Thursday, September 23, 2021

Olfacotry Camouflage


Scientists used 'fake news' to stop predators from killing endangered birds—and the result was remarkable
Mar 2021, phys.org

Amazing; you just don't hear about olfactory camouflage much:

Odors emanating from the shorebirds' feathers and eggs attract these scent-hunting mammals, which easily find the nests.

Five weeks before the shorebirds arrived for their breeding season in 2016, we mixed the odors with Vaseline and smeared the concoction on hundreds of rocks over two 1,000-hectare study sites. We did this every three days, for three months.

The predators were initially attracted to the odors. But within days, after realizing the scent would not lead to food, they lost interest and stopped visiting the site.

via: Grant L. Norbury et al. Misinformation tactics protect rare birds from problem predators, Science Advances (2021). DOI: 10.1126/sciadv.abe4164

Image credit: Lord of the Rings, scene where the Black Rider sniffs and misses.

Friday, September 10, 2021

Olfactory Training for Olfactory Dysfunction


Parking this here for future reference, and for anyone still having trouble getting their sense of smell back:

Hura N, Xie DX, Choby GW, Schlosser RJ, Orlov CP, Seal SM, Rowan NR. Treatment of post-viral olfactory dysfunction: an evidence-based review with recommendations. Int Forum Allergy Rhinol. 2020 Sep;10(9):1065-1086. doi: 10.1002/alr.22624. Epub 2020 Jun 25. PMID: 32567798; PMCID: PMC7361320. https://pubmed.ncbi.nlm.nih.gov/32567798/

Background: Post-viral olfactory dysfunction (PVOD) is one of the most common causes of olfactory loss. Despite its prevalence, optimal treatment strategies remain unclear. This article provides a comprehensive review of PVOD treatment options and provides evidence-based recommendations for their use.

Methods: A systematic review of the Medline, Embase, Cochrane, Web of Science, Scopus, and Google Scholar databases was completed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Studies with defined olfactory outcomes of patients treated for PVOD following medical, surgical, acupuncture, or olfactory training interventions were included. The Clinical Practice Guideline Development Manual and Conference on Guideline Standardization (COGS) instrument recommendations were followed in accordance with a previously described, rigorous, iterative process to create an evidence-based review with recommendations.

Results: From 552 initial candidate articles, 36 studies with data for 2183 patients with PVOD were ultimately included. The most common method to assess olfactory outcomes was Sniffin' Sticks. Broad treatment categories included: olfactory training, systemic steroids, topical therapies, a variety of heterogeneous non-steroidal oral medications, and acupuncture.

Conclusion: Based on the available evidence, olfactory training is a recommendation for the treatment of PVOD. The use of short-term systemic and/or topical steroids is an option in select patients after careful consideration of potential risks of oral steroids. Though some pharmacological investigations offer promising preliminary results for systemic and topical medications alike, a paucity of high-quality studies limits the ability to make meaningful evidence-based recommendations for the use of these therapies for the treatment of PVOD.

And don't forget:
Monell Center Scientists Find that Insulin is Necessary for Repairing Olfactory Neurons: Findings Point to Possible Treatment for Smell Loss
May 2021 - Monell Center

Thursday, September 9, 2021

Dark Taxa AKA Creating Taxonomies From Scratch


New norms needed to name never-seen fungi
May 2021, phys.org

There's 150,000 species of fungi known, yet a projected 2.2 to 3.8 million still waiting to be discovered (these are called dark taxa). But because of advances in DNA sequencing and microscopy, we're learning so fast that we need a new way to organize it all. 

This comes up in the context of biosecurity, where it can only work if "organisms detected can be reliably identified and have accurate names." For fungi, that's not really possible, because believe it or not, we don't have a good catalog of fungi. 
-via: Robert Lücking et al. Fungal taxonomy and sequence-based nomenclature, Nature Microbiology (2021). DOI: 10.1038/s41564-021-00888-x

We also don't have a good way to organize the words we use to describe everyday smells, and we don't have something like a "smell taxonomy." There are plenty of sub-domains that organize their relevant smells, found in subjects like coffee, wine, perfume, and culinary arts. They always seem to take the form of a wheel (not the most complex form). You can get a good start with everyday smells at the South Coast Air Quality Management District, who created a "Characterization of Odor Nuisance" odor wheel, with the help of environmental scientist Jane Curren at UCLA circa 2016. It was based on a bunch of phone calls made to the District where people were complaining about odors in their neighborhood. She took all the words they used and organized them. 

You could also look into Ann-Sophie Barwich who is a cognitive scientist who did her dissertion on olfactory categorization, and then wrote a book called Smellosophy. Probably one of the most interesting academics you will ever hear of. I mean, her master's thesis was about the relevance of  Leibniz causality on biological classification.

Image credit: Penicillin, Kew Royal Botanical Gardens for BBC

Notes:
State of the World's Fungi, by the Kew Royal Botanical Gardens (2018), is the first ever State of the World's Fungi report revealing how important fungi are to all life on Earth. [pdf]
[State of the World's Fungi]

International Commission on the Taxonomy of Fungi (ICTF)

MycoBank is the on-line repository and nomenclatural registry provided in collaboration between the International Mycological Association and the Westerdijk Fungal Biodiversity Institute. It provides a free service to the mycological and scientific society by databasing mycological nomenclatural novelties (new names and combinations) and associated data, such as descriptions, illustrations and DNA barcodes. Nomenclatural novelties are each allocated a unique MycoBank number to be cited in the publication where the nomenclatural novelty is introduced, to conform with the requirements of the International Code of Nomenclature for algae, fungi and plants.

Identification and quantification of nuisance odors at a trash transfer station. Jane Curren, et al.  PubMed, Waste Manag. 2016 Dec;58:52-61. doi: 10.1016/j.wasman.2016.09.021. Epub 2016 Sep 28.

Post Script:
I'm looking at a popular science article about fungi. The first two "interesting" points, when looked at together, remind me of why I always have the feeling like fungi are from outerspace:
  • Fungi are in a kingdom of their own but are closer to animals than plants
  • They have chemicals in their cell walls shared with lobsters and crabs (you do know we're all becoming crabs, right?)

Monday, August 30, 2021

Promiscuous Pattern Recognition


Study reveals how smell receptors work
Aug 2021, phys.org

Big smell news - for the first time ever, using cryo-electron microscopy, we can see an olfactory receptor in action. And as expected, it doesn't work like any other receptor.

Odorant receptors are known for their 'promiscuous chemical sensitivity;' that's a scientific term, by the way. It means that any one receptor might be sensitive to hundreds of molecules, so it's been really hard  to figure out what makes any particular molecule match with a receptor.

They looked at the jumping bristletail (surprise - not the fruit fly) because it has only five types of receptors, and because one of those receptors (OR5) is really broad, responding to 60% of the smell molecules they presented to it (promiscuous).

So they look at this receptor in its default state, and then again as they expose it to smell molecules (either eugenol or DEET).

And? Its ion channel pore dilates. That's it. Both of the competing theories about how smells work were wrong. It turns out they work via nonspecific chemical interactions -- they are not recognizing a specific chemical characteristic, but something more general about the molecule itself.

And there you have it! Olfaction is still one of the strangest senses we have.

Don't forget to thank cryo-electron microscopy, and the hundreds of scientists who have been trying to figure this out over the past hundred years.

via Rockefeller University: del Mármol, J., Yedlin, M.A. & Ruta, V. The structural basis of odorant recognition in insect olfactory receptors. Nature (2021). https://doi.org/10.1038/s41586-021-03794-8

Tuesday, August 24, 2021

Amoore' Anosmias Get a Tune-Up

Back in the 1960's, a scientist named John Amoore tried to get a number on how much our sense of smell varies from person to person. In his study (limited mostly to Europeans), he found that half are anosmic to something. That was long before we sequenced the human genome. This study goes a bit further:

There's a gene for detecting that fishy smell, olfactory GWAS shows
Oct 2020, phys.org
9,000 people in Iceland showed that not only do they smell licorice and cinnamon differently, but there's a mutation that makes rotten fish smell a little less fishy. (The odors they used weren't limited to these three, there were also lemon, peppermint, and banana.)

One of the genes is called a "non-canonical olfactory receptor gene" or a trace amine receptor, TAAR 5 in this case. People with a particular variant of this gene were more likely to not smell anything when presented with the fish odor or to use descriptors for it that were neutral or positive and not seafood related, such as "potatoes," "caramel," and "rose."

"Carriers of the variant find the fish odor less intense, less unpleasant, and are less likely to name it accurately," Gisladottir said. 

"We discovered a common variant in a cluster of olfactory receptors which is associated with increased sensitivity to trans-anethole, found in black licorice products but also in spices and plants such as anise seed, star anise, and fennel," Gisladottir said. "Carriers of the variant find the licorice odor more intense, more pleasant, and can name it more accurately. Interestingly, the variant is much more common in East Asia than in Europe."

The cinnamon variant influenced the perception of trans-cinnamaldehyde, the major ingredient in both Chinese and Ceylon cinnamon. Carriers of the variant can name the cinnamon odor more accurately, they report. They also find it more intense.

via deCODE Genetics in Reykjavik, Iceland: Current Biology, Gisladottir et al.: "Sequence variants in TAAR5 and other loci affect human odor perception and naming. DOI: 10.1016/j.cub.2020.09.012

Post Script:
Here's another way to measure the difference in how we smell things -- we have a 30% variation from person to person:
378-dimensional individual olfactory receptor subtype genome:
Individual olfactory perception reveals meaningful nonolfactory genetic information.
Secundo L, Snitz K, Weissler K, Pinchover L, Shoenfeld Y, Loewenthal R, Agmon-Levin N, Frumin I, Bar-Zvi D, Shushan S, Sobel N. Proc Natl Acad Sci U S A. 2015 Jul 14; 112(28):8750-5.

Friday, August 20, 2021

On Handshakes and Animal Behavior

AKA Olfactory Sampling

Non-human primates Mark Zuckerberg and Pope Francis shaking hands and about to smell each other's chemosignals once they start covertly raising their hands near their face in about 20 seconds from now.

After you shake someone's hand, you smell your own hand. Sometimes the shaking hand, and sometimes the opposite, depending on the gender match. They call it "olfactory sampling," but we call it "smelling your fingers," and despite its being in poor taste while in public view, we do it almost neurotically, albeit covertly -- so covertly that even we don't notice ourselves doing it. 

I'm surprised this didn't resurface at the outset of the pandemic when we were all paying so much attention to how often we touch our face. In fact, the authors set us up thus:
Consistent with previous studies (Nicas and Best, 2008), we observed that humans often bring their hands to their noses. Of 153 subjects, 85 (55.55%) touched their nose with their hand at least once during baseline before the greet. Idle subjects had a hand (either right or left) at the vicinity of their nose for 22.14% of the time. (that's a lot of time!)
But this isn't just about how you can't keep your own hands off yourself:
Whereas facial self-touching has been considered a form of displacement stress response (Troisi, 2002), akin to rodent grooming, the novel framework we propose here for this behavior is that of olfactory sampling.
In this really carefully controlled study, they videotaped  hundreds of people after shaking hands with a greeter at the lab, and even outfitted the subjects tubes near their nose to monitor their sniffing behavior. The results were "unequivocal," and remind us that we are in fact animals, sniffing up a storm:
We found that humans often sniff their own hands*, and selectively increase this behavior after handshake. After handshakes within gender, subjects increased sniffing of their own right shaking hand by more than 100%. In contrast, after handshakes across gender, subjects increased sniffing of their own left non-shaking hand by more than 100%. Tainting participants with unnoticed odors significantly altered the effects, thus verifying their olfactory nature. Thus, handshaking may functionally serve active yet subliminal social chemosignaling, which likely plays a large role in ongoing human behavior.

*For example, by touching their nose when they were in the room on their own; ... Criterion for scoring was any application of a hand to the face, as long as touching was under the eyebrows and above the chin; n=271 down to 153.
And later on in the report, things get even more complicated:
The body odor of some of the experimenters was tainted by perfumes or gender-specific odors. Volunteers who shook hands with these tainted individuals behaved differently; when the experimenter was tainted with perfume the volunteers spent more time sniffing their own hands, but when the experimenter was tainted with a gender-specific odor they spent less time sniffing of their own hands. This shows that different smells influenced the hand sniffing behavior of the volunteers.
Now that you know, you might notice yourself doing it constantly. What would be really interesting now would be to somehow get some anosmics up in the mix, maybe congenitally, maybe some recent long covid anosmics, and see how these numbers change?

Notes:
Frumin I, et al. [incl Noam Sobel] A social chemosignaling function for human handshaking. eLife. 2015 Mar 03;4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4345842/

Tuesday, August 17, 2021

Did Someone Say Cheese?

Those funky cheese smells allow microbes to 'talk' to and feed each other
Oct 2020, phys.org

The more you learn, the more complicated it gets. So we know that the funky cheese smell of isovaleric acid is produced by bacteria, and we know that (some) cheese has fungus growing on it. But now we're told that they're all talking to each other, using other odor molecules.

The "cheese microbiome." Cheese doesn't house only one bacteria species, and it doesn't make only one smell, although isovaleric acid is a pretty good representative. There's a whole cheese microbiome, made of bacteria, yeast and fungi. Each one of these organisms secretes goop that digests their food, in this case that's the cheese. Their goop is kind of like making the whole world your stomach, where your digestive juices aid your digesting al fresco. As their external digestion approach does its thing, the target nutrients get broken down, and a by-product of that breakdown are odorous volatile organic compounds. 

What these researchers have discovered is that fungi also release VOCs, but instead of being an important part of the smell of cheese, they communicate to bacteria. Some bacteria accelerate their growth in the presence of the right fungi-gas. Others get real shy and shut down. These fungus VOCs do real-time genetic modification on the bacteria, changing the way they metabolize nutrients. They also eat the VOCs themselves. They eat smells. We can't eat smells. 

Anyway, the cheese microbiome now contains a VOC-ome sub-component, and this study hints that one day we may be looking very carefully at these VOC-omes, especially in the bio-factories of the future. 

via Tufts University: Casey M. Cosetta et al, Fungal volatiles mediate cheese rind microbiome assembly, Environmental Microbiology (2020). DOI: 10.1111/1462-2920.15223

Thursday, August 12, 2021

Odeuropa's Olfactory Iconographies

€2.8M grant for research project on European olfactory heritage and sensory mining:

Odeuropa bundles expertise in sensory mining and olfactory heritage. We develop novel methods to collect information about smell from digital text and image collections. They will identify and trace olfactory information in text and image datasets using AI, and promote Europe’s tangible and intangible cultural heritage.

Here's one of their ongoing projects, seen in the picture above, an odor wheel based on art historical references to smells: The Odeuropa Art Historical Scent Wheel from the Mediamatic Aroma Lab.

The Odeuropa “Nose first art historical odour wheel” starting from scent families in the centre, connected to odorants in the second ring, and then to artworks and artefacts around that, ending with an outer ring with Iconclass codes. Iconclass is a multilingual online database that museums use to tag historical images and artworks. -link

This wheel is based on imagery like paintings that were then coded with words, allowing a machine-readable dataset of odors, which will become increasingly more popular as we apply this approach to larger and more recent datasets, such as the Wikimedia Commons, or the running corpus of Instagram's zero-liked images.
 
Speaking of datasets, there are many to choose, from dog breeds to aerial photographs to 3 million "Clickbait, spam, crowd-sourced headlines from 2010 to 2015," to "4,000 physical dimensions of abolone." Wikimedia commons has 7.5 million images.

Looking back at the odor wheel, there are some interesting associations here. But they do reflect the dataset. I'm having a hard time finding details on Iconoclass but it was developed by one person in the 1950's, and based I assume on Western Art. It's currently maintained by RKD Netherlands Institute for Art History.

Here's some examples -- "street scenes and horses;" not a common conjunction in today's world. "Unicorns and cinnamon," anyone? "Prostitutes and civet," less unexpected. The two "body odors" are armpit and vagina, fyi. 

The most interesting part of all this? The lead researcher Sofia Ehrich has "become familiar with detecting depictions of smell." She can smell words and pictures. 

And speaking of words and pictures: 
Ocularcentric - like a visual bias, like we as humans tend to have an ocularcentric view of the world, with our trichromatic vision and fancy visual cortices, etc. 

Notes:
Mediamatic (in Amsterdam) is an art centre dedicated to new developments in the arts since 1983. We organize lectures, workshops and art projects, focusing on nature, biotechnology and art+science in a strong international network.

IconoClass dataset -  specialized library classification designed for art and iconography.

Lifting One's Hat

Layers of IconClass system

This is an example of the layers of the IconoClass system, pretty deep stuff. You can see how the image has words attached to it, making it a machine-readable cultural object. This is how we will teach robots of the future how to better understand us, and maybe we can even teach them how to smell.

Mario Klongmann x BigGAN - 2019

Mostly Unrelated Post Script:
An AI Artist’s Twitter Feed Is an Art Gallery
The images and videos Mario Klingemann posted under the hashtag #BigGAN can only be appreciated by treating his Twitter feed as a digital exhibition. (Images taken from the ImageNet dataset)
Feb 2019, Hyperallergenic


This AI Creates Art From Instagram Posts With Zero Likes
“Zero Likes” is trained to create glitchy visuals from forgotten social media images.
May 2017, Vice

Melbourne artist and coder Sam Hains created Zero Likes, an AI trained to respond only to those lost and lonely images that miss out on attention.

Tuesday, August 10, 2021

Headline Party

My first master's degree was in architecture, and I graduated the day the United States housing market collapsed. So my second master's was in public health, and I got my first job the day Planet Earth went into pandemic lockdown. Expertise in indoor air quality and occupant exposure during an airborne pandemic will make your life pretty busy. Hence, a list of smell-related headlines I've been collecting in the meantime:

Unparalleled inventory of the human gut ecosystem
Jul 2020, phys.org
The Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes. These genomes encode >170 million protein sequences, which we collated in the Unified Human Gastrointestinal Protein (UHGP) catalog. 

via the European Bioinformatics Institute: Alexandre Almeida et al. A unified catalog of 204,938 reference genomes from the human gut microbiome, Nature Biotechnology (2020). DOI: 10.1038/s41587-020-0603-3
Fresh sea spray turns 'sour' after being airborne
Jan 2021, phys.org
"The smallest particles become 100,000 times more acidic than the ocean within two minutes," said Angle, first author of the paper.

via University of California San Diego: Kyle J. Angle et al. Acidity across the interface from the ocean surface to sea spray aerosol, Proceedings of the National Academy of Sciences (2020). DOI: 10.1073/pnas.2018397118
Researchers create a highly sensitive biohybrid olfactory sensor
Jan 2021, phys.org
So we decided to combine existing biological sensors directly with artificial systems to create highly sensitive volatile organic compound (VOC) sensors. We call these biohybrid sensors."

Takeuchi and his team essentially grafted a set of olfactory receptors from an insect into a device that feeds certain odors to the receptors and also reads how the receptors respond to these odors. 

via the University of Tokyo: T. Yamada el al. Highly sensitive VOC detectors using insect olfactory receptors reconstituted into lipid bilayers. Science Advances (2021). DOI: 10.1126/sciadv.abd2013
Male butterflies mark their mates with repulsive smell during sex to 'turn off' other suitors
Jan 2021, phys.org

Butterfly genitals secrete an odor that covers female genitals, deterring other males from mating with them. Occimene - it's the anti-aphrodisiac (for moths).

via University of Cambridge: Darragh K, Orteu A, Black D, Byers KJRP, Szczerbowski D, Warren IA, et al. (2021) A novel terpene synthase controls differences in anti-aphrodisiac pheromone production between closely related Heliconius butterflies. PLoS Biol 19(1): e3001022. 


Cosmic mouthful - Tasters savor fine wine that orbited Earth
Mar 2021, phys.org
This comes via the Institute for Wine and Vine Research in Bordeaux, and of course the International Space Station.
Researchers develop new smell test for Parkinson's, Alzheimer's and COVID-19
May 2021, phys.org
A new smell test developed by Queen Mary University of London researchers has been found to be easy to use in patients with Parkinson's disease, and could also be helpful in diagnosing COVID-19 in the broader population.

via  Queen Mary, University of London: A. Said Ismail et al. A novel capsule-based smell test fabricated via coaxial dripping, Journal of The Royal Society Interface (2021). DOI: 10.1098/rsif.2021.0039
Scientists invent an artificial nose for continuous bacterial monitoring
Jun 2021, phys.org
via Americans for Ben-Gurion University: Nitzan Shauloff et al, Sniffing Bacteria with a Carbon-Dot Artificial Nose, Nano-Micro Letters (2021). DOI: 10.1007/s40820-021-00610-w

Thursday, August 5, 2021

Diabetes x Anosmia

Interesting theme here; anosmia, insulin and Covid:

It appears that long-Covid has more to do with the pancreas and insulin regulation than we thought, and this has implications for the health of our olfactory receptors.

Research from the Monell Center found that insulin may be able to treat smell loss:
1. Insulin plays a critical role in the maturation, after injury, of immature olfactory sensory neurons (OSNs). 

2. The research team induced diabetes type 1 in mice to reduce levels of circulating insulin reaching the OSNs. The reduced insulin interfered with the regeneration of OSNs, resulting in an impaired sense of smell. 

3. In addition, the team injured OSNs, which have a unique ability to regenerate in mammals. This approach allowed the investigators to ask whether OSNs required insulin to regenerate, which they found to be true. What’s more, they discovered that OSNs are highly susceptible to insulin deprivation-induced cell death eight to 13 days after an injury. This time window indicates that during a critical stage newly generated OSNs are dependent on insulin. They also found that insulin must be applied to regenerating OSNs at this critical time point in the neurons’ growth to be able to restore a mouse’s sense of smell.

4. Insulin promotes regeneration of regenerating OSNs in both type 1 diabetic and nondiabetic mice.

Monell Center Scientists Find that Insulin is Necessary for Repairing Olfactory Neurons: Findings Point to Possible Treatment for Smell Loss, May 2021
Post Script:
July 2021, phys.org
An increase in new-onset hyperglycemia and abnormal hormone levels lasting months after Covid infection in Italy; "This study is one of the first to show that COVID-19 has a direct effect on the pancreas," says Fiorina.

via Children's Hospital Boston: Laura Montefusco et al, Acute and long-term disruption of glycometabolic control after SARS-CoV-2 infection, Nature Metabolism (2021). DOI: 10.1038/s42255-021-00407-6

Sebastiano Bruno Solerte et al, Sitagliptin Treatment at the Time of Hospitalization Was Associated With Reduced Mortality in Patients With Type 2 Diabetes and COVID-19: A Multicenter, Case-Control, Retrospective, Observational Study, Diabetes Care (2020). DOI: 10.2337/dc20-1521

Tuesday, August 3, 2021

Nanon Nanoff


Please ignore the potential environmental disaster of embedding nanoparticles all over the planet, and instead focus on how we are reverse engineering the process of chemosensation.

Plants communicate with chemicals the way we use words. Many, almost all, of the chemicals that populate the aromatic repertoire of the fragrance industry are plant-derived. If they do not come from the plant itself, as an essential oil, then they are synthetically produced in chemical reactors, yet, the target product will have originated to imitate the molecule found in nature.

Now, we get one example of synthetic biology doing the work. Imagine the scaled-up version, the chemical factory is now a biological plant, like a factory, but modeled on an actual plant, like lemongrass, but then run through bacteria programmed to produce citronellol.

Granted the nanosized sensors described in this article below are not producing any molecules, only sensing them. But any synbio fragrance plant would need a good sensor network. 

Also, "nanobionic plants" 

Carbon nanotubes embedded in leaves detect chemical signals that are produced when a plant is damaged
Apr 2020, phys.org
These sensors can be embedded in plant leaves, where they report on hydrogen peroxide signaling waves.

Plants use hydrogen peroxide to communicate within their leaves, sending out a distress signal that stimulates leaf cells to produce compounds that will help them repair damage or fend off predators such as insects. The new sensors can use these hydrogen peroxide signals to distinguish between different types of stress, as well as between different species of plants.

"Plants have a very sophisticated form of internal communication, which we can now observe for the first time. That means that in real-time, we can see a living plant's response, communicating the specific type of stress that it's experiencing," says Michael Strano, the Carbon P. Dubbs Professor of Chemical Engineering at MIT.

via Massachusetts Institute of Technology: Tedrick Thomas Salim Lew et al. Real-time detection of wound-induced H2O2 signalling waves in plants with optical nanosensors, Nature Plants (2020). DOI: 10.1038/s41477-020-0632-4
Unrelated image credit: Krzysztof Marczak via Deviant Art

Post Script:
Center for Strategic and International Studies Headquarters, Washington DC
February 6, 2020

Thursday, June 3, 2021

Artificial Olfactory Perception and the Olfactome


Chemical informatics, machine learning and the indispensable fruit-fly, Drosophila melanogaster have been used by researchers at University of California Riverside to predict odor perception. 

Olfactory prediction is kind of a holy grail of sensory perception. Sounds sus. Let's get into the data.

image credit: Diatom, by Dr. Jan Michels for Nikon Small World 2020

Using artificial intelligence to smell the roses
Aug 2020, phys.org

First sentence they're referencing Asifa Majid. That's a great start. Her work shows us that culture, language and experience influence individual odor perception. Nonetheless, the search for the human odor code continues.

After reducing a larger dataset of 84 olfactory receptors and 54 allelic variants (138 total), they took 34 receptors, each of which is controlled by a single gene, and trained machines to predict their descriptors. The descriptors, or "the words we would use to describe the smell," came from the Vosshall Keller Rockefeller University 2016 lexicon. They've got about 170 odorants, working on 34 receptors. 

Remember that each odor receptor gene can be activated by a number of chemicals, sometimes by only one, but usually by more than one. This is what makes things complicated. Olfaction is a combinatorial affair that breaks down at the granular level.

And they made a model for each receptor, 34 different models, and fed those models the odorants. They found that you could predict chemical properties of the molecules that match each receptor tested. So now, we can use the 450,000 library of chemicals, run them through each of the 36 artificial receptors, and predict what those receptors would perceive.

Figure 5A: Few Key ORs or Chemical Features Sensibly Cluster the Perceptual Descriptors
(A) Dendrogram representation of the Euclidean distances among perceptual descriptors based on overlap of perceptual response data (% Usage) from chemicals in the ATLAS study.
(B) Dendrogram from the top five ORs picked per perceptual descriptor.
(C) Dendrogram created from five randomly chosen ORs per perceptual descriptor.
(D) Dendrogram from the five best overall predictors including OR and chemical features per perceptual descriptor. Clustering is hierarchical and based on Euclidean distance (A) or the Jaccard distance (B–D). Cluster number (colored branches) inferred from gap statistic across bootstrap samples. [find the pdf for fine-resolution]

I think, and I could be wrong, but it seems the big deal here is that they made a model for each receptor, instead of just making one model for all receptors. Whereas others have created an n-dimensional predictive space to collapse the behemoth of the chemosphere into a single equation, this team just reverse-engineered the receptors themselves.

They haven't found the odor code, but they did write 34 of them. We have hundreds of olfactory receptors. That's not everything, but we are definitely getting there.

What it CAN do? It can help us discover new chemicals, and also to discover substitutes for other chemicals that are expensive, rare, or ethically-troublesome (fear-pheromones from tortured cats for example).

What it CAN'T do? It can't predict how an odor will smell to you, as an individual. It can approximate, however, and pretty good. They mention only getting 20% of the human olfactome, or human olfactory receptor repertoire.

via UC Riverside: Joel Kowalewski et al. Predicting Human Olfactory Perception from Activities of Odorant Receptors, iScience (2020). DOI: 10.1016/j.isci.2020.101361


Post Script:
They mention something called the ATLAS dataset, but I don't know what that is, other than a proprietary data analysis software. Maybe it's their own dataset through ATLAS?

And for fun, I'll report that they do mention "substantive portion of odor identity arises early in the processing stream" which is a good way of describing the the two-layer perception process of olfaction.

The second layer, and this is the one that Asifa Majid tells us is influenced by culture, experience, and language: "It is likely that the remaining portion depends on experience-dependent modulation, supporting a downstream model with reliance on distributed neuronal networks for human perceptual coding."

Further: "Unlike the retinotopic and tonotopic patterning observed in the visual and auditory cortices, representing spatiotemporal properties of visual and auditory stimuli as they are processed at sensory neurons, piriform activity appears randomly distributed, without a clear mapping of physicochemical features (Stettler and Axel, 2009)."

Interesting: "In our analyses, the OR specialized for musk was not a top candidate for
musk predictions but contributed strongly to predictions of 'sweaty.'"

Perhaps because the model isn't "smelling" it among other calculated fragrant mixtures such as perfumes, but rather "in the wild?" 


Post Post Script:
Can't talk about the odor code without mentioning code smell, a term for when something is wrong with your code, but we're not sure what it is. 

Also, going deep on the topic here:
The Dream of Olfaction Prediction

Thursday, May 20, 2021

Olfactory Overload


For centuries, smell has been considered the lowest sense. Even Science itself has avoided it. No more; olfaction is experiencing an absolute revolution.

Oh really? Yes. Consider for a moment, the €2.8M price tag on this European olfactory heritage and sensory mining project, called Odeuopa. That's a nice price tag for research on the history of smells.


I review a few hundred articles every week, pulling aside anything I see on olfaction. Some weeks there's a good article, maybe two, sometimes nothing. Much of the time, the article is about a development in hi-tech sensors or electronic noses, or how the East doesn't like "new car smell" and what Western car companies are doing about it... . 

But now, about once a month for seven months in a row, another piece of research surfaces to enrich our understanding of olfactory perception. Not just hype-cycle blurbles, but domain-foundation scientific breakthroughs are redefining how we think about olfaction, and our models of how it works.

The news is that each one of us employs a dynamic, combinatorial chemosensory system. It's capable of adapting in real time to an ever-changing environment, and it's using a combinatorial network of hundreds of genetically-determined olfactory receptors working in unison to identify and interpret any possible combination of odorous chemicals that we could ever be exposed to. 
 
First, a reminder of what it means to be using a "combinatorial" approach to perception. Epistemologically, combinatorics comes from mathematics, but combinatoric optimization and combinatorial dynamical systems are subfields of this domain, usually found in areas like graph theory or network theory. These areas overlap with the "brains" of our early 21st century artificial intelligence machines -- the deep learning neural networks you should be hearing about daily. 

But what does it mean for olfaction to be combinatorial? It means that olfaction is all gestalt. We don't use one type of neuron to smell one type of smell. We use a bunch for each, and they overlap too. In other words, it's a mess.

Some odorants, in theory, could activate (or inhibit) every receptor we have (roughly 400 functional). And it's the combination of all those excitations and inhibitions that create odor identity. That's a lot of combinations. And you would need all of them to identify that one odorant. And if you lost only one, by viral infection for example, that thing would not smell the same. In reality, this is not how it works because it's a lot more complicated, and there are so many exceptions to the rule that it's barely a rule. But it's getting clearer by the day. 

The main point of a combinatorial system is that you can't "map" it (it's a mess, remember?). This is something Science has been trying to do for a long time. Using language as an intermediary, this attempt to map the olfactory dimension started with the Dravnieks dataset, a bunch of odorous molecules mapped to descriptors produced by people who smell those molecules:

Dravnieks A. Atlas of odor character profiles. Philadelphia: ASTM; 1985.

Arctander is also used to organize the aromasphere by way of language: 

Arctander S. Perfume and flavor chemicals (aroma chemicals). Montclair, NJ: Author; 1969.

But then things changed. The DREAM dataset is produced, using huge chemoinformatics datasets for the individual molecules, mapped against equally huge semantic analysis datasets made of a bustling lexicon of odor words. This paper via Leslie Vosshall's lab in Rockefeller University sums it up:

Keller A, Vosshall LB. Olfactory perception of chemically diverse molecules. BMC Neurosci. 2016 Aug 8; 17(1):55. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4977894/

Multidimensional Folds - Lach - 2010

And now onto 2020, a big year for olfaction. Figures so much of this will be overshadowed by a raging global pandemic.

In March, a study from Hebrew University shows us that our olfactory receptors are not just activated but inhibited, and that they can change over time from one to the other. Back in 2006, Wilson and Stevenson's book Learning to Smell investigated this idea of the blank slate. The thing is, optogenetics wasn't invented yet. Well it may have been invented, but they weren't slipping glass fibers into mouse neurons to monitor their activity in real time. We're not looking at the psychology of smell anymore but the actual neurological behaviors of it. 

And they see that the receptors themselves do in fact learn, change, adapt, and even revert back to a previous state. I've repasted this description already elsewhere on this site, because it's such a big deal, but again:
The general profile of excitatory vs. inhibitory responses by mitral cells changed with learning and task demands. In naive animals, most responsive cells (71%) responded by excitation to the odours. Following the learning of the 5-decision boundary task, the ratio of excitatory/inhibitory responses reversed. After learning, the majority (71.4%) of neurons now responded by inhibitory calcium transients to the odours (Fig. 6C,E). The ratio of inhibitory vs. excitatory responses reverted back to normal after retraining the mice on the 1-decision boundary task. Specifically, 73.3% of responsive neurons were again excitatory on day 18.
via Hebrew University: Flexible Representations of Odour Categories in the Mouse Olfactory Bulb. Elena Kudryavitskaya, Eran Marom, David Pash, Adi Mizrahi. Hebrew University of Jerusalem. Mar 24 2020. BioRxiv. doi: https://doi.org/10.1101/2020.03.21.002006
https://www.biorxiv.org/content/10.1101/2020.03.21.002006v1.article-info

April. When you hear the phrase "more than the sum of its parts," that's codeword for things combinatorial. This one doesn't use the optogenetics described above, but an imaging technique called SCAPE microscopy:

Making sense of scents - 3-D videos reveal how the nose detects odor combinations
Apr 2020, phys.org
Using a cutting-edge 3-D imaging method called SCAPE microscopy, the Columbia team monitored how thousands of different cells in the nose of a mouse responded to different odors—and mixtures of those odors. They found that the information that the nose sends to the brain about a mixture of scents is more than just the sum of its parts.
...
The researchers expected to see that the cells activated by mixtures of odors would be equivalent to adding together responses to individual odors. In fact, they found that in some cases an odor can actually turn off a cell's response to another odor in a mixture [previously known via violet ionones]; in other cases, a first odor could amplify a cell's response to a second odor.
...
The team's data challenged the traditional view that the brain makes sense of a mixture of scents by figuring out all of the individual components. It confirmed what perfumers have long known: combining different scents can create a certain experience on its own, essentially becoming an entirely new scent that can provide a completely different experience.
via Stuart Firestein's lab at Columbia University: L. Xu el al., "Widespread receptor-driven modulation in peripheral olfactory coding," Science (2020). https://science.sciencemag.org/cgi/doi/10.1126/science.aaz5390

Multidimensional - Oliver Panthsdown - 2008

Skipping May, June shows us "synthetic olfactory perception" which is exactly what it sounds like.

Researchers at New York University's Langone Health Center simulated olfactory perception with a synthetic electronic odor signal. In laymen's terms, mouse noses were tricked into thinking they smelled something when it was actually just an electrical signal. This is kind of like the way you can open someone's skull and zap certain parts of their brain, and they will feel tingles in corresponding parts of their body, even though you're not touching those parts of their body (don't try this at home though).

There are also some interesting results from this study that support the mostly-uncontroversial yet definitely misunderstood theory of information processing in the olfactory bulb, which is that the detection of odor-representations is more of a combinatorial process, and less of a one-to-one system of odor molecules and neuron receptors. And, this combinatorial perception theory is a primary reason as to why we cannot comprehensively organize olfactory experience into subsets or primary odors. (And the reason for writing a book about the language of smell.)

via NYU Langone: Manipulating synthetic optogenetic odors reveals the coding logic of olfactory perception. Edmund Chong, Christopher Wilson, Shy Shoham, Stefano Panzeri, Dmitry Rinberg. Science 19, Jun 2020, Vol. 368, Issue 6497, eaba2357. DOI: 10.1126/science.aba2357

Later on, in July, Harvard Medical School releases a similar study, showing "flexible cortical representations in odor space" here:

via Harvard Medical School: Stan L. Pashkovski et al, Structure and flexibility in cortical representations of odor space, Nature (2020). DOI: 10.1038/s41586-020-2451-1. http://dx.doi.org/10.1038/s41586-020-2451-1 [alt link] https://www.newsbreak.com/news/1593236184136/structure-and-flexibility-in-cortical-representations-of-odour-space

Sum-of-its-parts strikes again, July. 

Engineering and philosophy combine for an emerging understanding of smell
Jul 2020, phys.org
Shi Nung Ching of the Preston M. Green Department of Electrical & Systems Engineering, and doctoral student Sruti Mallik developed computational models of neural circuits that mimic the sensory act of smelling. They found the models also manifest certain properties analogous to those observed in olfactory sensory processing in insect brains.

Researchers found that their sensory system model developed emergent properties—properties that are more than the sum of their parts, so to speak—similar to properties seen in an insect's antennal lobe, which is important for its sense of smell.
via Washington University in St Louis: Sruti Mallik et al. Neural Circuit Dynamics for Sensory Detection, The Journal of Neuroscience (2020). DOI: 10.1523/JNEUROSCI.2185-19.2020
http://dx.doi.org/10.1523/JNEUROSCI.2185-19.2020

Astral Fragments - Stacy Young - 2016

Onto August. They're looking at the rat hippocampus; because that's the place where memories are stored, and it's hardwired into the olfactory system, the limbic system. They're showing that the brain identifies things differently over time. In a way, saying that there is no objective reality, only subjective multitudes:

via the University of Technology Sydney: Laura A. Bradfield et al. Goal-directed actions transiently depend on dorsal hippocampus, Nature Neuroscience (2020). DOI: 10.1038/s41593-020-0693-8
http://dx.doi.org/10.1038/s41593-020-0693-8

September, "sum of parts" again:

Nose's response to odors more than just a simple sum of parts
Sep 2020, phys.org
"New research from Kyushu University shows that a much more complex process is occurring, with some responses being enhanced and others inhibited depending on the odors present."
via Kyushu University: Shigenori Inagaki et al, Widespread Inhibition, Antagonism, and Synergy in Mouse Olfactory Sensory Neurons In Vivo, Cell Reports (2020). DOI: 10.1016

October shows us that you can teach yourself to smell better. I am compelled to remind the reader that olfactory receptor cells are the only part of your brain that pokes outside the body, making them very vulnerable. This also makes them a great point of entry for viruses invading the body, but it's also the reason why these cells regenerate profusely throughout most of our lives. And that's a reason why you can train yourself to smell better. 

These scientists basically stopped sending odors in the air to one nostril, and found that neurogenesis slowed down (use it or lose it). The idea is that as these cells re-grow, they may be changing the cell types in order to adapt to a changing environment. This is called stimulation-dependent neurogenesis, and although it's still up in the air as to how it all works, get in on the ground floor:

Study finds odor-sensing neuron regeneration process is adaptive
Oct 2020, phys.org

via University of Colorado Anschutz Medical Campus: Carl J. van der Linden et al, Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors, Cell Reports (2020). DOI: 10.1016/j.celrep.2020.108210

November now. Not olfaction specifically, but memory, which is closely related. The common theory has been that each memory gets its own neuron, but now an alternative model is ascending, and it looks more like the same group of neurons store all memories.

All the data we have on this stuff comes from fMRI. But fMRI can't see individual neurons. If we look at the neurons one at a time, we see something very different happening. 

This is certainly an idea to get familiar with. It should also fill you with wonder at what else we will figure out with rapidly-advancing neuro-tech:

Human intelligence just got less mysterious, neuroscientist says
Nov 2020, phys.org

via the University of Leicester: Rey HG, Gori B, Chaure FJ, Collavini S, Blenkmann AO, Seoane P, Seoane E, Kochen S, Quian Quiroga R. Single Neuron Coding of Identity in the Human Hippocampal Formation. Current Biology : Cb. PMID 32142694 DOI: 10.1016/j.cub.2020.01.035 

Thursday, May 6, 2021

On Fruit Flies and the History of Brain Science


Researchers uncover brain mechanisms in fruit flies that may impact future learning
Jun 2020, phys.org

I was going to write something about the trifecta between much of the basis for modern neuro- and behavioral science and fruit flies and olfaction, but this researcher sums it up pretty well:
Paul Sabandal said olfactory conditioning in fruit flies has greatly contributed to overall understanding about the mechanisms underlying associative learning and memory. Historically, in fruit flies, dopamine is implicated in both punishment- and reward-based learning while octopamine is widely considered to be essential only for reward.

When he says "historically", he implicitly refers to the fact that fruit flies, along with the elegant roundworm C. elegans, are prime biological models for studying the brain and translating that information to humans.
via the University of Texas at El Paso: John Martin Sabandal et al, Concerted Actions of Octopamine and Dopamine Receptors Drive Olfactory Learning, The Journal of Neuroscience (2020). DOI: 10.1523/JNEUROSCI.1756-19.2020

image credit: Ovary of a Fruit Fly, Dr. Yujun Chen, Nikon Small World 2020


Biology blurs line between sexes, behaviors
Aug 2020, phys.org

Never heard this one before:
Typically, C. elegans males prefer searching for mates over eating, in part because they can't smell food as well as females do. But if a male goes too long without eating, it will dial up its ability to detect food and acts more like a female. The new research shows that TRA-1 is necessary for this switch, and without it hungry males can't enhance their sense of smell and stay locked in the default, food-insensitive mate-searching mode.
via the University of Rochester Medical Center: Hannah N. Lawson et al, Dynamic, Non-binary Specification of Sexual State in the C. elegans Nervous System, Current Biology (2020). DOI: 10.1016/j.cub.2020.07.007


Scientists may have found one path to a longer life
Jul 2020, phys.org

Aaaand now they're immortal. Just kidding but we're getting there:
Studying one of the most common laboratory models used in genetic research—the fruit fly Drosophila—John Tower, professor of biological sciences, and his team found that the drug mifepristone extends the lives of female flies that have mated.
via University of Southern California: Gary N Landis et al, Metabolic Signatures of Life Span Regulated by Mating, Sex Peptide and Mifepristone/RU486 in Female Drosophila melanogaster, The Journals of Gerontology: Series A (2020). DOI: 10.1093/gerona/glaa164

Friday, April 23, 2021

Fragrance Book of the Year 2021

The Essence: Discovering the World of Scent, Perfume & Fragrance


It's back -- the de facto fragrance compendium for the modern world has risen from beneath the pandemic infopocalypse to be nominated as Fragrance Book of the Year for 2021. 

Released in Europe in late 2019, then in the United States in early 2020, this book was immediately overshadowed by the pandemic, and has now come back to life. 

Nominated by the Perfumed Plume, it stands against the legendary author of culinary bible On Food and Cooking, Harold McGee, who just released his second major book in over 30 years. His new book is called Nose Dive: A Field Guide to the World of Smells. This is stiff competition for a book that could have been one of the earliest victims of the COVID-19 pandemic.

The Perfumed Plume has been awarding fragrance journalism and fragrance books since 2016. They shine a spotlight on writing that both informs and entertains us, offering an engaging view into the oftentimes clandestine, esoteric world of fragrance and olfactory experience. 

They couldn't have picked a better book for that. Described by Fragrantica editor John Biebel as a "highly aesthetic experience," The Essence is a 288-page, full color, hardcover, stitch bound book full of essays, research, inforgraphics, interviews, histories and photographs. The book is a world unto itself. Without reading a single word, this is one of the most beautiful books you'll ever hold. (Bias alert: I did contribute two essays to this book.)

The publisher, Die Gestalten Verlag, is known for their 600 books on art, architecture, design, photography and typography, and is the only publisher where all the editors are designers. And it shows. You put this book on your coffeetable and you might never leave your apartment again. (Sarcasm alert: some of us are still on lockdown due to the pandemic and can't leave our apartments anyway.) 

It's a visually compelling time capsule of fragrance, art, and history rolled into one thick volume. ... Also featured are many revealing essays about culture and smell, such as "The Smell of Fear", "Gender and Identity", and "The Future of Scent". The editorial finesse in a project like "Essence" comes about through the keen balance of compelling graphics, thorough research, and a "something for everyone" approach to content.
The Essence: Discovering the World of Scent, Perfume & Fragrance, edited by Robert Klanten, founder and CEO of gestalten as well as Carla Seipp, fragrance writer, is the first publication by gestalten recognizing the world of scent and the figures who shape the field.

Written in the pre-covid era, February 2020


Thursday, April 22, 2021

Odor Investigations

 

I do indoor air quality work with schools. Lots of schools are old, and suffer from indoor air quality problems. Odors are a common complaint, but they're a great diagnostic for bad ventilation. Here's a typical situation -- there's a classroom, and across the hall, a bathroom. The bathroom is supposed to have an exhaust fan running all the time, because a bathroom is a potent source of indoor contaminants (and not just from the obvious, but also for the powerful cleaning products used there). If this exhaust fan isn't working,  because maybe the rubber belt connecting the motor to the fan has deteriorated over time, then the air from the bathroom can get sucked into the classroom across the hall. 

This is a problem, obviously. But sometimes it's hard to convince those in charge that it needs fixing. Sometimes nobody knows how to fix it. (Because sometimes, just because you have a job doesn't mean you're good at it.)

When things get real crazy, the workers can convince their employer to get an "air test" in their classroom. This is usually not a good idea, because they will usually not find anything, whether it's there or not, and your problems will thenceforth be dismissed, regardless of their validity. There's other ways of diagnosing indoor air quality problems.

But sometimes it does work. I'm talking about a gas canister sample, sometimes called a TO-15. An environmental specialist will bring a metal canister into your room, twist off the top, and let it suck in the air in your room for a couple minutes. Then they close the canister, bring it back to a lab, release all the air that was sucked in from your room, and analyze it. Then they spit back a long list of the VOC's found, usually scary-sounding chemicals that are actually just your deodorant, hair gel, perfume, etc. But every once in a while, I get a hit on 1,4-Dichlorobenzene, and that's when I can say aha. The air from the bathroom is getting into your classroom. 

The VOC 1,4-Dichlorobenzene is the smell of a urinal cake, also described as "mothball-like." I don't know why it was chosen as THE smell of urinal cakes, but it is, and it doesn't belong in your classroom. 

Had we just fixed the exhaust fan in the first place, we could have skipped all the steps in between. But sometimes things have to be difficult. 

Thursday, April 8, 2021

Neuromorphic Buzzwords


Recent advances give theoretical insight into why deep learning networks are successful
Aug 2020, phys.org

It's just like olfaction.

If you didn't know what a deep learning neural network was in 2015 when Hidden Scents came out, you do now. Face recognition? Deep learning. Speech recognition? Deep learning. Deep fakes?? You guessed it. 

But why would someone spend an entire chapter of a book on smell talking about brain-like computing systems? Because the little part of our brain that smells is about as close as you get to a deep learning neural network.

And the story goes like this -- Big data brings Dirty data, which then brings the curse of dimensionality. It's not like mammals->dogs->poodles. It's like "that dog that bit me one time" and "the kind of dog that likes kids" and "dogs that were selected to hunt rodents" and "coyotes" and "pet cemetary" and "totem poles." Imagine a spreadsheet that has just as many columns as it has rows. For every rule there's an exception. 

What you probably know as a "computer algorithm" is just a bunch of rules. But when every rule has an exception, algorithms don't work so good anymore. This is the curse of dimensionality. 

This is also the chemosphere being described. Chemicals are myriad and ever-changing. Any means of chemosensation will have to employ something closer to a deep learning network than to an old-fashioned computer algorithm of IF/THEN functions. And that's why our olfactory system could really be called the deep nose, and why olfaction will become the representative sense of the Age of Approximation born of the datapocalypse. 

This thought-provoking paper does a much better job describing these networks, and makes implications for their use in society:

Tomaso Poggio et al. Theoretical issues in deep networks, Proceedings of the National Academy of Sciences (2020). DOI: 10.1073/pnas.1907369117

Thursday, March 4, 2021

Artificial Pheromones and Biomimetic Mind Control


Breathing may change your mind about free will
Feb 2020, phy.org

This reminds us how interconnected the olfactory system is with our body. "Osmetic Ontogenesis" by Hosek and Freeman in 2001 is a great dive into this subject, with a title that's hard to forget.
Scientists at EPFL in Switzerland have shown that you are more likely to initiate a voluntary decision as you exhale. 
via by Ecole Polytechnique Federale de Lausanne: Hyeong-Dong Park et al. Breathing is coupled with voluntary action and the cortical readiness potential, Nature Communications (2020). DOI: 10.1038/s41467-019-13967-9



Gut bacteria may modify behavior in worms, influencing eating habits
Jun 2020, phys.org
Specific gut bacteria in the worm may modify the animal's behavior, directing its dining decisions.

"In this way, the bacteria can take control over the host animal's sensory decision-making process, which affects their responses to odors and may influence food choices" said Dr. Sengupta.
via the National Institutes of Health: MP O'Donnell et al. Modulation of olfactory behavior by a gut bacteria-produced neurotransmitter. Nature, 2020. DOI: 10.1038/s41586-020-2395-5


Non-invasive nerve stimulation boosts learning of foreign language sounds
Aug 2020, phys.org

Can this be used for olfactory nerves as well?
Researchers significantly improved the ability of native English speakers to distinguish between Mandarin tones by using precisely timed, non-invasive stimulation of the vagus nerve.
via University of Pittsburg: Non-invasive peripheral nerve stimulation selectively enhances speech category learning in adults. Fernando Llanos et al. npj [Nature Partner Journal] Science of Learning volume 5, Article number: 12 (2020). https://www.nature.com/articles/s41539-020-0070-0


A lab that reads—and writes—our dreams
Apr 2020, phys.org

Well-known olfactory researcher Judith Amoore dispenses odors as subjects slip into sleep. In follow-up interviews, subjects report memories associated with the smells.

The device is supposed to trigger scents with positive associations during nightmares to help trauma and PTSD sufferers without them even being awake.

via MIT and the Dormio device

Augmented Reality, EPFL École polytechnique fédérale de Lausanne

Pregnancy test for water' delivers fast, easy results on water quality
Jul 2020, phys.org

Frankenstein as f***
In cell-free synthetic biology, researchers take the molecular machinery—including DNA, RNA and proteins—out of cells, and then reprogram that machinery to perform new tasks. The idea is akin to opening the hood of the car and removing the engine, which allows researchers to use the engine for different purposes, free from the constraints of the car. In this case, Lucks' team used molecular machinery from bacterial cells.

"We found out how bacteria naturally taste things in their water," Lucks added. "They do so with little molecular-level 'taste buds'. Cell-free synthetic biology allows us to take those little molecular taste buds out and put them into a test tube. We can then 're-wire' them up to produce a visual signal. It glows to let the user quickly and easily see if there's a contaminant in their water."

These reprogramed "taste buds" are freeze-dried to become shelf-stable and put into test tubes. Adding a drop of water to the tube—and then flicking it—sets off a chemical reaction that causes the freeze-dried pellet to glow in the presence of a contaminant.

In Paradise, California, after the recent wildfire disaster there, ... their teams tested ROSALIND alongside gold-standard water tests and discovered that ROSALIND was able to identify the presence of elevated toxic metals in the water supply. It also provided much faster and less expensive results.
via Northwestern University: Cell-free biosensors for rapid detection of water contaminants, Nature Biotechnology (2020). DOI: 10.1038/s41587-020-0571-7


Exhaled biomarkers can reveal lung disease
Jul 2020, phys.org

Inhalable nanosensors:
"We envision that this technology would allow you to inhale a sensor and then breathe out a volatile gas in about 10 minutes that reports on the status of your lungs and whether the medicines you are taking are working," says Sangeeta Bhatia, the John and Dorothy Wilson Professor of Health Sciences and Technology and Electrical Engineering and Computer Science at MIT.
via Massachusetts Institute of Technology: Chan, L.W., Anahtar, M.N., Ong, T. et al. Engineering synthetic breath biomarkers for respiratory disease, Nature Nanotechnology (2020). DOI: 10.1038/s41565-020-0723-4


Researchers develop sensors that detect human biomarkers and toxic gas
Nov 2020, phys.org

VOCs are going to be the new big data treasure chest.

via Penn State: Ning Yi et al. Stretchable gas sensors for detecting biomarkers from humans and exposed environments, TrAC Trends in Analytical Chemistry (2020). DOI: 10.1016/j.trac.2020.116085


AI-powered 'electronic nose' to sniff out meat freshness
Nov 2020, phys.org

Go figure it has to see it to smell it...
The e-nose developed by NTU scientists and their collaborators comprises two elements: a colored barcode that reacts with gasses produced by decaying meat; and a barcode reader that uses AI to interpret the combination of colors on the barcode. To make the e-nose portable, the scientists integrated it into a smartphone app that can yield results in 30 seconds.
via Nanyang Technological University: Lingling Guo et al. Portable Food‐Freshness Prediction Platform Based on Colorimetric Barcode Combinatorics and Deep Convolutional Neural Networks, Advanced Materials (2020). DOI: 10.1002/adma.202004805

The Cat Copter, for real.

A system for swarm robotics applications inspired by pheromone communication in insects
Jul 2020, phys.org

Biomimetic artificial pheromone signaling in robotic swarms:
One of the most promising systems developed so far is COSΦ, a system that uses light to emulate pheromone release in humans and animals.

So far, the researchers evaluated their artificial pheromone system in a series of experiments in which a swarm of small mobile robots moved around and adapted to different environmental factors. Their results were highly promising, as their system enabled effective communication and prompted the desired group behaviors among members of the swarm.
via the University of Manchester: Seongin Na et al. Bio-inspired artificial pheromone system for swarm robotics applications, Adaptive Behavior (2020). DOI: 10.1177/1059712320918936


Researchers find a chemical that makes locusts swarm
Aug 2020, Ars Technica

Distant future, we will also have pheromone programming or engineering, so that we don't "swarm" and so we can be more easily controlled

via the Chinese Academy of Sciences: 4-Vinylanisole is an aggregation pheromone in locusts
Xiaojiao Guo. Nature volume 584, pages584–588(2020). 12 Aug 2020. DOI: 10.1038/s41586-020-2610-4
https://www.nature.com/articles/s41586-020-2610-4


Researchers one step closer to bomb-sniffing cyborg locusts
Aug 2020, phys.org

An irresistible scent makes locusts swarm, study finds
Aug 2020, phys.org

'The Smellicopter,' an obstacle-avoiding drone that uses a live moth antenna to seek out smells
Dec 2020, phys.org

Awesome. Made me think of the catcopter though. Ah, old times.
"Nature really blows our human-made odor sensors out of the water," said lead author Melanie Anderson, a UW doctoral student in mechanical engineering. "By using an actual moth antenna ...
via the University of Washington: Melanie Joyce Anderson et al. A bio-hybrid odor-guided autonomous palm-sized air vehicle, Bioinspiration & Biomimetics (2020). DOI: 10.1088/1748-3190/abbd81