Thursday, March 2, 2017

Going Fictional: Introducing the Nick Zollicker Stories

I’ve always been fascinated by the portrayal of smell in fiction. I made a brief study of it in What the Nose Knows, and here on FN I’ve taken a close look at various authors and how they weave scent into their novels. Among the writers I’ve discussed or quoted are E.L. James, Tom Robbins, Vladimir Nabokov, Toni Morrison, and P.G. Wodehouse. (You can find these posts via the FN Review, FN Retrospective, and Olfactory Art tags.)

In most of these works scent is mentioned in passing. It functions to characterize a person or place or, especially in the case of Nabokov, to provide a sepia-toned sense of nostalgia. Smell is rarely a central theme in fiction. There are exceptions, like M.J. Rose’s The book of lost fragrances, Süskind’s Perfume: They story of a murderer, and Roald Dahl’s brilliant short story Bitch.

One would think the world of contemporary commercial perfumery is an ideal setting for fiction. The business is an unstable blend of creative fashion and technical chemistry. It straddles the magical and the mundane. It simultaneously touts its innovation and its longstanding traditions. It is filled with characters of Dickensian dimensions.

Another setting ripe for fiction is the world of academic smell research. University labs are stocked with weirdos and drones as well as the rare brilliant scientist. Scientists share a lifestyle—monk-like yet dissipated—that is remote from the experience of most readers. Their scientific obsessions are remarkable if not often bizarre. It’s all fertile ground for fiction.

Well, somebody needed to step up to the plate, and it appears that the someone is me. I have created a contemporary smell expert named Nick Zollicker. He lives in Berkeley, California where he runs a secretive private olfactory research institute. He has wide experience in the hard-edged world of commercial perfumery yet thrills to pushing the boundaries of olfactory science.

My first two Nick Zollicker stores An Imperfect Mimic and Smothering the Savage. They are now available digitally on Amazon. (You can read them on your Kindle or download the Kindle app onto whatever device you prefer.) I hope you enjoy them.

Thursday, February 23, 2017

Can We Predict a Molecule’s Smell from Its Physical Characteristics?

An extract of Yuanfang Guan’s winning code for odor prediction

A paper in this week’s edition of Science claims that computer models can predict the smell of a molecule. The paper describes the organization and outcome of an IBM Dream Challenge in which multiple laboratories competed to see whose model best predicts sensory characteristics from chemical parameters.

This crowd-sourced effort began with an olfactory dataset collected and published in 2016 by Andreas Keller and Leslie Vosshall. (Full disclosure: I previously collaborated with Keller and Vosshall on a different smell study.) They had 49 test subjects sniff and rate 476 “structurally and perceptually diverse molecules” using 19 semantic descriptors plus ratings of odor intensity and pleasantness.

In setting up the Dream Challenge, the organizers also “supplied 4884 physicochemical features of each of the molecules smelled by the subjects, including atom types, functional groups, and topological and geometrical properties that were computed using Dragon chemoinformatic software.”

There are several positive aspects to the challenge design. First, instead of recycling the decades-old Dravnieks dataset like so many other attempts at chemometric-based odor prediction, the sponsors supplied a fresh psychophysical dataset. Second, the study included a boatload of odorants, not the handful of smells found in most sensory studies. Third, the odor ratings were gathered from a relatively large number of sensory panelists. Forty-nine is not a super-robust sample size but it’s enough to encompass a lot of the person-to-person variability found in odor perception.

Here’s how the competition worked. Each team was given the molecular and sensory data for 338 molecules. They used these data to build computer models that predicted the sensory ratings from the chemical data. Sixty-nine molecules (absent the sensory data) were used by the organizers to construct a “leaderboard” to rank each team’s performance during the competition. The leaderboard sensory data were revealed to contestants late in the game to let them fine tune their models. Finally, another 69 molecules were reserved by the organizers and used to evaluate performance of the finalized models.

The models were judged on how well their predictions matched the actual sensory data using a bunch of wonky statistical procedures that look reasonable on my cursory inspection. (About the algorithmic structure of the competing models I have nothing useful to say, as “random-forest models” and the like are beyond my ken.) For the sake of argument I will assume that the statistical scorekeeping was appropriate to the task. My concern here is with the sensory methodology, the underlying assumptions, and the claims made for the predictability of odor perception.

Let’s begin with semantic descriptors. The widely used U.C. Davis Wine Aroma Wheel uses 86 terms to describe wine. The World Coffee Research Sensory Lexicon uses 85 terms to describe coffee. The Science paper uses 19 terms to describe a large set of “perceptually diverse” odorants which strikes me as a relatively paltry number. (The descriptors were: garlic, sweet, fruit, spices, bakery, grass, flower, sour, fish, musky, wood, warm, cold, acid, decayed, urinous, sweaty, burnt, and chemical.) Well, you might ask, can’t they just add more descriptors to include qualities like “minty” and “fecal” and “skunky”? It’s not that easy, as I discuss below.

The internal logic of the descriptors presents another issue. Some are quite specific (garlic), other very broad (spices), and still others are ambiguous (chemical). What are we to make of “bakery” as a smell? Is it yeasty like baking bread? Is it the smell of fresh cinnamon buns? (Or would that be “sweet”? Or “spices”?). The problem here is that words that are useful in an olfactory lexicon occur at different levels of cognitive categorization. This is reflected in the wine and coffee examples.

The Wine Aroma Wheel has twelve categories, each with one to six subcategories. For example, the Fruity category includes Citrus which consists of Lemon and Grapefruit. The higher level categories provide overall conceptual structure and are themselves useful as descriptors (e.g. a scent might be citrus-like while not smelling exactly of lemon or grapefruit).

Sensory specialists (including tea tasters, beer brewers, and perfumers) spend a lot of effort setting up lexicons that are concise and hierarchical, and which cover the relevant odor perception space. How were the 19 terms in the Science study arrived at? We do not know. How well do they cover the relevant perception space? We do no know. In fact, the authors state that “the size and dimensionality of olfactory perceptual space is unknown.”

These 19 terms are the basis on which the competing computer models were ranked. Thus a model's success at prediction is locked-in to this specific set of terms (plus intensity and pleasantness). In other words, this is not a general solution to smell prediction: it is specific to these odors and these adjectives. The authors openly admit this:
While the current models can only be used to predict the 21 attributes, the same approach could be applied to a psychophysical dataset that measured any desired sensory attribute (e.g. “rose”, “sandalwood”, or “citrus”).
So if one wants to predict what molecules might smell of sandalwood or citrus, one would have to retest all 476 molecules on another 49 sensory panelists using the new list of descriptors, then re-run the computer models on the new dataset. Easy peasy, right? Alternatively one could assemble a sensory panel and have the members sniff the molecules of interest and rate them on the new attributes of interest. Every fragrance and flavor house has such a panel. That’s how they currently evaluate the aroma of new molecules: they sniff them.

Thus the Dream challenge seems to be tilting at a windmill that the fragrance and flavor industry doesn’t see. The search for new molecules is not done by searching random molecular permutations. It is driven by specific market needs, say for a less expensive sandalwood smell or for a strong-smelling but environmentally safe musk. The parameters are cost, safety, and patentability, along with stability, compatibility in formulations, and (for perfumers) novelty.

Who knows, the smell prediction algorithms of the Dream challenge may turn out to be the first step in automating the exploration of chemosensory space. However I’d be surprised if this approach turns out to be generalizable and amazed if it proves useful in applied settings.

Don’t get me wrong. I like the idea of using Big Data to understand olfaction—have a look at my papers based on the National Geographic Smell Survey. I urged Keller and Vosshall to go big in terms of odorants and the number of sensory panelists for what became our co-authored paper in BMC Neuroscience. At the same time I respect the complexity of odor perception and the effort required to map its natural history. And I think the perceptual side of the equation got short shrift in this study.

The studies discussed here are “Predicting human olfactory perception from chemical features of odor molecules,” by Andreas Keller, et al., published online February 20, 2017 in Science, and “Olfactory perception of chemically diverse molecules,” by Andreas Keller and Leslie B. Vosshall, BMC Neuroscience 17:55, 2016.

Tuesday, January 3, 2017

Rate of Decay: The Case of Jonah Lehrer’s Twitter Account

Anyone active on Twitter experiences follower churn—the constant arrival of new followers and departure of existing ones. Some arrivals are follow-whores who will leave in short order if you fail to follow them back. Some are fake accounts attempting to build a legit patina. (Fake accounts are easy to spot and I delight in kicking them off my feed.) Then there are real-life porn actors and jihadists seeking to expand their reach. (Blocked and blocked.) Others follow you based on the odd single tweet and depart when they find your regular material is not to their taste. (de gustibus).

In general, one must tweet frequently to gain new followers. If you have a truly loyal set of followers they may stick around even if you tweet rarely.

But what happens at the limit, when an account ceases to tweet at all? In the absence of new material it is unlikely to attract new followers. Existing followers may eventually unfollow, or close their accounts, or be banned by Twitter. Thus we can expect an inactive account to shed followers gradually. But at what rate?

I have harvested data on a weekly basis from several Twitter accounts. One is that of Jonah Lehrer who enjoyed a brief vogue as a literary explainer of neuroscience. (I found him to be a superficial thinker and a lazy scholar; see the Proust chapter in What the Nose Knows.) After it became clear that Lehrer had recycled his own material and plagiarized the work of others he withdrew from the science journo-biz and, among other things, ceased tweeting.

The last regular tweet on @jonahlehrer was dated June 17, 2012. On February 13, 2013 he posted a link to the text of a speech he gave to the Knight Foundation in which he apologized for his behavior (and for which he was paid $20,000). After that, nada.

So how did Lehrer’s Twitter followers react after he went silent? Well, here’s the answer, based on weekly tallies from October 14, 2012 through December 31, 2016.

Over that period Lehrer lost 6,258 followers. Their number declined to 40,620 from 46,878. The steady decline was interrupted by three increases: a spike of 2,005 followers the week of October 28, 2012; a blip of 369 followers around May 2013, and another spike of 1,998 in the week of August 24, 2013. (Cynical readers might note that Twitter followers can be bought by the thousand online. Whether something like that happened here, I cannot say. The spikes remain a mystery.)

Aside from the anomalous spikes, the decline in followers shows a remarkably steady linear trend. I analyzed the 173 weeks following the second spike, during which the follower count dropped to 40,620 from 47,800 for a loss of 7,180. Over that interval, Lehrer lost on average -0.0935% of his followers each week. Based on this rate of decay, the half-life of his following is 741 weeks or about 14 years. In other words, he should be down to 20,000 followers in 2031. We can expect him to dip under 100 followers in the year 2140.

That’s one long, shallow glide path.

Is Lehrer’s case typical? Who knows. Maybe his followers are fanatically devoted and waiting, year after year, for him to return to Twitter. Or maybe they never noticed that he left in the first place. Having once clicked “follow” they remain fixed to his account like so many barnacles on the bottom of a boat.

Monday, November 28, 2016

It’s Cyber Monday and I’ve put the Kindle version of What the Nose Knows on sale at a deep discount: only $2.99. Why not grab a copy?

Do you have a friends or relatives who are into scent? You can buy them a Kindle copy! Just hit the “Give as Gift” button on Amazon. You can have it delivered to them instantly or you can schedule it to arrive on their device at any time and date you choose. Great idea for Christmas or Hanukkah.

Plus: plenty of time to order a paperback copy for old-school types. It’s already priced as low as it can go!

Sunday, September 11, 2016

Fifteen Years After 9/11

Fifteen years later and the emotions remain raw.

These are notes I made on the fifth anniversary of 9/11 when I still lived in Montclair, New Jersey.

September 11, 2006

Over morning coffee I read some blog essays remembering the attacks and where we stand five years later. S and I talked about our frustration with friends who don’t see the same threat we do; how we want to shake them by the shoulders and wake them up.

I couldn’t concentrate on my writing so I set off to do some mindless photocopying in town. Walking to the car I noticed the sky was a perfectly clear blue. Strange how the weather on the anniversary is almost always the same as the original.

I drove past K’s house [the 9/11 widow up the block] and noticed several pickup trucks parked outside. Her fireman friends keeping her company, as they do every year on this day.

I saw [my neighbor] D jogging down the street and pulled over to say hello.

“This is such a sad day,” he said.

“I know. It still gets to me too,” I said. (I had to look away.)

Then he blurted out, “It’s the same sky.” Now he was sobbing. “I’ve been crying almost my whole run.”

He walked off and I drove to the copy shop where I had to keep my shades on.

Thought I was back on an even keel. Then at four in the afternoon a Montclair Fire Department ladder truck came up the street with lights flashing, flying the Stars and Stripes. They paused a while in front of K’s house, blew their horn, and drove on.

I was a mess.

It’s dark out now. They’ve lit the two blue lights at Ground Zero. I still think it’s the best memorial.