Wednesday, September 28, 2016

Bionic Nose Implant World First

Just kidding. But there is this announcement of the first bionic eye implant. This can also be called a retinal prosthesis. There's also cochlear prosthetics, for the hearing impaired. And there's even people who can see with their tongues. (And don't forget the hand that feels.)

They all work by turning sensory stimulus, either photons or sound waves, into electrical signals for the brain to understand, and using whatever nerve fibers are available. These artificial sense organs are examples of reverse-engineering - to know how something works so well that you can detail its operations from beginning to end and everything in between.

It is generally understood that Science does not know enough about olfactory perception to reverse-engineer it, and will not know for a long time. The way aromatic molecules stimulate olfactory nerve receptors is still under debate (shape vs. vibration), and what happens after that is even less understood (although the popularity of deep learning neural nets might change that, as they have a lot in common with the olfactory bulb). Smell continues to be the most mysterious of our senses.

Not to mention, smell is (I think) the only sense where we can see evidence of evolution-in-action - people differ in the way they can smell things down to the individual genetic profile, depending on genes that are still in the process of change today. If you're reading this, you have a 2% chance of one of your 'smelling genes' being junk. So you can't smell asparagus-piss, or skunks, or semen, or sixty other possible candidates. Therefore, to create an artificial 'olfactory prosthesis' is to undoubtedly intervene in the trajectory of human evolution, in real-time.

read about our individual "smell fingerprints"

Wednesday, September 21, 2016


 AKA The Food Network

Bacon Flavor (2-Methoxy-4-methylphenol), surrounded by all the other flavors that use that same chemical-flavor; note that it's slightly modified for ease of viewing. 
There is only one chemical used to make the flavor of bacon.

To put it another way, the chemical that is used to make 'bacon flavor' is also used to make 'vanilla', 'jasmine', and 'clove', among others (including whiskey, which for the reason of lexical discrepancies does not show up on the graph).

Take a minute to play with this network graph - a compendium of flavors and fragrances and the relationships between them, using Aldrich's catalog of over 1000 chemicals.
(check out a youtube tutorial on how to use the network graphs)

 Not only does this seaweed taste like bacon, it looks like fine-sliced proscuitto.

Culinologist Jason Ball from Oregon State University’s Food Innovation Center (via University of Copenhagen’s Nordic Food Lab) and aquaculture researcher Chris Langdon from OSU Marine Science Center, July 2015

Friday, September 16, 2016

Microbial Turing Test

aka Do Eukaryotes Think?

I mean, what does it really mean to think? Don’t we associate thinking with active, purposeful, agency? I think; thinking isn’t something that happens to me. Or is it? Sometimes I wonder if anything we do has intent, if anything we do is of our own volition. When we move through a room, are we moving, or is the room moving us?

Do we wear earrings, or are the earrings wearing us (à la Kevin Kelly’s What Technology Wants, he asks if the earrings are actually using us to spread the wearing of earrings by others; I wear them, you think I look cool, and then you go ahead and wear them too, and so on, and so on).

Further afield, if we do not think the way we think we think (pardon me), then can we say the reverse – that other things thought not to-think are in fact thinking? What does a very simple multicellular organism do? Does it run decision making algorithms? Here’s a piece from the end of Hidden Scents in the chapter called “Olfactory Space and n-Dimensionality” where we’re talking about what space is, what dimensionality is, and what it means for us to be in it and moving through it. The thing is, our olfactory sense is more tied up with our sense of space than any other. In some ways, it is the thing that moves us, it is the same part of our brain that activates motion, or motility, as it is called in simpler organisms. Little cellular buggers do something called chemotaxis, where they follow a chemical gradient in their environment. As those critters evolve, they become more and more liberated from their chemical environment; they can decide whether they want to follow the gradient or not. This transition from reaction to decision, from being a slave to one’s environment, to somewhat of a master, is the story of the development of our own mind. And our sense of smell is a vestige of this ancient part of us. (And to call back to the original question here, once this organism is ‘liberated’ from its environment by its ability to decide, then does the decision-making system now control it? Does the decision-making system have its own rules and limitations which influence the liberated organism in way the physical environment used to?)

Snippets from Hidden Scents
The eukaryote reacts to the chemical information it encounters in at least two ways – positive or negative. Humans are no different, swimming in a soup of information. Cognition aside (or does the eukaryote think?), we navigate even the complexities of our world in this most primary way. Every piece of information we receive is placed on this hedonic gradient and weighed in light of all the rest until the moment we initiate an action. The eukaryote does not move of its own accord but, instead, in response to the things outside it. It needs these things in order to move. Ultimately, it does not move itself; they move it. For the chemosensing organism, space is not a void to be traversed. Space is a distribution of the potentiality for movement. The distance between things is not important: There is no distance, only contact.

Wednesday, September 14, 2016

Some Flowers Smell Bad

I often associate the smell of a rose with that of solid human waste, by way of restroom air fresheners; incidentally, the reason floral smells are so good in air fresheners, is that they share similar aroma compounds, like indole and skatole. image: Glorious Garden

Simon Cotton, The Conversation, via, July 9, 2015
[note this post is a bit outdated]

Most people already know about the world's smelliest flower. Here I'd like just take note of its associated lexicon, taken from the above article.

First let's hear about this "master of disguise":
"Its smell is designed to attract insects such as flies and carrion beetles, which normally feed on decaying flesh, which will help pollinate it. The spathe is green on the outside but the flower head is red, so it looks like meat. This plant is really cunning – as it blooms it gives out quite a lot of heat, up to 36°C, which encourages the molecules to spread out by helping them vapourise, and also confirms the impression of "warm meat". The insects crawl over the spathe to leave their eggs in what they believe to be rotten meat, in the process transferring pollen – and this pollinates the plant."

-Amorphophallus titanum
-corpse flower
-carrion plant
-hot, rotten flesh
-dimethyl disulphide (DMDS)
-dimethyl trisulphide (DMTS)
-'off-flavor' in beer (result of the fermentation process)
-"sweaty skin" acids
-human faeces
-"dead-horse arum"
-dimethyl sulfide (DMS)
-"smell of the seaside"
-black truffles underground in some parts of France.
(DMDS and DMTS are associated with the smell of Italian white truffles.)

*This list contains terms associated with plants of similar genus, and terms for molecules that may only contribute to, but do not wholly represent, their reference-term (indole is a component of human feces, but not the only one).

Friday, September 9, 2016

Revealing Salient Features of the Smell Network

aka On Sweetness and Flowers

pdf screenshot: Aldrich's Flavors and Fragrances Catalog, 2013. "Organoleptic properties index", pp145-169. 
If you work in the Flavor and Fragrance Industry, chances are you use the Sigma Aldrich catalog to reference the chemicals, the raw materials, of your craft. Sigma Aldrich produces and procures about 1,000 ‘smellable’ chemicals for distribution among the Industry.

It is the nature of volatile organic compounds (‘smellable’ molecules) that the same units can be used to make a variety of aromas. Although there are only 1,000 chemicals, they are indexed by over 3,000 descriptors, such as smoky, anise, spicy, or rose. One does not search for the chemical Geraniol, but instead looks up “Rose”, under the super-category Floral, and there will be Geraniol, along with all other chemicals used to intimate the aromatic impression of a rose. Further collapsing these roughly 3,000 descriptors into more general categories, again there is redundancy. The aromatic descriptor “Lemon” is categorized under the Citrus as well as the Woody groups.

Of all these descriptors, “Sweet” is the most redundant; it is repeated in four different groups, more than any other descriptor. In network science parlance, this is called centrality, or betweenness. Thus, Sweet has a higher centrality value than any other descriptor. It is a kind of glue, a hub, which holds the network together. (This is a flavor and fragrance catalog, after all.)

Using Sweet as a locus, a modified aroma network can be configured. Within this “Sweet network”, every super-category that contains Sweet as a descriptor is present. (Note that the chemical indexed by “Sweet” in one grouping, such as Fruity, does not necessarily refer to the same chemical as the “Sweet” in the Balsamic group.) The related super-categories that share Sweet as one of their descriptors, they happen to be the most ‘copiously described’ groups. Fruity has 850 descriptors, the most of any group. Balsamic has 540.

This revelation is becoming somewhat anti-climatic, as it would be expected that the more descriptors a group has, the more likely it would share one of those descriptors with another group. But what is this? If we look down, at the third-most populated grouping – Floral, at 296 – we see that it is absent from the Sweet network. If groupings with many descriptors tend to contain Sweet, and Floral has many descriptors, then it should also contain Sweet. It does not.

In the first place, Sweet is not a smell, it is a taste. But this is a flavor and fragrance catalog, you retort. But what then about sour, salty, bitter, and savory? They do not exhibit the same centrality as sweetness. Next, we do not eat flowers. In fact, a major part of the profile of a “floral” note is the smell of shit – not the most gustatorily satisfying of aromas.

The corpus of the Sigma Aldrich smell network is highly complex in its structure and associations, with stable patterns found few and far between. No matter the corpus, throughout history such has been the same for smells. At least for one of its infinite configurations, it can be observed that Sweetness and Flowers are very distinct entities in the aromasphere: We do not eat Flowers, and we do not smell Sweet.

Wednesday, September 7, 2016

Instant Grandpa

Just a nice picture of the late Oliver Sacks

Let me take a trip down memory lane here. I’m no longer a teacher, but it’s moments like these that made it so worth it. It’s not exactly the first day of school, but close enough. It's 9 a.m., I’m crouching down to help one of my students generate visually stimulating linear designs for our first art project. We had already sidetracked into a conversation about drawing cartoons or something. Mid-sentence, she looks me straight in the eye and drops this one on me – “You smell like my grandpa.”

First things first – I was 35 when this happened. Secondly, I’ve been teaching for 17 years and I never heard this one before. Thirdly, my students generally have no idea that their art teacher wrote a book about smells, and rarely do I go down this road with them. But this time, I simply couldn’t help it. And why? Because I knew exactly what she was talking about.

I’ll start with this: old people and old books have a lot in common, odor-wise. Let’s focus on the substance lignin. It's one the main classes of structural materials in the support tissues of vascular plants. It’s very rigid, and doesn’t rot easily. The word itself is derived from a Latin form of “wood”. It’s in books, obviously, and it’s in people, less obviously (until you consider that we eat hella plants in our lifetime, i.e. grasses, i.e. wheat, rice, etc.). To quote a scientist who investigated the smell of old books, their scent is a combination of “grassy notes with a tang of acids and a hint of vanilla over an underlying mustiness”.*

Why vanilla? Because it shares a similar structure with lignin, and although molecular structure and smell don’t necessarily correlate, they tend to, and in this case, they do. Babies, and in particular baby heads, smell like vanilla (Süskind calls it butterscotch). Babies drink breastmilk, which contains vanillin. This is part of the uroboric relationship between mother and child – the baby sniffs for a nipple, which has its own scent, and is rewarded by the milk, which reinforces the behavior by associating the smell and the satiation. Meanwhile the mother feeds her baby and is rewarded by the very specific smell of baby-head, which is then associated with all the other multimodal sensations of a cute, helpless little baby that we are hardwired to enjoy. It’s truly one of those beautiful circles of life that takes the metaphorical and actual physical shape of a yin-yang.

So babies smell like vanilla; and as we age, we smell more and more like a musty old book


During the school year I wear white cotton undershirts. During the summer I don’t. The day after the last day of school, I wash all my clothes and put them in the drawer where they stay for the next two months. I did notice that they weren’t 110% dry when I folded them and put them away, as it was really humid that summer day.

My drawers are made of wood, but the insides are what I’ll call particle board. That’s basically wood pulp and glue (i.e. the basic ingredients of a book). But wait, there’s more. The insides are surfaced with faux newspapers from the 19th century, which is simply ink printed on paper and adhered to the particle board. Put a stack of a dozen very, very slightly damp t-shirts in a drawer to marinate for two months in 90 degree heat, and there you have it: Instant grandpa.

*Bleached paper has had the lignin taken out of it, since that’s the reason it oxidizes and yellows, so “white paper” books do not develop the same smell as they age – note to all you self-publishing folk out there.

Artist Ingests and Sweats Dangerous Amount of Dye

Everything we consume eventually comes back out, and in other ways besides the most obvious. Many of the foods we eat are excreted through the skin via sweat, and lends itself to the many smells of body odor.

On a side note, the author can smell poison ivy being metabolized in his own body and excreted in this way. I can also tell the quality and type of milk product within 20 minutes after consumption - I might not notice "old butter" while I'm eating it on my toast, but I'll know soon enough. Gross. Milk smells not-so-much, and pizza cheese is the worst. I have a hard time finding people who know what I'm talking about, so if you do, please comment(!).

Post Script:

On transformative human effluence:
Scientist Christina Agapakis and olfactory artist Sissel Tolaas acquired and fermented human sweat to make cheese out of it. The big deal was the cheese made from Michael Pollan's stomach sweat (totally edible, even for vegans!).

And on the topic of disturbing performances:
Olivier de Sagazan's "Office Man", in the 2011 film Samsara, by Ron Fricke and Mark Magidson

Tuesday, September 6, 2016

When Data Has a Mind of Its Own

When good data goes bad.

Can’t hurt to post another example of dirty data, and this one is pretty cool (or not, if you’re a geneticist).

BBC News, Aug 2016

“Researchers trying to raise awareness of the issue claim that the spreadsheet software automatically converts the names of certain genes into dates.”

“Gene symbols like SEPT2 (Septin 2) were found to be altered to "September 2".”

“The researchers claimed the problem is present in "approximately one-fifth of papers" that collated data in Excel documents.”

“Excel's automatic renaming of certain genes was first cited by the scientific community back in 2004, the Baker IDI study claims. Since then the problem has "increased at an annual rate of 15%" over the past five years.

Friday, September 2, 2016

Dirty Data

I had someone ask me the other day, after reading a bit from my book, what is
“dirty data?” I was taken by surprise, because I thought that anyone under 30 knew what that was, you know, “digital natives” and all. Guess I should throw some definitions around:

Dirty data is inaccurate, incomplete or erroneous data, especially in a computer system or database. In reference to databases, this is data that contain errors. Sometimes called noise, as in signal noise, and is cleaned by a data janitor.” –wiki

Dirty data is part and parcel of Big Data and the Information Age. It’s inevitable and it’s everywhere. My autocorrect, for example, has some mis-spelled words accidentally added, and that messes up my texts, unless of course, I clean my personal dictionary. My phonebook has two different people named Nicole, obviously with two different numbers, and unless I go and disambiguate, there is no way for me to know which is which.

As a database, the “language of smell” is a stellar example of what it means to be dirty. Ask somebody what “musky” smells like, or “musty.” These are two very different smells, but because their names sound similar, people often substitute one for the other. Give someone the smell of an orange and then a lemon, and ask them which is which, but without telling them in advance. They can also both be called “Citrus.” As a database, the corpus of words we use to describe smells is a powerfully rich example of dirty data in action.

Snippets from Hidden Scents:

If knowledge is supposed to tell us which is which, and what is what, then how do we use it to study a thing that is inherently ambiguous? Smell is such a thing. In it, we have an example of an information-processing system that makes its sole purpose to ascertain ambiguous information. Moreover, during the entire process from primitive sensation to cognitive verbalization, it is fuzzy, noisy, and dirty.