldfish. They named them Dory and Nemo (of course). Dory killed Nemo. We flushed Nemo.

It's still a sad memory in our house.

bad wolf said...

I would not have made it through grad school without FFX/X-2. I had to delay my progress in XII to work on my thesis.

The frequency of references to FF in my thesis defense hopefully went largely unnoticed.

cow_2001 said...

Bad wolf, what kind of references?

Mevans, I thought that sequence was very good cinematics. I loved it. Made my eyes watery.

milkshake said...

Excimer, even though NEt3 is not that bad and many secondary amines (pyrrolidine for you, perverts!) are worse, there are are some tertiaty amines that are realy bad. N-methyl morpholine stinks like spoiled canned fish whereas trimethyl amine smells exactly like the unwashed Private Ryan, big time.

At the previous company we were scaling up a clinical candidate and unfortunately the phenols there were protected as methoxy groups and all material was pushed through with methoxys before we realized that it was very hard to purify the final product to 98%+ because of the impurities generated during phenol deprotection. So I spent a lot of time on finding a less messy deprotection method - and one of the good reagents to do that was a liquid complex of NMe3.HCl and AlCl3. The problem is that the hydrochloride ot trimethylamine is very hygroscopic and has a faint stink of the parent amine that tends to soak into things. It is very easy to spill a little around balances when working with the stuff on large scale, after some time you even won't smel it - but other people still do.