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