Friday, November 17, 2017

Why You Probably Don’t Know What Musk Really Smells Like

One of the big dogs of the perfume world is also a powerhouse of confusion. What the hell is musk? Do you know? Are you sure?

First, let’s disambiguate the basics. Musky and Musty are not the same thing. Musky is kind of like an animal smell – warm, sexy, intoxicating. Musty is related to moldy, it’s the smell of a dark hamper. Wet and dark, that’s musty. Thing is, body odor can be both musky AND musty, and this is one of the places where the two get intertwined. We can go on and on with this, because there’s this thing I call ‘river musk,’ which is absolutely intoxicating, to me at least, and is the by-product of stuff that lives in the river. Oceans have it too, but it tends to be mixed with dead fish. It’s a secondary metabolite, a kind of seaweed pheromone, which means it’s very similar to animal musk in that it’s a pheromone/chemosignal, but from plants. And yet, it’s related to wet things.

Parenthetically, body odor is actually not musty, for the most part. Usually it’s your dirty clothes that are musty, because they’ve been sitting in a pile on the floor, dark because they’re balled up, and damp because you just took them off, and your body is warm, and the air around you is less warm, so the water vapor in the air condenses on the clothes…either that or you were sweating just before you took them off. Either way, it’s your clothes that smell musty. That being said, we should also note that your armpits can get musty for the same reasons (it’s pretty dark in there). That isn’t what we call body odor, however.

Okay, so we got that out of the way. Sort of. Now for the anosmia part. Anosmia means you can’t smell something. Half the population is anosmic to something, and there are more people anosmic to musk than most other smells. Musk is a really big molecule, one of the biggest we can smell, and for some reason, bigger molecules tend to be invisible to us, but not in the way other anosmias work. It seems to go in-and-out.

Take the behemoth of the synthetic musks, Iso-E Super, which is so super that a perfume was made with only this as its only ingredient (and for non fragrance enthusiasts, that is totally unheard of). Lots of people can’t smell it. Saskia Wilson-Brown of the Institute for Art and Olfaction gave me a sample. I couldn’t smell it. Then I could. Then I couldn’t again. Anyway, because musk has this problem, or because we have this problem with musk, perfumers tend to use lots of musks in their formulas, to make sure that people will be able to smell at least one of the musks in there.

Next problem – the laundry detergent industry. Musks have this attribute where they do really well in fabrics and with detergents. They hold on for a long time (because they’re so big, as a molecule, among other reasons). They’re all over the world of laundry detergents; just about every laundry detergent smells like musk. But you probably don’t know that. You think that smell is the ‘smell of fresh laundry,’ not that of musk. When I tell people this, they don’t believe me, probably because they would rather not associate the smell of sweaty animal bodies with their freshly-laundered sheets. But alas, there it is: the smell of dirty is now the smell of clean.

What’s worse is that these sheets eventually end up in a dark hamper, and smell musty as well as musky. And so now you’re totally screwed. 

Friday, November 10, 2017

Ambiguity, Approximation and Probability

Logo (the programming language)

Probabilistic programming does in 50 lines of code what used to take thousands

I wanted to put some stuff up here about the state of computer programming, because the way we smell is akin to a special kind of computer program, and one which does not act like the kind we know.

I should start like this – I grew up on Logo, and then NES video games, therefore my experience with, and thinking upon, computer programming is ‘coded’ according to this top-down style. Someone writes the code, and the computer executes the code. There are no surprises (unless you have bugs to fix). You tell the turtle (that’s what they call the cursor in Logo) what to do and it does exactly that. Look at the picture above. That little triangle (the turtle) was told to go 100 spaces, rotate 90 degrees, then go 100 more spaces, etc, until a square is born.

King Koopa was told to jump every time you throw fireballs at him, or whatever he does. There is no fuzzy logic here. Everything is clear, concise, exact, predictable. (Again, that’s when the program runs as intended; surely this kind of programming is unpredictable when it goes wrong.)

Enter a new kind of programming. With the dual advent of big data and big processors to crunch it, we are seeing a different approach. The computing power is now so capable that it is asked to figure out its own program from the data given. This helps with a lot of the problems faced in computing today. With such variety in the data (this is ultimately what big data is about – not lots of quantity, but lots of different qualities) we can no longer write programs equipped to work with such variety. The program required for that ends up being as big as the dataset.

This is where we see the parallels to smells and olfaction. The amount of smells we could potentially be exposed to is infinite and multifarious. Vision has only a few categories. Things can look light or dark, a binary classification, or they can be categorized by their color on the spectrum, which is a discrete classification. They have a shape, a size, maybe a texture category. Odors, however, cannot be organized this way. There are too many and they are too different from eachother. Therefore, olfactory perception is distinct from our other senses. In order for us to create an artificial intelligence that can smell, we would have to come up with a different kind of programming.

Facial recognition provides a good visual analogy to the olfaction problem. What a face looks like isn’t really dependent on its color or its shape, but the combination of these features, the whole. And that makes a lot of initial parameters, in fact, infinite parameters. Face-rec uses these new types of programs, and they are almost the opposite, in every way, of what programming has been. I’ll let this guy describe them:

“When you think about probabilistic programs, you think very intuitively when you're modeling. You don't think mathematically. It's a very different style of modeling.” … “The code can be generic if the learning machinery is powerful enough to learn different strategies for different tasks.”
- Tejas Kulkarni, an MIT graduate student in brain and cognitive sciences,

In the same way that we are not born already knowing every smell we will ever encounter, these programs must ‘learn on the fly.’ This is an advance in computing, but also it foreshadows a very different world, where information is not distinct, discrete, exact, etc. It is instead more like that thing you smell but you don’t know what it is, but you swear you know yet you don’t know…you know what I’m talking about? Doesn’t sound like the kind of output your computer would produce.


[lots of good explaining in this article, so I just copied most of it]

A Grand Unified Theory of Artificial Intelligence

Embracing uncertainty

In probabilistic AI, by contrast, a computer is fed lots of examples of something — like pictures of birds — and is left to infer, on its own, what those examples have in common. This approach works fairly well with concrete concepts like “bird,” but it has trouble with more abstract concepts — for example, flight, a capacity shared by birds, helicopters, kites and superheroes. You could show a probabilistic system lots of pictures of things in flight, but even if it figured out what they all had in common, it would be very likely to misidentify clouds, or the sun, or the antennas on top of buildings as instances of flight. And even flight is a concrete concept compared to, say, “grammar,” or “motherhood.”

As a research tool, Goodman has developed a computer programming language called Church — after the great American logician Alonzo Church — that, like the early AI languages, includes rules of inference. But those rules are probabilistic. Told that the cassowary is a bird, a program written in Church might conclude that cassowaries can probably fly. But if the program was then told that cassowaries can weigh almost 200 pounds, it might revise its initial probability estimate, concluding that, actually, cassowaries probably can’t fly.

“With probabilistic reasoning, you get all that structure for free,” Goodman says. A Church program that has never encountered a flightless bird might, initially, set the probability that any bird can fly at 99.99 percent. But as it learns more about cassowaries — and penguins, and caged and broken-winged robins — it revises its probabilities accordingly. Ultimately, the probabilities represent all the conceptual distinctions that early AI researchers would have had to code by hand. But the system learns those distinctions itself, over time — much the way humans learn new concepts and revise old ones.

Thursday, November 9, 2017

Getting Schooled on Deep Learning

This image was produced by a neural network called the Deep Dream Generator

Despite their great usefulness, deep learning neural nets have been unexplained in terms of how they do what they do.

New discoveries are being made, however, that shed light inside the black box of these networks:

Oct 2017, WIRED

In one case, the researchers used small networks that could be trained to label input data with a 1 or 0 (think “dog” or “no dog”) and gave their 282 neural connections random initial strengths. They then tracked what happened as the networks engaged in deep learning with 3,000 sample input data sets.

This is an example of an experiment using a network of only couple hundred nodes. All the nodes have been tagged and watched to see how they evolve over iterations of the network. In other words the network is given a task, let's say to recognize face in a picture, and it attempts that task over and over.

The special thing about neural networks is that they learn how to do this task better with every iteration. When our brains do this we call it trial-and-error. We learn how to do things by trying over and over again, and hopefully we get better. These networks try over and over and eventually get better at what they're supposed to be doing.

What's happening while they try has been unknown, or we could say that it still is unknown. But experiments like this are helping us to learn more.

This is a good moment to recall that olfaction, or to be more specific – the olfactory bulb – is a biological neural network. The olfactory bulb is the brain of the nose; it is the nexus at which molecules in the air are translated into electrical signals that the brain can recognize as a smell.

The brain is a very large neural network. The olfactory bulb, on the other hand, is a very good model of this neural network phenomenon. It can be teased apart and separated from the rest of the brain very easily because it functions as its own brain.

Before we had a brain – the human part, the cortex, the one that helps to read this text – we had only a nose and the nose-brain. It can be said, in the spirit of metaphor of course, that the olfactory system was the first cortex, it was built on top of the limbic system, and it still connects to the limbic system in its own separate way.

Smell works differently than all the other senses; it has a direct line to the limbic system, which is the command center of the brain. It has a direct line to the White House, in other words...

So as we discover what neural networks are really doing in their hyperconnected webs, let us remember that the olfactory system did it first.

Post Script

Friday, November 3, 2017

Urban Scentsations

Odor investigators engaging in a smell hunt. source

Let’s take a minute to recognize this exceptional olfactory artist, Kate McLean. She works with human perception and the urban smellscape. She basically turns the city into her own little laboratory, running perception experiments on the people there, and coming back with sensory analyses that you just can’t get in an actual lab setting. She does smellwalks, smell sketches, and all kind of other activities to both help people explore and appreciate the most overlooked aspect of their urban environment. As a result of her work, we get these Smellmaps, something not taken up by Google yet…yet. Please check out her site here, and get upset that she already came to your neighborhood, or excited that she didn’t yet!

Research, analysis & design of Sensory Maps by Kate McLean

Thursday, October 26, 2017

Entomology vs Etymology

Personally I like words more than bugs, but I thought it would only be good form to give this guy some play…

Drosophila melanogaster, the lowly fruit fly, is the one creature whose olfactory system is the most extensively studied of any animal. Most of what we know about human olfaction was first studied via the fruit fly. Actually, a lot of what we know about human biology and genetics in general come from this, the most scientifically useful eukaryote there is. Caenorhabditis elegans (C. elegans, the lowly roundworm) is a close second for premier entomological fame, but their olfactory system is too different from ours (and I’m not really sure if worms are insects anyway).

Monday, October 23, 2017

At Your Fingertips

Oct 2017, BBC

"[Your fingerprint] contains molecules from within your body but also molecules that you have just contaminated your fingertips with, so the amount of information there potentially to retrieve is huge."
-Dr Simona Francese of Sheffield Hallam University for the BBC

And this information is now set to be used in courtrooms.

It comes as a surprise to me that this technique is only being used now. We've known since the dawn of the microscope that the labyrinthine ridges of our fingertips are stuffed with bacteria and whatever else in the world we recently touched. We've also been using this mass spectrometer tool since the 1900's, which is also when fingerprinting itself came out.

I’m adding this to the archives here because the mass spectrometer, combined with the gas chromatograph, is the primary tool for detecting odorous molecules. It’s the closest thing to an artificial nose that we have, and it’s the only we to determine with certainty what’s in a smell.

I’ve added below a chart taken from Sigma Aldrich, a supplier of essential oils for the flavor and fragrance industry. It shows the fingerprint, if you will, of the smell of orange.
The smell of orange, as seen in gas chromatograph analysis, courtesy of Sigma Aldrich.

As you can see, the smell of orange has in it way more than just “orange.” In fact, there’s nothing called “orange” in there at all. Limonene and Citronellol might sound like they belong there, but the others are probably foreign to most.

image: Imperial College London site, where you can grow your own fingerprint bacteria on an agar plate 

Friday, October 20, 2017

Chemotaxis vs Infotaxis

Hey, you dropped something. The back of your earring, it’s gotta be somewhere in this shaggy carpet. Hands and knees you search intently in a one foot radius of the spot you think it should be. After some time, your search-space widens, you move over a few feet, and begin again, very concentrated.

This is the foraging pattern. In searching for blackberries, you stop at this bush and look and look and look, and then you go to another bush altogether, and so on. It’s a lot like fractals, and a lot like Antonio Barabasi’s Bursts. The pattern of searching, or foraging, occurs in clusters. And the search-pattern within the clusters is repeated in the larger pattern of the clusters relative to each other.

Taken to its conceptual limit, we observe the common roundworm, neuropop celebrity extraordinaire, C. Elegans. If a worm thinks there is food somewhere, it will perform an intensive search in that local area, until 15 minutes are up, at which time they will literally make less turns, and explore a wider, more global area.

Humans usually rely on vision to search for things. Worms don’t; it’s much more effective for them to follow their nose. In this case, their search is informed by a chemical gradient. As they search for the source of an odor, they notice whether their target scent is getting closer or further. This is the chemical gradient, and it, in a sense, decides for the worm. All the worm needs is a memory big enough to store the last sniff, and compare it against the current one, and it can decide whether to go ahead, or to turn.

In reality, the worm has more than just a one-sniff memory capacity. It is in fact creating a gradient map of all the places it searches, as it searches. The seemingly infinite wonder that is the human memory begins with this basic foundation. And it is for this reason that smell and memory are such an intimate, indivisible pair.

What happens when the worm has no chemical gradient to help it decide? This is where it switches from chemotaxis to infotaxis. And I bring this up simply as an excuse to use the word infotaxis, because I really like it. Also, I was thinking about the future, and the idea of infotax, which, considering the advance of Bitcoin, might not be too far off. And then, there’s info-taxis, like taxi-the-car, which I can’t even imagine what that is or what it will do, but it will probably happen too.

Wednesday, October 18, 2017

Wörter und Sachen

Annoying Orange

Wörter und Sachen means "Words and Things" in German. It refers to a movement in Germany/Austria, in the early 20th century, that insisted we use the etymology of words to study the cultural products named by those words.

It’s also a 1959 book by Ernst Gellner* titled Words and Things: An Examination Of, and an Attack On, Linguistic Philosophy.

The study of the language of smells requires a most astute clarification of the words from the things, which is made most difficult by the fact that smells are the things their words describe. The smell of an orange is an orange. The color of an orange is not. The color of anything is instead white light being reflected off of a surface, the color being the portion of that white spectrum not absorbed into the surface. So the color of a thing is almost like the opposite of the thing.

*Gellner is a personal favorite of mine; I have many posts on my other blog inspired by him or in reference to another work of his, Plough, Sword and Book (1988).

Tuesday, October 17, 2017

Mutation in Media Res

Alex Grey

Neanderthals didn't give us red hair but they certainly changed the way we sleep
Oct 2017,

Just thinking here about the intersection of genes and culture and their effects on our olfactory world.

This article mentions that one of the differences between people with lots of Neanderthal genes (Caucasians and to a lesser extent Asians) and people without so many Neanderthal genes (Africans) is that the Africans have a distaste for pork. I'm not an expert here, please note. But I do recall a variation on a gene that codes for pork, making male boar taste like piss to some folks but sweet to others. There's another one, not related to cavemen (as far as I know), that makes cilantro taste like soap to some people and yet a delicious herb to others.

The fact that these examples even appear in the news is because taste is far more conspicuous than smell (despite the fact that most of what we taste is actually smell). But these examples of varying genes for coding sensory perception are at least a good reminder of the fact that our sense of smell is proof that we are still evolving.

Two percent of our genome is devoted to smell - of our 10,000 genes, 250 are for smelling. The way genes work is complex, and simple arithmetic is no way to measure it, and 2% might not even sound like a lot, but still - these 250 smelling-genes are the largest of all the gene families. What's more, many of these genes have variations, called alleles, like hair varying from black to brown to red to blonde. That means the way something smells to you may differ from that of other people.

While listening to a talk on this stuff given by a smell Nobel, Richard Axel, I discovered that the gene, or genes, that code for some of the aroma compounds in broccoli have variations. That means some people taste the bad part of broccoli more than others, or that some people taste the good part more than others. Bottom line is that broccoli is not the same for everyone. And this goes for lots of things.

As far as we know, there is no allele on the genes that we use for vision. We have three photoreceptors, controlled by 3 genes (again I'm not an expert, maybe it's more complicated than this). We agree on colors, which is to say that we all see the same colors in the same way. This means that we are done evolving in regards to color (yes?). But when you see this many [olfactory] mutations occuring throughout the population, well, it means that we are still in the process of evolving. We aren't growing extra toes, or losing tails, but we are still going through the process.

Back in the day, part of this process involved a Homo Sapien seducing a Neanderthal, and making mutant cross-species babies. Before that, it meant walking on the ground instead of swinging in the trees. Today, I think we would have no idea what is really steering our species in one direction or another, but the fact that we all have such a variety of different smelling-genomes is proof that it's still happening. 


Scents and Sensibility: Representations of the Olfactory World in the Brain
Richard Axel, Columbia University, 2015

Related Links:

Human Evolution in Action

From Network Address:

Milk Does a Body, 2017

FurFuryl Mercapton, Abstract Foods, and Flavor Networks, 2012

Seeing Red, 2013

Wednesday, October 11, 2017

On Dryer Sheets

M.C. Escher's Drawing Hands, lithograph, 1948

Solar-powered self-mowing lawnmowers are the most mind-numbing thing there is, when you think about it.

Second in line is the fact that we have had to build structures to keep the Alaskan gas pipeline from sinking into the  earth due to global warming.

Lastly, 'synthetic musk' is the thing in dryer sheets that makes you want to make love to dryer sheets. (Also called fabric softener.)

Wednesday, October 4, 2017

Darwin’s Children

Voldemort has nothing to do with Charles Darwin, or Greg Bear, but he has no nose.

Darwin’s Children, scifi book by Greg Bear, 2003
Children communicate by using psychoactive chemical scents made from their own bodies. A beautiful twist on the idea that smell is a vestigial organ or perception. At one point, a boy consciously secretes from his own body a mind-controlling scent, wipes it on sheets of paper, crumples them up and throws them at the seat next kidnapping bus-driver, who becomes overtaken by the boy’s vaporous emissions.

Wednesday, September 27, 2017

Hyperosmia and the Elastic Mind

Design and the Elastic Mind, MOMA, 2008. James Auger and Jimmy Loizeau, Design Interactions Dept., Royal College of Art. 

Penicillium Saprophyticus is a kind of mold that comes around in autumn, when the living tissue of the woodlands begins its seasonal decomposition. At the helm of the HMS Entropy are the roaming swarms of saprophytes that live off of dying plants. In small doses their smell can be intoxicating. The haunting smell of crushed leaves in autumn is not without a touch of this mold.

Just as the seasons, weather events bring their own aromatic indicators. The smell when it’s about to snow, river musk on now-dry floodplains after a severe summer flooding, the smell of the beach on the same floodplains after severe hurricane flooding, and plenty of mold during a mismatching of seasonal characteristics – these all announce the ever-changing and rebirthing of an ecosystem. 

Some people smell strongly of civet, some simply have evaporated cat piss all over them, and sometimes it’s hard to tell the difference. Civet, like lots of smells, is good at low doses, but bad when high, and people become desensitized over time. Many perfumes use civet, on purpose, for this reason. Many grandmothers are avoided, for the same. (Blackcurrant buds give off the same smell, and are used in perfumery.)

Furfural mercaptans are strong – coffee, cannabis, skunkpiss. They intermingle, both in molecular presence, and redintegrated perception. In a classroom, one might smell diesel exhaust, barely perceptible, somehow coming through a labyrinth of antiquated air vents.

Then there is the smell of lactose being processed in the body, on a scale from skim milk, through butter, to mozzarella cheese. Poison ivy (which I get every August) smells like something, though I cannot name it – it is the smell of my own body metabolizing urushiol.


Where Science and Design Collide, a Few Weird Sights to Behold
John Schwartz, February 26, 2008, nytimes
ART AND SCIENCE: The show “Design and the Elastic Mind,” at the Museum of Modern Art in New York, features items like “Smell +,” left, whose designer, James Auger, said he wanted to underscore the diminished importance the sense of smell had in our lives by creating a device that allowed people to smell each other’s bodily scents before they met.
Design and the Elastic Mind
Paola Antonelli, MoMA, 2008
James Auger and Jimmy Loizeau
Design Interactions Dept., Royal College of Art, viaMoMA

Saturday, September 23, 2017

The Japanese Aesthetic

 Reading a bit about urban planning lately, and this one comes up a lot:

Around the year 2000, Japan’s Ministry of the Environment decided to establish protection for 100 sites around their country because they smell good. Yup – here in the US, we’re having trouble protecting our own damn water supply, and Japan is thinking about their national smellscape. I’ve read about this more than once now, but an internet search makes it seem like it’s not real.

And I keep coming across the same passage:

…sea mist of Kushiro to the Nanbu rice cracker of Morioka, not to mention the distinct smell of glue that hangs in the air around the doll craftsmen’s homes in Koriyama, all now have protected status...
-seems to have been written by Victoria Henshaw in her book Urban Smellscapes, 2013.

But here’s another one:

…vegetation (‘a hundred thousand peach blossoms at a glance’), food (‘rice cracker of Morioka’), and urban odours (‘streets of used bookstores’)

And since we’re talking about Japan, we can’t forget that really important thing about how smell is regarded differently across cultures. In Japan, and other Eastern countries, fragrance is not something that you wear on your body, but something that is in the environment around you. Maybe, or probably, this has something to do with the fact that the Japanese, and other Asian cultures, have no body odor. If you don’t believe me, you might want to ride the subway in Tokyo during rush hour.

Wednesday, September 20, 2017

Anthropogenic Aroma Compounds

aka Human Body Odor
aka apocrine bromhidrosis, axillary osmidrosis
aka Is that Me [I Smell]?

Body odor network graph

Sweat doesn't smell, per se; what smells is the metabolism of skin flora. These are colonies of bacteria that live on your armpits, but can also be found around the areola, anogenital, and navel regions.

Kids don't smell the same as adults, because the bacteria haven't colonized their bodies yet. Old people, it seems, smell different because they produce a chemical referred to as, simply, "old people smell" (see below: trans-2-Nonenal).

Below are some aroma compounds produced by the human body, via either sweat or urine:

Methyl hexanoate
ethereal, pineapple

Methyl octanoate
citurs-like, fruity, green-like

Methyl nonanoate

Methyl decanoate
oily, fruity, wine-like

all methyl -noates
fatty acid esters; found in human sweat, possibly related to odor preference mate selection; some share the same chemical formula with Propyl hexanoate aka propyl caproate, ethyl heptanoate, butyl pentanoate; scent of propyl hexanoate described as blackberries, pineapple, cheese or wine

4-Hydroxybutanoic acid lactone
caramel; perhaps related to Hydroxybutyric acid (GHB) -
produced as a result of fermentation, and so is found in small quantities in some beers and wines; structurally related to the ketone body beta-hydroxybutyrate, although that is technically a carboxylic acid; perhaps related to diabetes and hangovers

lemon, lime, orange, oily, rose, apple, coconut, grape, grapefruit, melon, peach, meaty, nutty, vegetable-like, waxy; aka Nonanaldehyde, pelargonaldehyde; an alkyl aldehyde; produced by the human body and attracts mosquitos; responsible for the “smell of metal” along w decanal and the main component Oct-1-en-3-one (1-octen-3-one)

ethereal, apple; propanone; active ingredient in nail polish remover and paint thinner; normally present in blood and urine. People with diabetes produce it in larger amounts; it is the ketone produced by the body in the metabolism of fats; produced by the liver whenever the liver has to produce glucose at a very high rate, such as in diabetes

Vanillic acid
chocolate, creamy, grape, nutty, wine-like

4-hydroxy-3-methoxybenzoic acid; a dihydroxybenzoic acid derivative; oxidized form of vanillin; found in the root of Angelica sinensis, and Açaí oil Euterpe oleracea; main natural phenol in argan oil; found in wine and vinegar; main catechins metabolites found in humans after consumption of green tea infusions

Butyric acid
cheese; systematic name butanoic acid; found in milk and as a product of anaerobic fermentation (including in the colon and as body odor); fishing bait additive, component of vomit, used in stink bombs; fermentation of butyric acid is also found as a hexyl ester hexyl butyrate in the oil of Heracleum giganteum (a type of hogweed) and as the octyl ester octyl butyrate in parsnip (Pastinaca sativa)

animal-like, chocolate, honey, vanilla, musty, earthy, butter, cheese, fatty, jasmine, grape, vegetable-like, wine-like; an amine; aromatic heterocyclic organic compound; produced by bacteria as a degradation product of the amino acid tryptophan; occurs naturally in human feces and coal tar; intense fecal odor; flowery smell concentrations; natural jasmine oil contains around 2.5% of indole

Floral; 3-methylindole; belongs to the indole family; occurs naturally in feces (it is produced from tryptophan in the mammalian digestive tract) and coal tar; strong fecal odor; flowery smell in low concentrations; found in orange blossoms, jasmine, and Ziziphus mauritiana; used by U.S. military in its non-lethal weaponry

floral; shrub of genus Jasminum; chemical constituents include methyl anthranilate, indole, benzyl alcohol, linalool, and skatole

Fumaric acid
sour; found in fumitory (Fumaria officinalis), bolete mushrooms (specifically Boletus fomentarius var. pseudo-igniarius), lichen, and Iceland moss; Human skin naturally produces fumaric acid when exposed to sunlight; product of the urea cycle; provides sourness; a Trans-Butenedioic Acid

Lauric acid
fatty; systematically: dodecanoic acid; saturated fatty acid; faint odor of bay oil or soap; as a component of triglycerides, comprises about half of the fatty acid content in coconut oil, laurel oil, and in palm kernel oil; found in human breast milk (6.2% of total fat), cow's milk (2.9%), and goat's milk (3.1%)

Isovaleric acid
animal-like, cheese; a fatty acid; strong pungent cheesy or sweaty smell; major component of the cause of unpleasant foot odor, as it is produced by skin bacteria Staphylococcus epidermidis (which is also present in several strong cheese types) metabolizing leucine; volatile esters have pleasing scents; produced by the oxidation of hop resins in beer, where it is seen as a defect

Phenethyl acetate
balsamic, floral, citrus, fruity, wine-like; Part of the characteristic odor of Camembert cheese, along w biacetyl (buttery flavoring for popcorn), 3-methylbutanal, methional (degradation product of methionine), 1-octen-3-ol and 1-octen-3-one (degradation products of fats), 2-undecanone, decalactone

fatty, waxy; 4-Hydroxynonenal; a,ß-unsaturated hydroxyalkenal; found throughout animal tissues; found in Clitopilus prunulus, commonly known as the miller or the sweetbread mushroom; cucumber odor of this species has been attributed to trans-2-nonenal, which is present at a concentration of 17 µg per gram of crushed tissue; see 2-Nonenal: an unsaturated aldehyde; with human body odor alterations during aging, old-person smell, smell of old books, aged beer and buckwheat

Oleic acid, natural
fatty; a monosaturated fatty acid; occurs naturally in various animal and vegetable fats and oils; monounsaturated omega-9 fatty acid; term related to olive, predominantly composed of oleic acid; makes up 59-75% of pecan oil, 61% of canola oil, 36-67% of peanut oil, 60% of macadamia oil, 20-85% of sunflower oil (the latter in the high oleic variant), 15-20% of grape seed oil, sea buckthorn oil, and sesame oil, and 14% of poppyseed oil; constituting 37 to 56% of chicken and turkey fat and 44 to 47% of lard; most abundant fatty acid in human adipose tissue; emitted by the decaying corpses of a number of insects to signal removal of dead bodies

Trimethylamine solution
oily, fishy, meaty; tertiary amine; strong "fishy" odor in low concentrations and an ammonia-like odor at higher concentrations; Trimethylaminuria is a genetic disorder in which the body is unable to metabolize trimethylamine from food sources, Patients develop a characteristic fish odour of their sweat, urine, and breath after the consumption of choline-rich foods

medicinal; major component in pig odor, human sweat; traditionally extracted from coal tar

trans-3-Methyl-2-hexenoic acid
(TMHA) is an unsaturated short-chain fatty acid that occurs in sweat secreted by the axillary apocrine glands of Caucasians and some Asians.[1]
Hexanoic acids such as TMHA have an hircine odor. Of the fatty acids contributing to Caucasian men's axillary (underarm) odor, TMHA has the most prominent odor.

*Information taken from Sigma Aldrich Flavor and Fragrance Catalog, 2013.
**wiki-scraped description fragments are meant for contextualization/disambiguation only.
***see this chart for visualization of the body odor smell network:  fusiontables

"The Smell of Ammonia in Your Sweat"

When too much nitrogen is present in your system, your body depends on the kidneys to process the excess nitrogen. This process creates urea, which can then be expelled through your urine. However, when there is too much for the kidneys to even process, then the excess nitrogen is secreted as ammonia through your sweat. When you exercise and sweat at a greater rate than normal, enough ammonia escapes for you to actually smell it…(or when your kidneys are under stress, thus processing less, and sending more through as sweat?).

Saturday, September 16, 2017

On Allergies and Sensitization

Writing about smell will get you thing about nuisance odors and about folks who think that smells are making them sick. A lot of this has to do with allergies, and allergies can be a tricky thing. There is no threshold for the amount of a thing that will elicit a reaction, and so allergies tend to be modulated by our own minds, at least to some extent. In other words, if you’re stressed, or if you’re thinking way too much about these allergies and their allergens and the environment where they come from, you may amplify the effects, and you may start sneezing or scratching at the most miniscule of exposures.

The way allergies work in the body is pretty damn confusing. There’s different kinds of allergies, some are hardwired, we might say, and some are ‘learned’ by the body. Some allergies can be deadly, like a shellfish allergy that closes your throat. Some can be just annoying, but won’t kill you or send you to the hospital (unless your body gets so hijacked by your own histamines that you smash your head into a wall).

All this being said, when I came across this short explanation on how allergies work, and I found it to be somewhat comprehendible, I thought I should repeat it here.

Most chemicals and their metabolic products are not sufficiently large enough to be recognized by the immune system as a foreign substance and thus must first combine with an endogenous protein [something that comes from inside the body not outside, endo- vs exo-] to form an antigen (or immunogen). Such a molecule is called a hapten. The hapten-protein complex (antigen) is then capable of eliciting the formation of antibodies. Subsequent exposure to the chemical results in an antingen-antibody interaction, which provokes the typical manifestations of allergy that range in severity from minor skin disturbance to fatal anaphylactic shock.
-Essentials of Toxicology, Casarett and Doull

Got all that? The “allergic reaction” is really an antigen-antibody reaction. It is your body fighting an intruder, and you are the collateral damage.


Please take a look at another post called “The Dangers of Smell and Perfumes in the Workplace” (forthcoming), but it’s based on this article: perfume in the workplace, which is an interesting look inside the work of an HR worker who has to deal with employees complaining about their smelly coworkers, and soothing the hypersensitive worker who thinks their coworker’s perfume is making them sick (it’s not; unfortunately, it’s your own mind doing that). 

Wednesday, September 13, 2017

Olfaction and Mental Health

Image: Ship of Fools, a reference to Michel Foucault's Madness and Civilization

The following article/abstract is quoted here as an introduction to the practice of using olfaction to better understand mental health:

Grete Kjelvik , Hallvard R. Evensmoen , Veronika Brezova , Asta K. Håberg, Journal of Neurophysiology. Published 15 July 2012. Vol. 108, No. 2, 645-657 DOI: 10.1152/jn.01036.2010

Odor identification (OI) tests are increasingly used clinically as biomarkers for Alzheimer's disease and schizophrenia.

ODOR IDENTIFICATION (OI) tests examine an individual's ability to correctly name an odor. In the clinic OI tests have been shown to have high sensitivity and specificity for predicting Alzheimer's disease (AD) at an early stage. This OI deficit is considered a central phenomenon as olfactory threshold, detection, and discrimination abilities are preserved (Arnold et al. 1998; Morgan et al. 1995; Serby et al. 1991; Wilson et al. 2007, 2009). Since AD pathology is first observed in entorhinal cortex and subsequently in the hippocampus (Braak and Braak 1992), OI impairments may arise from medial temporal lobe (MTL) pathology. Indeed, the early and specific OI deficit in AD correlates with the number of tangles in entorhinal cortex and the hippocampus (Wilson et al. 2007), and left hippocampal atrophy (Murphy et al. 2003). Structural changes in the entorhinal cortex and hippocampus are also present in patients with schizophrenia (Baiano et al. 2008; Bogerts et al. 1985; Ebdrup et al. 2010; Schultz et al. 2009; Witthaus et al. 2009), another group of patients with a specific OI deficit (Atanasova et al. 2008; Moberg et al. 1997, 2006; Rupp 2010). The utility of OI tests as a clinical tool depends on a better understanding of the neuronal processes underlying OI, and how OI differs from passive smelling (PS).

This point about smelling mental illness is fantastically queried by the odor author Annick Le Guérer in Scent the Mysterious and Essential Powers of Smell (1992), where she plays with the possibility of the “odor of sanctum” reported to emanate from certain saintly corpses as a result of extensive abnormal mental states which lower, or encumber the metabolic rate, leading to incomplete combustion of aromatic materials in the body. She reciprocates by suggesting such lower metabolism as a result of sustained meditation. Regardless, it is a general understanding that psychosis brings with it an identifiable smell.

Wednesday, September 6, 2017

Avian Navigation

Pigeons were fitted with mini Ticka watch cameras in 1908 by Dr Julius Neubronner to take aerial photos.
Aug 2017, BBC
Researchers from the universities of Oxford, Barcelona and Pisa temporarily removed seabirds' sense of smell before tracking their movements. … They found the birds could navigate normally over land, but appeared to lose their bearings over the sea. … This suggests that they use a map of smells to find their way when there are no visual cues.

Is there ever such thing as an animal that doesn’t use smell to navigate? Or anything for that matter? Humans use smell to “navigate.” We find the nipple by smell. We find mates by smell. (This is one of the few things about “pheromones” that’s unequivocally evidenced – it’s not the pheromones, and besides we don’t have pheromone receptors, but we do tend to like smells from people with compatible immune systems.) I really love how Alexandra Horowitz, in her book Being A Dog, describes the dog actively mapping its environment by its smells. I like how pet detectives find your escaped cat by drizzling your own urine outside your apartment complex so they have a point of familiarity to home-in on. And how could you not love this Florida woman who bottled her own scent so she could be found later as an Alzheimer’s wanderer.

Thursday, August 31, 2017

Olfaction Meets AI

Headline reads like this:

Aug 2017, BBC

And inside:

Nigerian Oshi Agabi’s modem-sized device - dubbed Koniku Kore - could provide the brain for future robots. It is an amalgam of living neurons and silicon, with olfactory capabilities — basically sensors that can detect and recognise smells.

And an explanation:

While computers are better than humans at complex mathematical equations, there are many cognitive functions where the brain is much better: training a computer to recognise smells would require colossal amounts of computational power and energy, for example.

The prototype device shown off at TED - the pictures of which cannot yet be publicly revealed - has partially solved one of the biggest challenges of harnessing biological systems - keeping the neurons alive. "This device can live on a desk and we can keep them alive for a couple of months," Agabi told the BBC.

And what do we think about this?

As much as this story is pretty nuts (if the sentence “They can live on a desk” doesn’t make your head spin…), it’s all too common a story in the tech world. Not that it’s fake news or anything, but let’s just say it is misleading to talk about “smelling robots” in this way.

The less interesting truth is that they can only be trained to smell specific molecules, not even signatures, or combinations, of molecules. A system able to smell “anything that might come up,” and able to use that information for something important, such a system could not be trained. Well, hmmm,  we get trained to do this from birth, in fact we are already learning about our olfactory environment in utero.

So if we want AI to meet olfaction, what we need to do is keep them alive for a lifetime, and give them a body, and friends and a job. You know, just like a real person. They would need to learn from the ground up, just like a real person.

However ---

There is a point being made here by Mr. Agabi that is totally in-line with the thesis of Hidden Scents. The way we use computers today will eventually be supplanted by something else. Traditional computation will still be useful, but something else will take us beyond the capacities of today’s technology (whole lotta talk in the sci-fi sphere of quantum computing, for example).

As of now, neural networks are taking us in a new direction. Granted they were used back in the 80’s, but only recently have they become a marked change in computing technique. (I like to note here the contemporaneous link between the architecture of neural networks and how it is the same thing used to mine bitcoins – the processor is no longer the key component, it’s how many graphics cards you have all wired together.)

The olfactory bulb, the crux of the olfactory system, from an information processing point of view, is a model neural network. And the fact that it’s already connected to the limbic system – the thing that makes us move, the thing that makes our bodies work, and even our emotions – this makes it a model system for so much more.

*Anyone with more comp sci knowledge than me please feel free to correct as I am no expert and speaking in pretty broad, possibly misunderstood, terms.  

Wednesday, August 30, 2017

On Sotolon

Sotolon is also related to fenugreek, and more specifically, fenugreek urine. It can be found in the scent of roasted tobacco and cannabis. If your car smells like maple syrup, you're leaking coolant. If your cannabis-smoking pipe smells like Sotolon, you're running low on cannabis. Vermont, and Canada in general, both smell like Sotolon, but because of maple syrup, not because of a lack of mechanics or lax drug laws.

Esther Ingus-Arkell,, Oct/24/2014

William F. Wooda, Jay A. Brandes, Brian D. Foy, Christopher G. Morgan, Thierry D. Mann, Darvin A. DeShazer. Biochemical Systematics and Ecology. Volume 43, August 2012, Pages 51–53

Post Script:
Only because I mentioned celery and fenugreek (a component of curry) do I list these descriptions.
Celery note: Due to vertofix, a IFF molecule (methyl cedryl ketone) which smells like vetiver/leathery. It can therefore hide as "vetiver" and musky notes in a fragrance notes pyramid.
Curry note: Usually a combination of spices, one of which has to be cumin. It also includes coriander and sometimes "dirty" musks. See L'Autre by Diptyque.
- Taken from Perfume Shrine

Saturday, August 26, 2017

Gene Editing for Behavior Design

Illustrated by Bill Butcher for The Economist

Because ants are social creatures, an ant colony is really a superorganism, making them a valuable model for studying complex biological systems. And because of the way they reproduce, scientists can edit whole colonies in one stroke.

Although ants have 350 odor receptor genes (similar to humans), they also have this thing called a coreceptor gene that every odor gene has to go through to work. Shut that one off, and you shut down the whole system.

And what happens when ants can't smell? They stop talking to other ants, stop doing their job, and they get lost from the group. That's not it though, they also saw changes in brain anatomy, where some sensory substructures didn't grow at all.

Scientists are hoping these studies can help understand how social behavior changes the way neurological disorders like schizophrenia or depression work, and how sensory development in general change the brain.

Now, as I stretch on a heavy tangent here, I think about how there are developers on the other side of candy crush and facebook whose job it is to model your behavior and then tweak it to make you stay using the product. Game theory maybe, the science of addiction perhaps? Behavior design, according to this article (an earlier attempt termed it captology). Not sure what we're calling this, but everything from dating websites to the weather channel are using these techniques to keep us tapping into the pleasure centers of our brains and therefore coming back for more. In a distant future, I wonder if we might want to try knocking out the olfactory receptors in people in order to make them more malleable. If we take away people's sense of smell, maybe they will be more easily influenced to do what we want them to do.

Researchers use CRISPR to manipulate social behavior in ants
Aug 2017,

From two different studies:
Cell, Trible et al: "orco mutagenesis causes loss of antennal lobe glomeruli and impaired social behavior in ants." , DOI: 10.1016/j.cell.2017.07.001

Cell, Yan et al: "An engineered orco mutation produces aberrant social behavior and defective neural development in ants" , DOI: 10.1016/j.cell.2017.06.051

Post Script:
The Scientists Who Make Apps Addictive, Ian Leslie, Nov 2016, The Economist

good explanation of behavior design in computer programming/software development:

When you get to the end of an episode of “House of Cards” on Netflix, the next episode plays automatically unless you tell it to stop. Your motivation is high, because the last episode has left you eager to know what will happen and you are mentally immersed in the world of the show. The level of difficulty is reduced to zero. Actually, less than zero: it is harder to stop than to carry on. Working on the same principle, the British government now “nudges” people into enrolling into workplace pension schemes, by making it the default option rather than presenting it as a choice.

When motivation is high enough, or a task easy enough, people become responsive to triggers such as the vibration of a phone, Facebook’s red dot, the email from the fashion store featuring a time-limited offer on jumpsuits. The trigger, if it is well designed (or “hot”), finds you at exactly the moment you are most eager to take the action. The most important nine words in behaviour design, says Fogg, are, “Put hot triggers in the path of motivated people.”

Unconscious impulses are transformed into social obligations, which compel attention, which is sold for cash.

see also: Addiction by Design, by Natasha Dow Schüll, Princeton 2013

Wednesday, August 23, 2017

On Imprecision

second from the bottom, does it say fake or false?

I like to say that big data is leading us from the Information Age into the Approximation Age. More data doesn't always mean more precision, and although dirty data is a negative term today, I wonder if in some time to come, we may begin to see the value in uncertainty. In fact, regarding autonomous vehicles, this seems to be where we're already headed already.

Here's a little ditty on using imprecision in algorithm development:
“A paper he wrote as a postdoc at Microsoft Research, Escaping From Saddle Points—Online Stochastic Gradient for Tensor Decomposition, describes how a programmer can use the imprecision of a common machine learning algorithm, known as stochastic gradient descent, to his advantage.

[related to unsupervised learning]
“Hopefully we will see more growth in this field, especially interesting results such as this which find that the weaknesses associated with a certain algorithm can actually be strengths under different circumstances.”

Saturday, August 19, 2017

Local Odor Vocab

Curren's SCAQMD Urban Odor Dictionary

You’re looking at a smell network based on the work of UCLA post-grad named Jane Curren. She took all the words used in odor complaints in southern California, and found the source of those complaints. These odor sources can be anything from a hidden garbage dump to a local restaurant. The size of the blue nodes doesn’t indicate smelliness; it indicates more descriptors. Restaurants have more descriptors because they have 1. More people near them and 2. A greater diversity of things that smell. (I’m guessing this.) What this chart does show is the most common odor complaints in the middle of the cluster – we smell burnt things a lot. Also rotten eggs/sulfur/natural gas.

Below, Curren went further and found the specific chemical source of these smells, and I listed them below. Next time you smell something funny, check this list. (And the next time you’re in New Jersey, take a tour of the New Jersey Turnpike mobile museum of olfactory delights, you’ll smell firsthand many of the odors on this list!)

Curren's Urban Odor Lexicon
Descriptor                           Odorant
solvent                                 2-butanone
petroleum                          2-methyl-1-propene
pungent                               2-pentanone
sweet                                   2-pentanone
lemon                                   acetaldehyde
alcohol                                  acetaldehyde
acrid                                      acrolein
pungent                               ammonia
sweet solvent                   benzene
sweet                                   dichloromethane
decayed cabbage             ethyl mercaptan
pungent                               formaldehyde
rotten egg                           hydrogen sulfide
woody                                  m-cresol
resinous                               m-cresol
medical                                                m-cresol
woody                                  o-cresol
resinous                               o-cresol
medical                                                o-cresol
woody                                  p-cresol
resinous                               p-cresol
medical                                                p-cresol
medical                                                phenol
sweet                                   phenol
irritating                               propanal
fruity                                     propanal
empyreumatic                  pyridinec
irritating                               sulfurdioxide
aromatic                              toluenec
fishy                                      trimethylamine
pungent                               trimethylamine
sweet                                   acetone
minty                                    acetone
sweet solvent                   benzene
woody                                  cresol
resinous                               cresol
medicinal                             cresol
sour                                       dimethyl disulfide
onion                                    dimethyl disulfide
decayed cabbage             dimethyl sulfide
decayed cabbage             ethyl mercaptan
garlic                                      ethyl mercaptan
aromatic                              ethylbenzene
pungent                               formaldehyde
rotten eggs                         hydrogen sulfide
skunk                                    i-propyl mercaptan
sour                                       methyl mercaptan
garlic                                      methyl mercaptan
decayed cabbage             methyl mercaptan
skunk                                    n-butyl mercaptan
skunk                                    n-propyl mercaptan
medicinal                             phenol
sweet                                   phenol
irritating                               propanal
sweet                                   p-xylene
sharp                                     thiophene
skunk                                    thiophene
rubber                                  toluene
moth balls                           toluene
aromatic                              1,2,4-trimethylbenzene
aromatic                              1,3,5-trimethylbenzene
vinegar                                 acetic acid
sour                                       acetic acid
chemical                              acetone
sweet                                   acetone
acrid                                      acrolien
pungent                               ammonia
sweet                                   a-pinene
pine                                       a-pinene
sweet solvent                   benzene
malty                                     butanal
burnt                                     butanal
rancid                                    butyric acid
sour                                       butyric acid
perspiration                       butyric acid
fruity                                     butyl acetate
dead body                          cadaverine
disagreeable sweet        carbon disulfide
almond                                 chlorobenzene
sweet                                   chloroform
ethereal                               chloroform
pungent                               crotonaledehyde
gasoline                               decane
ethereal                               dichloromethane
sour                                       dimethyl disulfide
onion                                    dimethyl disulfide
decaying vegetation       dimethyl sulfide
aromatic                              ethylbenzene
oily                                         heptanal
musty                                   heptanal
woody                                  heptanal
fatty                                      hexanal
green                                    hexanal
rotten egg                           hydrogen sulfide
sharp                                     isopropyl benzene
aromatic                              isopropyl benzene
sharp                                     cumene
aromatic                              cumene
lemon                                   limonene
decayed cabbage             methyl mercaptan
moth balls                           naphthalene
tar                                          naphthalene
sweet                                   m-xylene
gasoline                               octane
sweet                                   o-xylene
pungent                               pentanal
sharp                                     propanal
vinegar                                 propanoic acid
sour                                       propanoic acid
sweet                                   p-xylene
solvent                                 styrene
rubber                                  styrene
sweet                                   tetrachloroethene
rubber                                  toluene
moth balls                           toluene
sweet                                   tricholoroethane
fishy                                      trimethylamine
fecal                                      valeric acid
sour                                       valeric acid
sweet                                   vinyl acetate

Suffet and Rosenfeld's Urban Odor Lexicon
*much of Curren’s work came from Suffet and Rosenfeld, so I added their leftover terms here

Descriptor                           Odorant
Coffee                                  Furfruryl Thiopropionate
earthy                                   Geosmin
musty                                   2-Methyl isoborneol
moldy                                   2,4,6-Trichloroanisole
grassy                                   Cis-3-hexen-1-ol
dead animal                       Putresine
rotten vegetable              Dimethyl Trisulfide
fishy                                      Dimethyl Amine
fishy                                      Methyl Amine
plastic                                   Methyl Methacrylate
fecal                                      Indole
manure                                  Skatole
burnt                                     Guiaicol

Primary document: Curren, J. 2012. Characterization of Odor Nuisance. UCLA.

Supporting document: Suffet, I.H., and P.E. Rosenfeld (2007). The Anatomy of Odour Wheels for Odors of Drinking Water, Wastewater, Compost and the Urban Environment, Water Science and Technology 55(5), 335-344.

Research note: The descriptor names come from the above source and supporting documents, whereas the odor causing compounds were matched against varying sources which will not be listed here; see instead the source document for those references