Wednesday, January 25, 2017

Identifying the Smell-Language Interface

Olfactory Artist Peter De Cupere

Re: Research investigating the physiological basis for odor naming via event-related potentials (ERPs) and fMRI.

The scientists fed subjects cues, either visual or olfactory, followed by words either matching or not matching the cue. A picture of a rose followed by the word “Rose”, the scent of a rose followed by the word “Rose”, or maybe the word “Lemon” instead. What parts of the brain light up when they recognize the match or the mismatch?

The results show that the “cue-modality”, whether it was visual or olfactory, affected different areas of the brain. Performance in recognizing either a match or a mismatch was slower when presented with an olfactory cue versus a visual cue. It was also discovered that the same areas responsible for recognition of an olfactory cue-word match lit up before the word appeared, suggesting less ‘flexibility’ in semantic identification of odors.

Furthermore, when the word is presented for match validation, the cue is reactivated, or re- experienced. But for olfaction, the entire olfactory perception system is not activated, only the parts which had initially coded the sensation semantically. This echoes the assertion that smells cannot be “imagined” in the same way as visual stimuli.

Let's not forget that smell originally functioned as an automatic system with no intervention of cortical processing. Activate - inhibit, that is the way of chemo-sensation. The buck does not cognize the scent of the doe, it reacts. Most of our models or analogies for thinking are visually based. The interface between olfaction and language is akin to the inner mental space in its entirety. The Olfactory-Language Interface, on the other hand, is more like a short cut through this mental space. There is no time for deliberation against the simulated perception, such a thing was impossible or unknown to our organic ancestors.

The chemically-sensitive organism (a redundancy in itself), whether plant or animal, is tied to its environment. The separation between the body and the environment is ultimately what we call this mind space, and it is the thing that makes us human.

(olfactory literature double whammy)

A few simple stereotypes demonstrate the paradoxical nature of the sense of smell. Olfaction as the sense of lust, desire, and impulsiveness is associated with sensuality. Smelling and sniffing are associated with animal behavior. If olfaction were his most important sense, man's linguistic incapacity to describe olfactory sensations would turn him into a creature tied to his environment. Because they are ephemeral, olfactory sensations can never provide a persistent stimulus of thought. Thus the development of the sense of smell seems to be inversely related to the development of intelligence.

Monday, January 23, 2017

Bad Information vs Good Information

Deep Learning, An MIT Press book by Ian Goodfellow, Yoshua Bengio, Aaron Courville, 2016

I'm not sure exactly how they got this image, but it sure looks like it came from the Google Deep Dream project where a deep learning network was asked to 'dream' about images and produce 'overpreceived' images, which look a lot like hallucinating on psychoactive mycotoxins.

Is there such a thing as Bad Information? If so, what is the difference between Good and Bad? How do we know that difference?

Artificial intelligence, but information theory in general, is a common theme in Hidden Scents. How can you not write about it these days? We are computers. At least, we are becoming computers. Or they us. At least, that's what they say. Do we know anything aside from the analogies we use? (We should probably be asking Douglas Hofstader about that one)

Back when pneumatics was the technology du jour, we thought the nervous system worked according to pressure in the nerve fibers. That was correct for the circulatory system, but the utility of that analogy ended there. Eventually, the computer analogy will run out, but until then, we are computers. And these days, specifically we are computers learning to recognize patterns in our environment using forward-feebacked layers of feature detection.

This brings us to the premier of a new infotech textbook.

“The Deep Learning textbook is a resource intended to help students and practitioners enter the field of machine learning in general and deep learning in particular.”

Deep Learning is a (new) textbook, so it's too technical for the interested layperson. But there is some good introductory materials that could help straighten things out for people who want to know what it is, but don't have the context-specific knowledge to digest the whole thing.

Here's from the chapter on Information Theory

“Likely events should have low information content, and in the extreme case, events that are guaranteed to happen should have no information content whatsoever.

“Less likely events should have higher information content.

“Independent events should have additive information. For example, finding out that a tossed coin has come up as heads twice should convey twice as much information as finding out that a tossed coin has come up as heads once. “

The text then goes on to translate these maxims into mathematical formulae.

Sometimes someone says something and I'm like, wow, that was really stupid. But then later on, when I try to think about why it was stupid, I find it difficult to articulate. In the text quoted above, we have a good rationale for explaining why a particular statement is 'stupid' or not: It depends on how much information it has. And this is how we measure that information.

In laymen's terms, we would call this the Captain Obvious principle. If you just said something that everyone already knows or should expect, but you said it like it's got good information value (as if nobody knows or expects it) then that would come across as stupid.

There we go again, turning a branch of applied mathematics into a magnifying glass for human behavior; probably not what the authors of this text intended to be done with their work.

Anyway, back to the text. I like their word “hard-coding.” They use it to describe the 'older' way of writing-in knowledge about the world into a program (instead of 'letting the program figure it out for itself,' as these newer deep learning programs are done).

They point out in the introduction that "A person's everyday life requires an immense amount of knowledge about the world. Much of this knowledge is subjective and intuitive, and therefore difficult to articulate in a formal way. Computers need to capture this same knowledge in order to behave in an intelligent way. One of the key challenges in artificial intelligence is how to get this informal knowledge into a computer." Instead, when computers get their own data, by extracting patterns from raw data, this is known as machine learning. Deep learning is a type of machine learning.

Still, figuring out which details are valuable and which are inconsequential is the hardest part. Disentangling is a word emphasized by the authors. That's a favorite word in Hidden Scents as well. So is inextricable, the information-opposite of disentangle. So is disambiguate, the big brother of disentangle.

If you're into this stuff, and a bit more on the application side than the theoretical side, you might want to check this book out. And if you're just into machine-generated hallucinations, or if you've ever tripped on psilocybin mushrooms and want to see something reminiscent – very reminiscent – unnervingly reminiscent – check out the front cover.

Analogy as the Core of Cognition, Douglas Hofstadter, Stanford lecture, 2006

Friday, January 20, 2017

Sound Symbolism and Universal Language

In this context, we have no choice but to summon Kiki and Bouba, two letters of an alien alphabet that although no person has ever heard it, they still known which is which, because one feels sharp and the other round, and that is called synaesthesia.

A nose by any other name would sound the same, study finds

“A study that shatters a cornerstone concept in linguistics […] two-thirds of the world's languages shows that humans tend to use the same sounds for common objects and ideas, no matter what language they're speaking […]the research demonstrates a robust statistical relationship between certain basic concepts—from body parts to familial relationships and aspects of the natural world—and the sounds humans around the world use to describe them […] For example, in most languages, the word for "nose" is likely to include the sounds "neh" or the "oo" sound, as in "ooze." The word for "tongue" is likely to have "l" (as in "langue" in French).”

Morten H. Christiansen, professor of psychology and director of Cornell's Cognitive Neuroscience Lab: “There does seem to be something about the human condition that leads to these patterns. We don't know what it is, but we know it's there.”

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.

Sunday, January 15, 2017

Hot Breath Cancer Detector

Turn your brozilla breath into a disease detector.

You Are What You Exhale: Different Diseases Have Distinct Chemical Signatures

The team uses an "artificially intelligent nanoarray" called the Na-Nose. This artificially intelligent sensory system uses gold nanoparticles and carbon nanotubes.

They’re looking for 13 chemicals, but not just for their presence; they’re looking for distinct profiles of those molecules – “odor signatures” says Prof. Hossam Haick from Israel Institute of Technology.

It’s quick and invasive and was 86% correct (but still not accurate enough for clinical diagnosis).

This needs to mentioned – Science still doesn’t know how olfaction works. Is it a shape-based interaction between receptors and aromatic molecules, or is it the vibrations of those molecules that stimulate receptors? Still don’t know. Science certainly doesn’t have to wait, however, to approximate an artificial nose. Examples of these sensory devices for specific purposes are becoming more common.

Regardless, none of these technologies does what our olfactory system does. They are pre-programmed to identify specific molecules. They are already given the things they are meant to look for. Our olfactory system, and the thing that makes it so special, is that it is ready for anything. There are an infinite number of molecules to be identified, and we cannot be born ‘pre-programmed’ for all of them. Still, exciting stuff.  

Friday, January 13, 2017

Use It Or Lose It

Losing your sense of smell and how to get it back

Frito Feet – a smell sorely missed by acquired-anosmic dog lovers. source

I had the opportunity to interview a young woman who temporarily lost her ability to smell. For anyone interested, I’ll give a brief rundown of events.

Before anything else, however, I must make a distinction. Not being able to smell is called Anosmia. But there is Congenital Anosmia for people born without it, and Acquired Anosmia for people who lose it after they already know what it is to smell. Acquired Anosmia usually happens as a result of physical trauma, like a blow to the head, or a sinus infection. But, one can also lose their sense due to prolonged disuse. In this case of the young woman I interviewed, it was disuse that led to her loss.

Ok, so let’s say one day you realize you have a spontaneous cerebral spinal fluid leak. Chances are you’re in for a rough time. The headache that never ends is from your brain tissue drying out and slowly dying. Daily, relentless, suicidal pain. The sinus problems are from your brain juices spilling out of your skull and into the pockets behind your face. You’ll probably get a spinal tap blood patch to refill your losses, and in the meantime (this can take months to refill) you get hallucinations. Auditory, like K-pop; visual like phantoms and UFO’s; maybe even olfactory. The thing about migraines-and-smells is that all smells turn into bad smells. All sensory stimuli sucks, but smell will trigger that deep, involuntary limbic system response – too much to ask for the migraine-suffering mind.

Back to the spontaneous cerebral spinal fluid leak. Now that your brain fluid has pillowed and deformed your sinus cavities, you should finish up your suite of procedures with some sinus reconstruction. Ahhh, looks great in there. Wait a month for the river of blood to dry up in your nose, get the scabs vacuum-sucked, and you’ll be good as new.

Just one more thing – since you’ve had a nose full of blood for the last several weeks, and you haven’t smelled a damn thing in quite a while, you’ve now lost your sense of smell. It doesn’t work at all.

Again, there are all types of things that can happen to make you lose your sense of smell, it doesn’t have to be a cerebral spinal fluid leak. You could faceplant in a rock-climbing accident, like this character written by the olfactory-science-fiction author Deji Bryce Olukotun. Or you could have your GI system removed and replaced with a bunch of tubes, like this gentleman on Radiolab. He couldn’t eat through his mouth anymore, and that eventually disabled his nose. His wife caught him one night in the kitchen with his digital members stuffed into a warm cake, and by some sensory shell-game, squishing its essence through his fingers and into the aromatic centers of his brain (necessity is the mother of invention). Anytime you stop using your nose – even by way of not-eating, you can lose it.

But there’s still hope. They can jumpstart your olfactory bulb in a couple of ways. Here, have some modified estrogen.* Oh, you can’t have estrogen? Sure, sniff these nose steroids through a baby bottle. In a week or so, you smell the steroids, and the rubber nipples, especially the “rotten fish” portion of the profile. The bad smells come first, and then the rest, one at a time. And that’s if you’re lucky. Sometimes it just doesn’t work, and may never come back, in which case you should read Oliver Sacks’ Hallucinations.

*Women smell things better than men, and fertile women better than anyone.

Post Script
Fifth Sense - UK-based, volunteer-led charity supporting people with smell and taste disorders

Post Post Script
Q: Is it true the early success of your product stemmed from the fact that Ben, the official ice-cream taster, has a smelling problem?

BEN: I've never had a very good sense of smell, and if you don't have that, you don't have a good sense of taste. When we began, the game was for Jerry to make a flavor I could taste with my eyes closed. To do that, he had to make ice creams that were intensely flavored. Also: because of this disability, I have an excellent sense of mouth feel.Creaminess and crunchiness are very important to people who can't taste.

JERRY: This led to our putting bigger than standard chunks of fruit and candy into our ice creams. It turned out that people really liked these highly flavored, extra-chunky ice creams. We were offering them something unique.

On Dog Paws
“Dog feet are a great place for bacteria and yeast to take up residence because there's a lot of moisture and little to no air circulation in the folds and pockets of skin between the toes and foot pads. Bacteria flock there and reproduce with exuberance.”

“All these microorganisms emit their own distinct odors (they're what give us BO), and the popcorn/corn chip smell on some dogs' feet could be due to yeast or Proteus bacteria. Both are known for their sweet, corn tortilla–like smell. Or it could be Pseudomonas bacteria, which smell a little fruitier—but pretty close to popcorn to most noses.”

Wednesday, January 11, 2017

Smell Everything

I’m not sure why this shows up when I search ‘google nose’ 
Here’s something about the good old April Fool’s Joke by Google, touting the ability to ‘google smells’ -- Smell Everything with Google Nose!

In Dog Years

Talking about smells is like when people talk to each other about their dogs:

"Oh, what a nice dog, what's your name?"
"How old are you, Frodo?"
"He's 5. (That's 35 in dog years.)"

***now in smell talk***

"Oh my God, do you smell that?"
"Eughhhh, seriously, can't they do something about that?"

(The smell never gets named.)

Tuesday, January 10, 2017

Evolvable Chemical Systems

Mitochondrion with endoplasmic reticulum, Center for Molecular Microscopy

Chemists create 'artificial chemical evolution' for the first time

“[The team from the University of Glasgow's School of Chemistry led by Professor Lee Cronin] created an evolving chemical system using a robotic 'aid' and could be used in the future to 'evolve' new chemicals capable of performing specific tasks.

“A robot monitors and selects for further development droplets of different chemical compounds, mimicking natural selection to produce 'fit' compounds.”

It is an attempt to produce new chemical life forms.

microscopy, pollen

The matter compiler in Neal Stephenson’s Diamond Age makes things molecule-by-molecule. It is fed by huge lines of individual atoms. They use it to make things like clothes and cutlery. The process described above is instead used to discover new chemicals combinations. In the world of perfumery, for example, this could be very helpful.

I also can’t help but mention, at the very end of the article, we hear about inorganic-chemical cells “built from molecules of metal and exhibit some of the same abilities as living cells.” Will killer robots smell fear, that’s all I want to know.

Friday, January 6, 2017

Bacteria, Molecules, and Other Small Things That Sense and Remember

Here I’ve compiled some articles from my notebook that look at how our senses work when it comes to simpler forms of life, like bacteria. There’s even something about how molecules – very far from what we consider ‘living things’ – uses a form of memory. All this has been put together to reinforce an idea presented in Hidden Scents which suggests that our awe-inspiring brain is similar to things less inspiring, like the lowly eukaryote.

Some of these things are really old, and most of the text here is copied from the links provided. Overall I hope it’s interesting enough to keep your attention:


“…there is a distinction between an organism reacting to a chemical that it encounters directly (in analogy to the sense of taste) and a reaction to a chemical that is floating around in the air, says Reindert Nijland, lead author of the study.

"The compounds detected by olfactory organs are generally much more volatile than things you can taste like 'sweet' or 'salt', and therefore can provide information about things that can be much further away; you can smell a barbecue from a few blocks away whereas you have to physically touch and eat the steak to be able to actually taste it."

***, Feb 2016

“ "Very little is known about the microbes of the built environment," microbiologist Maria Gloria Dominguez-Bello of New York University, who led the pilot study, said at a meeting of the American Association for the Advancement of Science.

“Her team found that as people living in the Amazon rainforest become more urbanized, the kinds of bacteria in their homes change from the bugs mostly found in nature to those that typically live on people, she reported Friday.

In fact, in city dwellings, the researchers could tell just by the microbial fingerprints of the walls that "this is a kitchen or this is a bathroom or this is a living room. That's amazing," Dominguez-Bello said.

“Despite fewer occupants, the more urbanized a dwelling, the more human bacteria lived on its walls and floors, the researchers reported in the journal Science Advances. In Manaus, a collection of microbes normally found in the mouth, including various species of strep bacteria, and in the gut were the most important in telling rooms apart. The more crowded jungle and rural homes nonetheless were filled with more bacteria commonly found in soil and water than with human microbes.”

The microbiome has become a big deal lately. As much as it is invisible, it’s not unrecognizable.

Its kind of funny how, first, we didn’t know what microorganisms were one hundred years ago, and are only now beginning to understand the role of microbes (in their totality, as the microbiome) in human health, and yet, I would conjecture that the smell of the microbiome, its dynamic states of existence and effects, have been well known to us for quite some time. I cannot see your body odor, even if I look really close. But I know it’s there.

***, Feb 2016

This isn’t about smelling, but sensing nonetheless…

“Dmitri A. Nusinow, Ph.D., assistant member at the Danforth Plant Science Center and researchers in his lab studying plants' circadian clock have discovered a gene that allows plants to remember daylight during the long nights of winter, helping them tailor their growth appropriately to the seasons.”

BBC, Feb 2016

“After more than three centuries of scientists eyeballing bugs under microscopes, Prof Mullineaux said it was remarkable that nobody had picked up on this before.”

“the entire organism acts like an eyeball”

“Cyanobacteria, including the Synechocystis species used in the study, are an ancient and abundant lifeform. They live in water and get their energy from photosynthesis - which explains their enthusiasm for bright light.”

Can’t resist mentioning that cyanobacteria are what make the ‘smell of the seashore;’ it emanates from their little bacteria bodies as they metabolize, and we can also call it seaweed sweat or seaweed pheromones or seaweed seeking sex.

***, Jan 2016

“This device, reported in the Jan. 28 issue of the journal Nature, is the first fully integrated electronic system that can provide continuous, non-invasive monitoring of multiple biochemicals in sweat.

“The advance opens doors to wearable devices that alert users to health problems such as fatigue, dehydration and dangerously high body temperatures.

"Human sweat contains physiologically rich information, thus making it an attractive body fluid for non-invasive wearable sensors."

[and on that note...], Feb 2016

"Thousands of bacteria species have the potential to live on human skin, and in particular in the armpit," says Rob Dunn, a professor of applied ecology at NC State and co-author of the paper. "Just which of these species live in any particular armpit has been hard to predict until now, but we've discovered that one of the biggest determinants of the bacteria in your armpits is your use of deodorant and/or antiperspirant."

"We found that, on the first day, people using antiperspirant had fewer microbes in their samples than people who didn't use product at all - but there was a lot of variability, making it hard to draw firm conclusions," Horvath says. "In addition, people who used deodorant actually often had more microbes - on average - than those who didn't use product."

“By the third day, participants who had used antiperspirant were beginning to see more microbial growth. And by day six, the amount of bacteria for all study participants was fairly comparable.

"However, once all participants began using antiperspirant on days seven and eight, we found very few microbes on any of the participants, verifying that these products dramatically reduce microbial growth," Horvath notes.

“The participants who had been regular antiperspirant users coming into the study had wildly different results. Sixty percent of their microbes were Staphylococcaceae, only 14 percent were Corynebacteria, and more than 20 percent were filed under "other" - meaning they were a grab-bag of opportunistic bacteria.

[aaaandddd], Nov 2015

“Swarm robotics is an emerging approach to the coordination of multi-robot systems, which takes inspiration from the natural world to examine the possibilities for improved interaction between robots and their surrounding environment.

“Until now, researchers specialising in swarm robotic applications have been unable to replicate all the aspects of pheromone communication that occur in the natural world.

“Specialists from the University of Lincoln's School of Computer Science have now produced a novel artificial pheromone system that is reliable, accurate and only uses 'off-the-shelf' components …[which] allows users to simulate several pheromones and to change their strength.

“Led by Farshad Arvin, PhD researcher in the School of Computer Science, the Lincoln team developed the system using their own Colias platform. They created Colias - an open-platform system that can be used to investigate collective behaviours and be applied to swarm applications - in 2014 in collaboration with experts from Tsinghua University in China.”

Wednesday, January 4, 2017

The Fragrance Industry Speaks

The inquisitive soul will immediately come upon two major entities acting as the gatekeepers of odorant-information. These are the fragrance industry and the scientific discipline of organic chemistry. Each one has its own way of making it very difficult to make sense of the smells around us – but in particular the aroma compounds that combine to make up those smells.

Flavor and fragrance are certainly enmeshed, and so the food industry is very close. Both are organized into only a handful of companies. It is with great power and airtight secrecy that they operate. The discovery of new aroma compounds, and of cheaper methods of replicating known ones, is a critical endeavor for their business. Keeping these discoveries unknown to competitors is even more critical.

In instances where a significant aroma has been synthesized, a trade name is given – but that is all. No other chemical clues are released, as not to inform the competition. In fact, in the case of the synthetic musk Phantolide, the international body of chemical nomenclature had no name for the molecule for years after it was discovered by the fragrance industry. Anecdotally, many of these “discoveries” by the fragrance industry were actually accidents of other pursuits, such as explosives (synthetic musk) and anti-depressants (“marine”/Calone).

Fragrance companies don’t supply the public with information about aroma compounds, but about Fragrance – artfully crafted combinations of aroma compounds. And in the case of masking-fragrances, where the intent is to use a good smell to camouflage a bad smell, the scent is invisible by design, and the public isn’t even supposed to know it exists in the first place, let alone seek information on its molecular components.

And so not only is it in direct opposition to the business model of a fragrance company to divest information about its products’ ingredients, their desire and capacity for discovering new compounds is greater than publicly-funded, publicly-accessible scientific discoveries.*

There is no such thing as a public arts fund for Fragrance, and so there is no knowledge acquired in the process of this craft that can be availed to the public. A passing thought: in comparison to the visual arts and music, smell-as-art is completely “patronized” by private industry.

*The presence of the amateur perfumer community warrants mention on this subject. The online community of is one of the few places one can go to search through conversations about smell from such a diverse and knowledgeable people.