Thursday, September 7, 2023

Science Fiction Can Smell Too

Hella is a science fiction book by David Gerold from 2020. If you like science fiction, it's a good book by a good writer. (posting the bookshop link here in an attempt to support local bookstores?).

They take off their helmet on an alien planet for the first time. "Tell me what you smell." I sniffed. A little at first. Then a little more. "I'm not sure," I said. I inhaled again. "Something sweet. Is that grass? Something else too." I looked up at him. "Does blue have a smell?" "That's what air smells like when it doesn't come from a can." (p27)

The electronic supernose: The conical rebreather on the front of the helmet adds enough carbon dioxide to every breath so that the wearer doesn't accidentally go hyper-toxic from too much oxygen, but more important, it also sniffs the air for all kinds of particles -- it's an electronic supernose. Thehelmet integrates all this information and superimposes the augmented data onto the display. It even includes a visual presentation of all the various smells and odors and scents it can recognize. It shows us which way the scents are blowing and that helps us know from which direction any carnivores are most likely to approach. (p29-30)

About the Author - David Gerrold has been writing professionally for half a century. He created the tribbles for Star Trek and the Sleestaks for Land Of The Lost. His most famous novel is The Man Who Folded Himself. His semi-autobiographical tale of his son's adoption, The Martian Child won both the Hugo and the Nebula awards, and was the basis for the 2007 movie starring John Cusack and Amanda Peet.

Thursday, August 3, 2023

Odor Hunter Extraordinaire Cliff the Z Man Zlotnick

Cliff the Z Man Zlotnick on IAQ Radio

If you suspect a dead animal hiding in your walls (because you're house smells like a dead animal), here's what Cliff the Z Man Zlotnick does, as described back in 2007 on the IAQ Radio Show:

Put a handful of raw ground beef in a garbage bag in a wastebasket and leave it outside. Within minutes, flies will be attracted to the meat. That's when you close up the garbage bag, bring it inside, open it back up, and watch as the flies fly straight to the problem. The gases that emit from a dead animal pass through the wall itself, and the flies can smell that. 

Mandatory shout out to Avery Gilbert and his I Smell Dead People Column on his First Nerve blog (or his newer substack).

Friday, July 28, 2023

Smells Like a New Car

That new-car smell may be a sign of exposure to a host of hazardous chemicals
Apr 2023,

They tested chemicals released into the air by just one vehicle -- a brand-new, midsize, plug-in hybrid SUV in a local outdoor parking lot tested every day for 12 consecutive days using gas chromatography-mass spectroscopy.

  • Air temps ranged from 21°C to 63°C (75F - 145F)
  • 20 common volatile organic compounds tested
  • Emissions dependent on material surface temperature rather than air temp
  • Formaldehyde exceeded Chinese government safety standards at some points by up to 35%*
  • Acetaldehyde exceeded standards by 61%*
  • Benzene levels described as being unsafe for drivers breathing it for long drives
  • They suggest new car buyers ride with the windows open

via mechanical and civil engineers and occupational health scientists with several entities in China and School of Mechanical Engineering and College of Architecture and Civil Engineering at Beijing Institute of Technology, Beijing Vehicle Emissions Management Affairs Center, Beijing Products Quality Supervision and Inspection Institute, Department of Occupational and Environmental Health Sciences at the School of Public Health of Peking University, and Department of Environmental Health at Harvard T.H. Chan School of Public Health: Haimei Wang et al, Observation, prediction, and risk assessment of volatile organic compounds in a vehicle cabin environment, Cell Reports Physical Science (2023). DOI: 10.1016/j.xcrp.2023.101375

*GB/T 27630 - Guideline for Air Quality Assessment of Passenger Cars - Standardization Administration of China, Beijing - 2011

Further Reading on the Smell of the New and a sommelier describing a bunch of new cars’ smells for Car and Driver magazine back in 2003:
Baked Goods, Network Address, 2018

And for those who venture the New Jersey Turnpike:
What Exit? The Smells of the New JErsey Turnpike, Network Address, 2016

Thursday, July 13, 2023

Plume Tracking and Odor Mapping Algorithms

A deep reinforcement learning model that allows AI agents to track odor plumes
Feb 2023,

Insects track odor plumes to find mates. (And there was a similar study done recently here.)

"Instead of running a traditional laboratory wind-tunnel experiment, we used a complementary 'in-silico' approach using artificial neural networks," Singh explained. "This helped us develop an integrative understanding of plume tracking across multiple levels, including emergent behavior, neural representation and neural dynamics."

To train their plume-tracking agents using DRL, the researchers first simulated an odor emanating from a source located within a windy arena with a total area of approximately 120 m2. When their agents identified where the source of the odor was located, they received a reward. In contrast, if they lost track of the odor plume and left the arena, they were "punished."

"The behavior that emerges in our trained artificial agents bears a striking resemblance to the behavior modules biologists have previously observed in flying insects performing plume tracking," Singh said.

via University of Washington and University of Nevada: Satpreet H. Singh et al, Emergent behaviour and neural dynamics in artificial agents tracking odour plumes, Nature Machine Intelligence (2023). DOI: 10.1038/s42256-022-00599-w

Thursday, July 6, 2023

E Noses Never

Read this to learn how basically e-noses are relegated to science fiction for the next 20 years at least:

How to make electronic noses smell better
Apr 2023,

via Xi'an China Northwestern Polytechnical University: Taoping Liu et al, Review on Algorithm Design in Electronic Noses: Challenges, Status, and Trends, Intelligent Computing (2023). DOI: 10.34133/icomputing.0012

'Electronic nose' built with sustainably sourced microbial nanowires could revolutionize health monitoring
Feb 2023,

Grown by bacteria. Great, but each nanowire needs to be programmed for each molecule, so a typical top-down approach.

via University of Massachusetts Amherst: Yassir Lekbach et al, Microbial nanowires with genetically modified peptide ligands to sustainably fabricate electronic sensing devices, Biosensors and Bioelectronics (2023). DOI: 10.1016/j.bios.2023.115147

A robot able to 'smell' using a biological sensor
Jan 2023,

10,000 times higher than the usual electric-based sensors, these are now biological sensors (not sure the difference). And then they program a "library of smells", so keep in mind that, like all other smell sensors out there, these don't just smell anything that happens to be in the environment -- they can only smell things that have been pre-selected and trained-on. 

via Tel Aviv University's Sagol School of Neuroscience and School of Zoology: Shvil Neta et al, The Locust antenna as an odor discriminator, Biosensors and Bioelectronics (2022). DOI: 10.1016/j.bios.2022.114919

New devices for conveying olfactory stimuli in virtual reality
May 2023,

Aerosols and atomizers add bulk to VR gear and entail bottle filling and cleaning. This new approach uses paraffin imbued with scents, released by a temperature-sensing resistor that controls a heating element - the more heat the more scent. But wait -- magnetic induction coils pull heat away from the face to cool the wax quickly when the scent is no longer needed. 

The removal of scent is actually the harder problem to solve than the introduction of scent in these kinds of systems.

via City University of Hong Kong, Beihang University and Shandong University: Yuhang Li, Soft, miniaturized, wireless olfactory interface for virtual reality, Nature Communications (2023). DOI: 10.1038/s41467-023-37678-4

Tuesday, June 27, 2023

Inhibition Is So Hot Right Now

First, whoever says scientists don't have a sense of humor don't have a sense of humor.

Image credit: This imaginary perfume bottle illustrates the role pheromones play in Drosophila courtship decisions by featuring the silhouettes of a male chasing a courted female. Naming this fictional eau de pheromone “Dew Lover” was inspired by the etymological origin of the genus Drosophila, which is based on the modern scientific Latin adaptation of the Greek words drósos (“dew”) and phílos (“loving”). Vernier et al.  show that the coupling of the perception and production of some mating pheromones is regulated by the action of a pleiotropic pheromone receptor. Credit: Digital art by Yehuda Ben-Shahar, Washington University in St. Louis

Now for the main point -- up until recently, much of our understanding of olfactory perception came from looking at receptor activity. You expose a receptor to an odor and see if it lights up, and with that you make a kind of odor map coordinating odorant molecules and receptor proteins. 

Things are different now, because instead of just looking at how receptors are stimulated by odors, we also look at how they are inhibited, because it turns out there is just as much to be learned from receptor inhibition as there is activation. And, the interplay of activate-inhibit sure sounds a lot like the ons and offs of computer processing, meaning that the nose-brain may be a lot more useful as a model for a primitive computer than we thought.

Examining the chemicals involved in insect mating
Jan 2023,

Researchers reported that a single protein called Gr8a is expressed in different organs in male and female flies and appears to play an inhibitory role in mating decision-making. The findings point to one of the ways that flies could put up behavioral barriers to protect against mating with the wrong kind of partner.

"A single pleiotropic protein can function as both a receptor for pheromones in sensory neurons, as well as contribute to their production in the pheromone-producing cells (oenocytes) of males, by way of a less-understood process."

The scientists still have not pinpointed exactly how the chemoreceptor affects the way the signal is produced, but they do know that it causes quantitative and qualitative differences in pheromones. And even small changes in pheromones could be enough to keep closely related flies from finding each other attractive—and change their mate choice behaviors.

"Based on what we have observed, mutations in a single gene could provide a molecular path for a pheromonal communication system to evolve while still maintaining the functional coupling between a pheromone and its receptor," Ben-Shahar said. "Our research uncovers a potential avenue for pheromonal systems to rapidly evolve when new species arise."

Or when a species decides to rapidly evolve itself; looking at you mass population control.

via Washington University St Louis: Cassondra L. Vernier et al, A pleiotropic chemoreceptor facilitates the production and perception of mating pheromones, iScience (2022). DOI: 10.1016/j.isci.2022.105882

Post Script - Pheromones Again
Pachyderm perfume: How African elephants use odor to communicate
Apr 2023,

We tested the DNA, glands, urine and manure of 113 African elephants in wildlife parks in Malawi to identify family groupings," and "We found a number of chemicals were common to group members, but others that were unique to each individual, and found that smell was used to distinguish characteristics including age, health, reproductive status and family relationships between elephants.

"We observed elephants greeting each other by squealing and flapping their ears," he said.

"We believe they're pushing their pheromones towards the other elephant as a sign of recognition.

"When elephants charge each other flapping their ears, rather than making themselves look bigger, we believe they're blowing their pheromones as a warning not to mess with them."

"Some of the animals in the study were bred in captivity, and one of the tricks they'd been taught was to take a tourist's hat and smell it," he said.

"When the tourist came back hours later the elephant would be able to immediately identify who the hat belonged to."

via University of Queensland: Katharina E. M. von Dürckheim et al, A pachyderm perfume: odour encodes identity and group membership in African elephants, Scientific Reports (2022). DOI: 10.1038/s41598-022-20920-2

Tuesday, June 20, 2023


This discovery provides a great example of how machine learning and optogenetics are blowing open our doors of perception.

In this case, scientists created an artificial olfactory receptor (this one derived from OR5A2). You can think of it like the ultimate musk receptor, because after matching it against 100 mammal-nose-brain gene sequences, it's the best-fit for all the animals at once.

But it doesn't really exist in any one animal; it's simply the most in-between of all of them. They call it a "consensus protein". I call it a frankenstein receptor. 

That was machine learning to the rescue, but then they called their friend optogenetics -- they further engineer this artificial protein to produce light when activated. This is a common technique these days that allows us to measure the receptor activity; it's like being able to ask an animal to tell you whether it smells something or not. Then they go back and find all the odorants that match this new frankenstein receptor -- if it lights up, it's a match.

They found no new musks actually, which suggests we know all of them already, but this could work for other odors:

Chemists propose unifying theory of musk - Engineered olfactory receptor may explain why structurally diverse molecules smell similar.
Chemical and Engineering News, Nov 2022

The three receptors known to recognize musk compounds only respond to a subset of musk-scented compounds.

The researchers compared the amino acid sequences for a given odorant receptor across 112 mammal species to determine the most common amino acid at each position and made a receptor with this so-called consensus sequence.

The engineered protein differs from human OR5A2 at 25 of its 324 amino acids ... .

Using the structures of compounds that do and do not activate the receptor, the researchers developed a machine learning model and used it to screen a database of odorant structures and human perceptions. The model, Mainland says, claims to identify known musk molecules much better than prior models trained only using the database. Although they do not report any new musky compounds in the study, the authors say that the Kao Corporation has filed patents related to the work.

via Duke University and Kao Corporation, Tokyo: Proc. Natl. Acad. Sci. U.S.A. 2019, DOI: 10.1073/pnas.1804106115

And this is a pretty big deal in smell science:
First molecular images of olfaction open door to creating novel smells
Mar 2023,

First molecular-level, 3D picture of how an odor molecule activates a human odorant receptor.

Odorant receptors are notoriously challenging, some say impossible, to make in the lab for such purposes. The Manglik and Matsunami teams looked for one that was abundant in both the body and the nose, thinking it might be easier to make artificially, and one that also could detect water-soluble odorants. They settled on a receptor called OR51E2, which is known to respond to propionate—a molecule that contributes to the pungent smell of Swiss cheese.

This molecular snapshot showed that propionate sticks tightly to OR51E2 thanks to a very specific fit between odorant and receptor. The finding jibes with one of the duties of the olfactory system as a sentinel for danger.

"This receptor is laser focused on trying to sense propionate and may have evolved to help detect when food has gone bad," said Manglik. Receptors for pleasing smells like menthol or caraway might instead interact more loosely with odorants, he speculated.

"We've dreamed of tackling this problem for years," he said. "We now have our first toehold, the first glimpse of how the molecules of smell bind to our odorant receptors. For us, this is just the beginning."

via University of California, San Francisco: Aashish Manglik, Structural basis of odorant recognition by a human odorant receptor, Nature (2023). DOI: 10.1038/s41586-023-05798-y