Thursday, October 25, 2018

Eau De Coli

I should begin by pointing out that I am not a perfumer. Actually I should begin by pointing out that there is such a thing as bacteria art, also called agar art, as seen above. Let me start again – I am not a perfumer; I am a writer interested in the language of smells. Obviously, perfume is a big part of that. But when I learn that bacteria are used to make perfumes it comes as a surprise to me, and I feel like I missed something. (And when I had been an art teacher for over ten years and I realize there’s such a thing as bacteria art, I also feel like I missed something, except for the fact that I only discovered radiation art a month ago.)

Apparently, fragrance experts are also a bit surprised. Engineering microorganisms to make specific odorous chemicals are a new addition to the typical methods of expression, steam distillation, and solvent extraction.

 It all started with a project done by a scientist named Reshma Shetty and a team at MIT. I'm almost as excited about the name as I am the project - it was called Eau De Coli, after the dignified Escherichia coli.  And it can be translated as "water of the colon."

E. coli isn't just for making you sick, or for making Chipotle go Chapter 11, it's also for scientists trying to research bacteria. E. coli is the model organism for scientific study, probably because of the compendium of literature already amassed due to its dangerous nature, and maybe just because it's easy to work with.

Regardless, dissertation-defending Shetty and her group engineered this archetypal organism to be a smell-generating machine. Usually E. coli smells like crap, literally, so they first had to find a mutant strain that had no genetic propensity for producing that smell. (This smell comes from the molecule Indole, by the way, and is related to Skatole, which doesn't sound like "skat" by accident.)

The next part was right out of a science fiction novel. They found enzymes that would produce the smells of wintergreen (methyl salicylate) and banana (isoamyl acetate), and they programmed the bacteria to produce those chemicals. So now, instead of smelling like crap, they smell like mint and bananas!

This is called odor engineering - a kind of genetic engineering that is used to make odor chemicals from bacteria. The researcher here, Dr. Shetty, suggests using this technique to probe bacteria at an industrial scale. Imagine you engineer the bacteria in your business to produce different smells at different stages in its metabolism. You could then tell what the bacteria are doing just by sniffing them.

Then there's others who are simply coaxing bacteria to produce otherwise difficult fragrance chemicals. Folks at the Joint BioEnergy Institute at Lawrence Berkeley Labs were originally trying to get bacteria to make biofuels. But after they accidentally discovered a way to make methyl ketones, the fragrance industry perked up.

Combining genetic-metabolic engineering and fragrance production may be a breakthrough for the industry. Now if only we could find a way to engineer ourselves not to secrete isovaleric acid from the soles of our feet!


Dr. Shetty's genetic odor engineering Eau de Coli project:
Shetty, R. P. Applying Engineering Principles to the Design and Construction of Transcriptional Devices. Department of Biological Engineering, MIT (2008).

Lawrence Berkeley Labs bioengineering efforts:
From Petri Dish to Perfume, Berkeley Science Review

Post Script:

While I research odor engineering, I find some things that fall well outside the realm of fragrance.

Odor Science & Engineering, Inc. will research environments that stink and develop products that don't. Instead of using bacteria, they rely on good ol' nose megaphones (see below, a screenshot from their site.)


Here's some of the odor-absent products they have helped to develop:
High performance athletic wear
Hunting clothing
Cat litter
Trash bags
Room deodorizers
Shoe/Sneaker deodorizers

Post Post Script

Just when you let your guard down, the internet provides you with Bacteria Art, aka Agar Art. Yup.

Bacteria Art

Bacteria Art
Check out this entire gallery of bacteria art.

Monday, October 15, 2018

Motherlode of All Microbiomes


With microbiomes being the new big thing, it’s no surprise that a specimen of chunky sewer grease is now decomposing live for our viewing pleasure.

We have all heard of the fatbergs plaguing London. They’re an agglomeration of fat and baby wipes, congealed into a monster the size of an entire sewer drain (one was bigger than a 747). The first one to be discovered became an instant celebrity, and was subsequently added to the dictionary within a couple years. Presently, a small portion of it enjoys a place in the Museum of London where we can all watch it decompose into perpetuity

This fatberg is only a small fragment of the kind found in London's underground (the other underground).

It’s pretty gross to have a lump of human feces and spit toothpaste placed on a pedestal in public view. Not only is it gross, but it’s a health hazard. The lump was quarantined for months. It grew mold, it hatched flies, and then it was contained in a triple-thick glass case and put on display.

Being gross and dangerous also makes it intriguing. After its debut, it became a sort of icon, the subject of plays and poems. Apparently there’s a fragrance artist on the loose making fatbergs representing different neighborhoods but I can’t find any further mention of this.

Needless to say, we can’t smell the thing. During the process, it was said to transform from its raw, unbridled state of pungent effluence to a milder olfactory incarnation as a damp basement. Anything more is left to our imaginations.

It now sits as part of the permanent collection; livestream from quarantine.

Image source - Getty

Aug 2018, Ars Technica

Here is the lab analysis report for the fatberg. They give a list of fatty acids, metals, and fecal indicators. Most of the sample was made of unsaturated fats from cooking oils. The report also gives you a rudimentary understanding about how fatbergs may accumulate (make sure to brush up on your Saponification lessons first).

Post Script:
Scopophilia or scoptophilia (from Ancient Greek: skopeo, "look to, examine"), is when we get pleasure from looking at something. 

And of course it's evil twin, Scopophobia, the fear of being looked at.

Thursday, October 11, 2018

Be a Bad Beer Expert


Today we're talking about beer taints. Yup, beer taints. Sure this has to do with flavor* but right in the middle of my poking-around for info on the "smell of rain," I seduced by this lexicon of bad beer problems that you can buy to help you make better beer, and just to be a better beer drinker in general. (If I can recognize more of the features of the beer I'm drinking, does that make me a better beer drinker?)

Another term synonymous with beer taint is staling compounds, or simply "off-flavors." Regardless, oxidization is the culprit. In fact, oxygen messes up lots of things, like apples, avocados, and even your body. (You know the old joke of how "Scumbag Oxygen" is required for you to live, yet kills you slowly.)

In beer, oxidization can happen for all kinds of reasons, from air trapped in the head space before putting the cap on, to how long it's been in the bottle, to the storage conditions.

The bottom line is, we want beer to taste good, so if you're making it, we want you to know how to recognize the bad stuff. That's where the test kits come in.

It seems like the concept isn't too old, starting maybe circa 1995 by a gentleman named Dr Bill Simpson working at the Brewing Research Foundation in England.

I'm getting all this at the AROXA site. They make flavor standards and sensory software for beverages. And for beer taints.

I'm taking the following lexicon from their beer taint kit. However, I'm adding some descriptions from a few things I found elsewhere; these extras are separated by a semicolon. And I'm doing this because sensory lexicons are great. This one doesn't have any common names (except for Geosmin), but we'll have something to say about that below.

AROXA (etc) Beer Taint Kit:

“Chlorophenol, like antiseptic mouthwash”

“geosmin, like sugar beets or damp soil”

“Earthy, like green pepper"

“Earthy, like potato skins or dug soil”

"Catty, like blackcurrant juice or tom cat urine"; 2,5-dimethylpyrazine - catty, tomato plant

“Earthy, mouldy, like peat or compost”

sodium bicarbonate
“Alkaline, like caustic or detergent”

"Musty, like corked wine with a rubbery overtone”

“Musty, like corked wine or a damp cellar”

"papery" at the threshold concentration, "cucumbery and green-malty" at twice that value, and "fatty and leathery" at three times the threshold value; I'm adding this although it's not on the AROXA list, because it shows how different concentrations affect perception.

"moldy, earthy, tobacco-like;" and this one because it is an oxidized form of humulene.

Dr. Morten Meilgaard’s Beer Flavor Wheel, 1970s

AROXA has all kinds of flavor standards; I'm only copying the ones for bad beer.

FlavorActiv is another name I should mention, being that they declare themselves the global beverage industry standard for sensory needs since 1996, and have something to do with AROXA.

They make reference standards as well, and have a lexicon of 57 flavors.

And finally, I have to add my favorite word found on this topic - Lightstruck! It's another word for "skunked."

 *Let's not forget, however, that most of what we taste is smell. If it's not from the sweet-salty-bitter-etc profile, it's smell we're talking about. But we'll let this slide.

Post Script
Other important entities in the beverage industry:

Camden BRI - providing practical scientific, technical, regulatory and information support (also selling a beer taint recognition kit)

Siebel Institute of Technology - in the North American yeast-brewing business since 1872 providing all kinds of services (also have sensory training kits)

Here's a book about all this:
MJ Saxby, 1996

And you can't talk about beer without mentioning coffee:

(Yet I leave out all the wine stuff for another day!)