Showing posts with label lingua anosmia. Show all posts
Showing posts with label lingua anosmia. Show all posts

Thursday, October 14, 2021

Neuromorphic Odor Translator Helps Robots Express Their Feelings


Neural network trained to properly name organic molecules
Aug 2021, phys.org

Do you ever have a problem naming that smell? It's not just you. Science has this problem too, but maybe not for long. 

Smells are volatile organic compounds that have evaporated and entered your nose. Although they almost always occur in combination with others and not in isolation, us humans want to reduce smells to their individual components, and then name them. After all, in order to think about something, you have to know it's name. (Is that true?) 

The problem is that organic molecules are big, with lots of chemicals joined together in lots of ways, so coming up with a naming convention for all these permutations is hard. IUPAC, the International Union of Pure and Applied Chemistry, sets the convention for naming molecules. And boy is it complicated.

Take sugar, a common molecule known to us by its simple name "sucrose;" in IUPAC, it's called (2R,3R,4S,5S,6R)-2-[(2S,3S,4S, 5R)-3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol.

Since we do live in the computer age, folks want to automate this naming process for when they discover new molecules. But as you can imagine by looking at the IUPAC name for sucrose, the algorithm at the core of that naming convention is really hard to write. So they decided to use a neural network instead.*

*I'm casually calling a neural network "neuromorphic," but in the past few years, real neuromorphic computers have forced a distinction here that I'm ignoring here for the sake of a more clickable title. 

This new artificially intelligent chemical translator is not a magical structure-to-name translator that can just look at a chemical and give it a name; that's still out of reach. It does, however, translate between IUPAC and another naming convention called SMILES.

Trained on PubChem's 100 million molecules, this translator ultimately shows how the utility of the new approach of using neural networks to help us write algorithms from the bottom up instead of the top down, which really is a revolution in computing. 

And if you think it would be cool to have robots that can smell, or to ensure that future humans maintain their sense of smell as they evolve into hyperdimensional algorithms, then making odors machine-readable is how you do that.

via Skolkovo Institute of Science and Technology, Lomonosov Moscow State University and start-up Syntelly: Lev Krasnov et al, Transformer-based artificial neural networks for the conversion between chemical notations, Scientific Reports (2021). DOI: 10.1038/s41598-021-94082-y

Thursday, April 23, 2020

Normosmia Has No Name



I have really met my match. In the world of smell, where language is a game more than a utility, there is one group of researchers who have finally said f*** it. They took all the words out, smashed all the molecules together, presented a bunch of people with their sniff panel, and recorded the responses. (This study is from 2013, but still worth writing about, since this is pretty important point in smell science.)

And it worked. They found that we don't smell molecules; we smell mixtures of molecules. In their words: "The algorithm that worked best was one that treats the odor-mixture as a single value, rather than a bunch of values reflecting each of its components."

They also found that "Pleasantness is the primary odor dimension in human olfactory perception," but we already knew that.

The Study
They use mixtures of 1 to 43 different components, making each 191 mixture-pairs in total, each having 1433 physiochemical descriptors (via the Dragon dataset), and gave them to 48 people.

The Findings: Pairwise Distance Model for Predicting Odorant-Mixture Similarity
They pit the molecular mixtures against each other and have people rate their similarity.
Again, "We found that the mean pairwise Euclidean distance over all the descriptors of all mono-molecular components comprising any two mixtures was a poor predictor of perceptual similarity between the two mixtures." But it gets even better, because apparently they're saying that the weak predicting capacity is because the data is screwed up by the monomolecules' comparisons to themselves! Maybe I'm wrong here, but I think they're saying  people gave different ratings for the same pairs of molecules at different times in the test, and those ratings changed so much from time to time, that they make the model no good.

The Findings: Angle Distance Model for Predicting Odorant-Mixture Similarity
This is the meat of the study. They came up with a statistical regime to turn the odor mixtures into a perceptual whole, that way it could be manipulated as if they it was an individual odor.

Just about every smell-science experiment like this will use odors that have been very carefully isolated – single molecules with single names (let's not kid anyone here, any particular molecule can have a dozen different names, from the local vernacular to the formalized IUPAC designation). The point is that molecules are typically isolated. Because science likes that. Lumping molecules together is messy. But that's also how we interface odors in the real world.

So they made this study more like the real world. They take all the physiochemical components of each molecule, add them together, and divide by the norm. That makes the mixture-odor as if it were a single odor, with a single vector (a single point in multi-dimensional odor-space). And this was the model that worked.

If you take its higher logical plateau, you end up with Olfactory White, one of the most mindbending osmological facts you'll ever comprehend: if you add enough molecules together, it doesn't make "brown paint" like colors do, it makes the mixture smell like nothing. Sure enough, these researchers found that the more components you add to the mixture, the closer the mixture gets to every other mixture (approaching 30 components).

A very important note here is that these odor mixtures were made to be all the same intensity. (This was done in the Olfactory White study as well.) Odors can have very different perceived intensities, and it's more than unlikely that this would ever happen in the wild. I can't help but get into some quick industrial hygiene here: the odor detection threshold for Ammonia is 50ppm; Acetone 100ppm, Trimethyl Amine (rotten fish) 0.0002ppm, Hydrogen Sulfide (rotten eggs) 0.005ppm.

Another extension of this study is maybe not so logical, but certainly an important point in smell science: we can't identify individual components of a mixture of only 4 components. You think you know what peanut butter smells like. And pineapples, and cinnamon. But if you add one more thing to that mixture, they all fall away, losing their identify on your great epithelial equalizer.

Conclusion
"The olfactory system treats odorant-mixtures as unitary synthetic objects, and not as an analytical combination of components."

Limitations
Being that they have three clear limitations, they should be included here:

1. The mixtures were intensity-normalized. This is not natural, because perceived odor-intensity changes drastically across odors. See mention above.

2. The odorants represent only a limited portion of olfactory perceptual space (not much we can do about that, since it's kind of infinite).

3. Many physicochemical features such as boiling point or vapor pressure remain unrepresented (they narrowed down the features from ~4,000 to 25).

Post Script
If you don’t know what the word steganography means, you do know: camouflage. Think about it – you don’t like broccoli? Blend it with enough other smells and you won’t even notice!

Olfactory White also its own name, and it’s called Laurax.

Notes
Semantic free approach to structure-odor prediction, general perceptual primaries rather than individual odorant primaries:
Predicting odor perceptual similarity from odor structure.
Snitz K, Yablonka A, Weiss T, Frumin I, Khan RM, Sobel N
PLoS Comput Biol. 2013; 9(9):e1003184.

Olfactory White:
Weiss T, Snitz K, Yablonka A, Khan RM, Gafsou D, et al. (2012) Perceptual convergence of multi-component mixtures in olfaction implies an olfactory white. Proc Natl Acad Sci USA 109: 19959–19964.

Odor Thresholds:
Gregory Leonardos , David Kendall & Nancy Barnard (1969) Odor Threshold Determinations of 53 Odorant Chemicals, Journal of the Air Pollution Control Association, 19:2, 91-95, DOI: 10.1080/00022470.1969.10466465

Wednesday, October 16, 2019

The Stink Bug



Descriptively-named, yet elusive in the description of its most striking feature, the Stink Bug has been invading America for a few decades. In New Jersey specifically, it was a good summer for stink bugs (or a bad summer for humans).

The stink bug is like a skunk but in bug form. I guess a skunk would be called a "stink rat" if it was also an invasive species. The bugs are a bit less problematic; they can only squirt 3 inches not 3 feet. Thing is, skunks don't get into your house. The bugs do, especially as winter nears and cold weather sends them seeking shelter inside your walls etc. In Spring, they reappear, this time trying to get back outside.

They don't bite, but they smell. But they only smell if they're threatened. Or if you squish them, releasing their obnoxious defense secretion. And what does that secretion smell like?


I'm paranoid, but for smells. When it comes to my own house, my place of work, or anywhere I have to spend a lot of time, I am constantly, actively smelling my surroundings. Noticing, investigating, researching, remembering. It started with a moldly basement apartment, but now I am hyper-aware of the entirety of my osmic environment.

Hype-aware, that is, except for the things I can't smell. I'm anosmic to putrescene (can't smell semen). You're anosmic to something too, probably. It's common. I once did an "experiment" in my workplace where I had an old smelly tube of paint; it smelled like rotten fish. Some of my coworkers couldn't smell it, and I thought it was strange, so I passed it around to everyone, about thirty people. Three of those people, the ones who didn't jerk their head away after sniffing, they were anosmic to trimethylamine, the smell of rotten fish.

What's more interesting is that one of those people was 50 years old, and he had no idea that he couldn't smell rotten fish. A whole life of smelling, and yet totally unaware of something like that. Around the same time I met a young man who was totally anosmic; he can't smell anything at all. He didn't realize it until he was ten years old, while playing a board game called P.U. The Guessing Game of Smells.


Back to stink bugs. I hear a lot about stink bugs, and being an odor aficionado, I find it hard to believe that I don't "know" what they smell like. (Granted I could settle this by ruthlessly smashing the next one I see, but I'm also so sensitive to smells that the thought of potentially dosing myself just sounds stupid.)

I ask people, lots of people, and you know what they say? They all say the exact same thing, "I don't know...it just smells bad."

I do some superficial searches: For a bug called the Stink Bug, you think there would be more descriptions of its stench. I need to contact an exterminator and ask them. Meanwhile, the best and really the only description is this list of slightly-related descriptors:

Pungent onions
Skunk odor
Strong herbs and spices
Intense-smelling herbs and spices
Rotten cilantro and coriander
Smelly garbage
The odor from the stink bug is due to trans-2-decenal and trans-2-octenal. The smell has been characterized as a "pungent odor that smells like coriander."
-Henderson 2006 below

trans-2-decenal descriptions from The Good Scents Company:
waxy, fatty, earthy, coriander, green, mushroom, sweet aldehydic with a chicken and pork fat nuance, diffusive orange odor with floral, rosey topnotes, citrus peel, citrus flavors especially orange and grapefruit, fruit flavors especially tropical, fried taste somewhat citrusy in dilution

trans-2-octenal descriptions from The Good Scents Company:
fresh, pungent, cucumber, spicy cucumber, green, leafy, herbal, vegetable, banana, waxy, oily, fatty, brothy, sweet, citrus peel, citrus especially orange, fatty notes of nuts especially hazelnut

Image sources:
Stink Bug Side View (pinterest = no copyright protection, good thing for watermarks? PBS)

Notes:
Brown Marmorated Stink Bug - Halyomorpha halys
Green Stink Bug - Acrosternum hilare

Oct 2019, NJ.com


Detecting Stink Bugs/Damage in Cotton Utilizing a Portable Electronic Nose. Henderson, Will; Khalilian, Ahmad; Han, Young (July 9–12, 2006). Oregon Convention Center; Portland, Oregon: Clemson University. [PDF]

Post Script:
The stink bug is an invasive species in the United States. All the invasive species, plants or insects or whatever, seem to be from Asia. I think the real question here is this -- Do they have "invasive species" in Asia? Are our insects invasive to them? And how come I've never heard anyone ask this before?

Post Post Script:
By the way, the stink bug's natural predator? Samurai wasp.

Wednesday, January 18, 2017

The First Rule of Fragrance is You Do Not Talk About Fragrance

Ladies Love Cool James

Seriously though, it has recently come to the attention of researchers that the very concept of word-of-mouth is inactive in the global community of female fragrance wearers. Women do not buy fragrance for other women and they don't tell other women what fragrance they wear. And for good reason.

Like any accessory worn on the body, fragrance forms part of a personal identity. But a scented accessory is different, and for many reasons. It's invisible, it's silent. Unlike a piece of jewelry which may go in and out of fashion, looking garish one day and played-out the next, people tend to stick with a trusty fragrance for a long time. This is not to say that fragrance is unperturbed by the whims of fashion, but that people tend to form strong emotional associations with their chosen scent, and such relationships die hard.

It goes deeper than that, however. Scent is a secret weapon in the war of sexual selection. The power of this weapon is immediately halved by the number of others who smell the same as you; keeping your armory secret is the first rule of fragrance. A coauthor of the above-mentioned study reports another finding: "When they dislike a scent, they won't purchase it for themselves or their boyfriend, but they will buy it for a female friend.”

I stopped by the by Kilian boutique in New York City . One of his signature components is the packaging of his juices. And not just the bottles, but the elegant lacquered cases in which they are meant to be stored. The well-informed gentleman handing me samples of olfactory art retells the centuries-gone practice of storing one’s valuable perfume in a locked box, to keep curious children and suspicious maidservants from pilfering.

Centuries later, not much has changed - people still want to keep their scents personal. Ironically, as my vendeur éclairé points out, fragrances technically smell different from person to person due to the chemical breakdown that occurs between the ingredients and the individual’s sweat composition, and so there is no need to be so secretive. Nonetheless, we are. And in the quest to learn the Language of Smell, this is added as another reason for the silent sense to stay in the shadows.



Friday, July 22, 2016

Disambiguator Supreme

 aka Common Misperceptions in the World of Smell


Polymathic artist/scientist Elena Vosnaki keeps a very different kind of perfume site. It focuses as much on the raw materials of fragrance and their omnicategorical contexts as much as the fragrances themselves.

Vosnaki authored one post in particular that is so informative to the curious nose that I wish I could add it as an appendix to my book. It is a breakdown of the "vocabulary of scent," a lexigraph connecting chemical names, perfume notes, and everyday descriptors for so many of the smells that surround us in our daily lives.

As I point out repeatedly in Hidden Scents, there is no such thing as a language of smell, and for such a variety of reasons as to require a book of explanation. From the way the smells enter our minds and the language parts of it, to the lack of general public discourse about olfactory experience, to the lack of intellectual property protections on fragrance, which severely limits public access to information about the ingredients of fragrances, for all of these reasons, it is so difficult to talk about smells and to think about them. Additionally, because this language is usurped by chemistry, which is too complex for the layperson to use, and by advertising, which relies on prestidigitation of experiential cues, any information we do get about smells is clouded by confusion, superstition and outright dirty data.

So what Perfume Shrine does here is great – she has generated her list in response to user comments by regular people, confused people, curious people. She takes that list and clarifies and disambiguates a few dozen terms, or odor entities as they might be called, from the smell of nail polish to play-doh to "barnyard." I wish that this list could be posted in every kindergarten room in the world; one generation may be all it takes to dispel from our society this Lingua Anosmia.

“In the end, getting to know the vocabulary of scent not only facilitates a common language reference among fellow fragrance enthusiasts, but also enriches the experience itself, much like getting to know the parameters of art critique enhances the appreciation of art itself.”

Please check this out, if you've ever wondered, "What is that smell?" or "Why does that girl smell like cat piss?" (hint: it's blackcurrant buds in her perfume, not her 15 cats and the piss-soaked apartment she lives in).

Without a doubt, and as with anything else, the more you know, the more you notice. Inform yourself with this little lexicon and watch as you slowly become a Sherlock Holmes of scent.

 What Smells like Nail Polish/ Metal/ Sweat/ Horses/ Hairspray/ Burnt Toast/ Baby Powder/Dirty Socks etc?
-Perfume Shrine, Feb 2011