Wednesday, November 30, 2022

Living With Friends

Above we see a microscopic view of the Paenibacillus bacteria, found in coffee machines and where coffee is prepared. It's been used as a probiotic for both chickens and bees, and might have something to do with the idea that coffee is good for your health. 

But that's just coffee. Onto the real story -- nobody lives alone, and that includes even those of us who don't live with other people. We're talking about the vast array of microbes that share our domestic biome with us. They outnumber us by the billions (uncountable really) and could have a strong influence on our health, maybe even our behavior (looking at you Toxoplasmosis), all by way of the mediating effects between our microbiome and our immune system. And they smell. Not all of them, but where there's life, there's smells. It's our own domestic ecology of smells.  

Each one of us affects the microbiome we live with, depending on who we are, what we eat, what we do for work and in our spare time, how we clean, how often and how thoroughly we clean, ad infinitum. The home is a dynamic place, and very different from a scientific laboratory, in almost every way, and so we don't have a good idea of what's happening in our homes, not on a biological basis, and not even on a chemical basis. 

And then came the HOME house, the HOME Chem model house, a chemical-lab-house, put together by 60 scientists from 13 universities in Austin, Texas circa 2020. They do regular-house things and measure the chemical profile of the air inside the home over time while they cook, clean, eat, sleep. It might sound mundane, but it's the first time we're getting real world indoor air quality data from the domestic frontier.

Most air quality data comes from outside air. We haven't been thinking about the indoor air for very long, and much less resources and scientific inquiry have been devoted to it. The HOME project gives us the first glimpse of what's really happening to our indoor environment while we live there.  

With roommates, it's all about chemistry, molecularly speaking
Jun 2022,

An experimental test home was erected in Austin, Texas during the summer of 2018. The house was designed for ordinary use and included bathrooms, a kitchen, gathering and work areas. Overnight stays were prohibited, but 45 study participants, plus visitors, spent time in the house, occupying it for approximately six hours per day for 26 days, during which they performed scripted activities, such as cooking, cleaning and socializing.

The house was deep cleaned with a bleach solution. Nonetheless, researchers said traces of molecules associated with humans were still present. After almost of month of human occupation, the house was alive with molecular and microbial abundance and diversity, albeit unevenly distributed.

Not surprisingly, the kitchen and toilet were hotspots of molecular and microbial diversity, though numbers fluctuated with surface cleaning and sanitation. "It appears that, even when a subset of chemistry is removed because of the cleaning, it is only temporary and/or partial, as the sum total of cleaning and human activities overall results in an increase in accumulation of richer chemistry," the authors wrote.

via University of California San Diego, Colorado State (Delphine Farmer), and University of Colorado: Alexander A. Aksenov et al, The molecular impact of life in an indoor environment, Science Advances (2022). DOI: 10.1126/sciadv.abn8016

Here's more links on HOME:

And here's some information on how bad we are at perceiving air quality indoors:
  • Teachers did not accurately perceive mechanical ventilation sufficiency
  • Air quality and temperature are conflated
  • Dramatic difference in IAQ perception (but not quality) in summer vs winter
  • Occupants misperceive temperature as a proxy for indoor air quality; they think cooler air is better, and confuse warm air with "stuffy, stale" air
  • Teachers in classrooms with worse ventilation were more satisfied with classroom temperature
  • Occupants don't understand how the systems work, and think incoming cold air in winter is a defect, for example (when in fact it is the system adding fresh air to the mix); they then say the system isn't working, and therefore they must have bad IAQ; they also think the only time the system brings fresh air is when the AC is on, which is the complete opposite of what's happening
Source: Pistochini T, Mande C, Modera M, et al. Improving Ventilation and Indoor Environmental Quality in California K-12 Schools (CEC-500- 2020-049). Sacramento, CA: California Energy Commission; 2020.

Thursday, November 17, 2022

Everyone Likes Vanilla

People around the world like the same kinds of smells
Apr 2022,

Odor preference is molecular. People share odor preferences regardless of cultural background. Traditionally it has been seen as cultural.

First of all, the thumbnail for this article, of the girl smelling the flower in profile view, is used every time a smell article comes up on
Girl Smelling a Flower in Profile - Petr Kratochvil

So I ran it through the Stable Diffusion library at, "girl smelling a flower in profile," and got top image above, what I'll call "Woman Eating a Flower by William-Adolphe Bouguereau and Gustav Klimt" [link]

Second of all, look that the list of collaborators here -- this is not your average smell study:

Department of Clinical Neuroscience at Karolinska Institutet, School of Life Sciences at Arizona State, Centre for Languages and Literature at Lund, Department of Anthropology at University College London, Colegio de Ciencias Sociales y Humanidades at Universidad San Francisco de Quito in Ecuador, Instituto de Investigaciones Filológicas at the National Autonomous University of Mexico, School of Languages and Linguistics at University of Melbourne, Monell Chemical Senses Center, Department of Neuroscience at University of Pennsylvania (Asifa Majid as corresponding author)
The secret? 

Many of the researchers are field workers working with indigenous populations. For this present study, the researchers selected nine communities representing different lifestyles: four hunter-gatherer groups and five groups with different forms of farming and fishing. Some of these groups have very little contact with Western foodstuffs or household articles.

"Since these groups live in such disparate odiferous environments, like rainforest, coast, mountain and city, we captured many different types of 'odor experiences'," says Dr. Arshamian.
The results:

The study included a total of 235 individuals, who were asked to rank smells on a scale of pleasant to unpleasant. The results showed variation between individuals within each group, but global correspondence on which odors are pleasant and unpleasant. The researchers showed that the variation is largely explained by molecular structure (41 percent) and by personal preference (54 percent). 

^One other study measured about 30% difference between any two people, this now says 54%, just keeping track.

The odors the participants were asked to rank included vanilla, which smelled best. This was followed by ethyl butyrate, which smells like peaches. The smell that most participants considered the least pleasant was isovaleric acid, which can be found in many foods, such as cheese, soy milk and apple juice, but also in foot sweat.

I think we knew vanilla was the universally liked odor, but this study is likely more reliable. 

via Karolinska Institutet, University of Oxford, Lund University, Stockholm University, University College London, Arizona State University, Monell Chemical Senses, Universidad San Francisco de Quito (Ecuador), University of Melbourne, and National Autonomous University of Mexico: Artin Arshamian, Richard C. Gerkin, Nicole Kruspe, Ewelina Wnuk, Simeon Floyd, Carolyn O’Meara, Gabriela Garrido Rodriguez, Johan N. Lundström, Joel D. Mainland, Asifa Majid, The perception of odor pleasantness is shared across cultures, Current Biology (2022). DOI: 10.1016/j.cub.2022.02.062

AI Art - Emma Watson in a Tunic Holding a Flower by Rubens - 2022
Emma Watson wearing green tunic holding a flower. Painted by Rubens, high detail [link]

Post Script:
(Personal opinion not backed by science) I think cultural influence on odor preference only works for bad smells, and specifically the "quantum hedonic" smells like parmesan cheese, kimchi, durian fruit, etc. That's where the signal is for cultural influence (and if put in the same dataset as vanilla and peaches would get lost).

Thursday, November 10, 2022

The Past Doesn't Smell Like It Used To

Scientists find ways to study and reconstruct past scents
Apr 2022,

They're trying to develop "an archaeology of scent," which is hard because smells are ephemeral, and last only as long as their source. But because of advances in chromatography, mass spectrometry, sequencing technologies and modern bioinformatics, which include metabolomics, proteomics and genomics; they can identify the organic remains preserved on surfaces like walls, ceramic vessels, incense burners, perfume flasks, cooking pots, dental calculus, mummies, and entire streets:

Advanced biomolecular and ‘omics’ sciences enable more direct insights into past scents, offering new options to explore critical aspects of ancient society and lifeways as well as the historical meanings of smell.

The whole paper is very interesting, and although I encourage anyone interested in ancient history to read it, for those who don't, I bring back only this -- palaeofaeces -- it's a thing in archaeology, and now in olfactory archaeology too: "in an Iron Age roundhouse in Scotland, chemical characterization of floor sediments provided insight into living conditions, hygiene practices and the temporary sheltering of animals in human living areas during this period."
-Mackay, H. et al. J. Archaeol. Sci. 121, 105202 (2020). [pdf]

via the Department of Archaeology at the Max Planck Institute for the Science of Human History in Jena, Germany: Huber, B., Larsen, T., Spengler, R.N. et al. How to use modern science to reconstruct ancient scents. Nat Hum Behav 6, 611–614 (2022).

via James Gilleard and Justin Gerard

Post Script:
Speaking of human history, the Odeuropa project is taking a completely different angle -- they use computer science to identify, scrape, and coordinate pictures that contain smells in them, either by visually recognizing objects tagged as related to smells, or by reading the text captioned with the image. Sensory mining they call it:

Odeuropa is a European research project which bundles expertise in sensory mining and olfactory heritage. We develop novel methods to collect information about smell from (digital) text and image collections.

Thursday, November 3, 2022

Chemical Intelligence

'E-nose' sniffs out mixtures of volatile organic compounds
Jun 2022,

Electric nose with porous metal-organic framework films that distinguish xylene isomer mixtures for environmental health monitoring.

Previously, researchers used gas chromatography analysis to identify the three forms of xylene. But this procedure requires large instruments that are expensive, and the analyses are time intensive. 

The researchers prepared six different porous MOF films known to adsorb xylene isomers and applied them to gravimetric sensors in an array called an "e-nose." By analyzing the sensor array data with a machine learning algorithm, the team could determine the composition of the mixtures with 86% accuracy for the 10-ppm mixture and 96% accuracy for the 100-ppm mixture

via Karlsruhe Institute of Technology's Institute of Functional Interfaces and University of Pittsburgh Department of Chemical & Petroleum Engineering: VOC Mixture Sensing with a MOF Film Sensor Array: Detection and Discrimination of Xylene Isomers and Their Ternary Blends, ACS Sensors (2022). DOI: 10.1021/acssensors.2c00301

a detailed blueprint of god, top - secret document 

Nano-sensor detects pesticides on fruit in minutes
Jun 2022,

Current techniques for detecting pesticides on single products before consumption are restricted in practice by the high cost and cumbersome manufacturing of its sensors.

Uses flame-sprayed nanoparticles made from silver to increase the signal of chemicals, "The flame spray can be used to quickly produce uniform surface-enhanced Raman scattering (SERS) films across large areas, removing one of the key barriers to scalability,"

To test the sensors' practical application, the researchers calibrated them to detect low concentrations of parathion-ethyl, a toxic agricultural insecticide that is banned or restricted in most countries. A small amount of parathion-ethyl was placed on part of an apple. The residues were later collected with a cotton swab that was immersed in a solution to dissolve the pesticide molecules. The solution was dropped on the sensor, which confirmed the presence of pesticides.

via Karolinska Institutet: SERS Hotspot Engineering by Aerosol Self-Assembly of Plasmonic Ag Nanoaggregates with Tunable Interparticle Distance, Advanced Science (2022). DOI: 10.1002/advs.202201133

Damaged plants and fake perfumes can be identified rapidly and reliably in real time
Jun 2022,

Chiral detection:

Most natural chiral substances are found in two mirror-image forms present in different relative quantities. Therefore, every plant and every perfume must have its own individual chiral signature.

The relative ratios of the two enantiomers of pinene naturally vary in the emissions of such plants, but critically depend on the state of health of the plant.

Fake perfumes will have a chiral signature that differs from that of the originals.

The Mainz-based researchers have developed a cavity-enhanced polarimetric method for optical chiral analysis to detect the differing optical rotation effects of chiral molecules under polarized light. The researchers have been able to achieve a sensitivity that is better than that of the current state-of-the-art equipment by several orders of magnitude.

via Universitaet Mainz and the Max Planck Institute for Chemistry: Lykourgos Bougas et al, Absolute optical chiral analysis using cavity-enhanced polarimetry, Science Advances (2022). DOI: 10.1126/sciadv.abm3749


Thursday, October 27, 2022

Advances in Olfactory Perception

Scientists use machine learning to predict smells based on brain activity in worms
Jan 2022,

Putting this here because they used graph theory aka network science to decode the otherwise cacophony of neuronal crosstalk involved in smelling.

Also, why C. elegans? It has only 302 neurons, that's why:

Chalasani's team set out to study how C. elegans neurons react to smelling each of five different chemicals: benzaldehyde (almond), diacetyl (popcorn), isoamyl alcohol (banana), 2-nonanone (cheese), and sodium chloride (salt).

The researchers engineered C. elegans so that each of their 302 neurons contained a fluorescent sensor that would light up when the neuron was active. 

By looking at basic properties of the datasets—such as how many cells were active at each time point—Chalasani and his colleagues couldn't immediately differentiate between the different chemicals. So, they turned to a mathematical approach called graph theory, which analyzes the collective interactions between pairs of cells: When one cell is activated, how does the activity of other cells change in response?

The algorithm was able to learn to differentiate the neural response to salt and benzaldehyde but often confused the other three chemicals.

via Salk Institute, Cold Spring Harbor Laboratory and UC San Diego: Javier J. How et al, Neural network features distinguish chemosensory stimuli in Caenorhabditis elegans, PLOS Computational Biology (2021). DOI: 10.1371/journal.pcbi.1009591

a highly detailed, macro shot of a human nose, 8k, depth of field

The art of smell: Research suggests the brain processes smell both like a painting and a symphony
Apr 2022,

"These findings reveal a core principle of the nervous system," using a model to simulate the workings of the early olfactory system. This is a reminder that the olfactory system is an ideal model for understanding the brain.

In their computer simulation, they found that centrifugal fibers switched between two different modes -- one worked on a specific instant in time, while the other worked on the neural patterns across time.

This is where I make a further interpretation, which might be incorrect, but it seems like one is for comparing a smell to the body's repository (is this good or bad for me? have I smelled this before? where? who was I with?) and the other mode is for comparing the smell against itself, over time, perhaps to learn whether it's getting stronger or weaker. One uses autobiographical, physiological memory, and the other uses basic chemotaxis. One ontogeny and the other phylogeny?

Anyway, another reminder by one of the authors that the olfactory system is a good model: "Computational approaches inspired by the circuits of the brain such as this have the potential to improve the safety of self-driving cars, or help computer vision algorithms more accurately identify and classify objects in an image." -Krishnan Padmanabhan, associate professor of Neuroscience at University of Rochester School of Medicine and Dentistry

via University of Rochester Medical Center: Zhen Chen et al, Top-down feedback enables flexible coding strategies in the olfactory cortex, Cell Reports (2022). DOI: 10.1016/j.celrep.2022.110545

Sniffing out the brain's smelling power
Oct 2022,

(Out of order but seemingly related to the above) Here's another way of thinking of the two processes to smelling -- We said mitral cells are what do the smelling, but mostly because those were the ones we could see. Tufted cells were harder to see, up until now -- they find that the mitral cells were faster, more discriminating, and more broadly-tuned. 

The authors think the mitral cells only enhance important smells, but the tufted cells are part of a background process for identity and intensity. 

via Cold Spring Harbor Laboratory: Honggoo Chae et al, Long-range functional loops in the mouse olfactory system and their roles in computing odor identity, Neuron (2022). DOI: 10.1016/j.neuron.2022.09.005

a straight smooth vertical tube with the texture of human skin, highly realistic, hyper-real, 4k, Octane render 

Researchers map mouse olfactory glomeruli using state-of-the-art techniques
Apr 2022,

While other research teams previously examined the organization of glomeruli in the olfactory bulb, so far they only identified the positions of a limited subset of these clusters. As a result, the relationship between the location of glomeruli and odor discrimination has been very difficult to infer.

They used a combination of single-cell RNA sequencing, spatial transcriptomics and machine learning techniques. This allowed them to create a map that outlined the brain regions where most of the sensory neurons in the mouse olfactory bulb sent odor-related information.

via University of Massachusetts Medical School, Broad Institute of Harvard and MIT, and Stanford University: I-Hao Wang et al, Spatial transcriptomic reconstruction of the mouse olfactory glomerular map suggests principles of odor processing, Nature Neuroscience (2022). DOI: 10.1038/s41593-022-01030-8

How mosquito brains encode human odor so they can seek us out
May 2022,

Of the two nerve centers, one responds to many smells including human odor, essentially saying, "Hey, look, there's something interesting nearby you should check out," while the other responds only to humans. Having two may help the mosquitos home in on their targets, the researchers suggest.

First genetically engineer mosquitos whose brains lit up when active, and then deliver human-flavored air (with decanal and undecanal).

"When I first saw the brain activity, I couldn't believe it—just two glomeruli (out of 60) were involved. That contradicted everything we expected, so I repeated the experiment several times, with more humans, more animals. I just couldn't believe it. It's so simple."

via Princeton: Carolyn McBride, Mosquito brains encode unique features of human odour to drive host seeking, Nature (2022). DOI: 10.1038/s41586-022-04675-4

Thursday, October 20, 2022

Body Building for the Odor-Indulgent Robot

When Hidden Scents was written, back in 2015, it was certain that we wouldn't see an artificial smelling machine akin to the state of visual object recognition at the time, until we created robots that were indistinguishable from humans -- robots that grew up like a child did, complete with it's own physiological and emotional response to its environment, especially its social environment, and of course with its own resulting autobiography. 

Not until then would a robot, or even a simple computing device, be able to perform anything even close to the phenomenon of olfactory experience. And that's mostly because every one of us smells things differently, whether its genetics inherited before birth, anosmic dysfunction from viral infections, olfactory desensitization from old age, or just difference in cultural or personal preference. Without all this mess, no matter how hard you try to replicate the process of olfaction, you can't really call it the same thing as smelling unless you have an authentic adult human in the equation.

Granted there are reverse engineered electronic noses implanted on the bodies of roboticized locust cyborgs that have been programmed to detect explosives. Or less sci-fi e-noses used to detect fake whiskey. But that's not what we're talking about here. 

The headlines pasted below show us the dawn of the baby-bots, robots started from scratch, to understand themselves, and maybe even to accumulate an autobiographical identity. 

Researchers trained an AI model to 'think' like a baby, and it suddenly excelled
Jul 2022,

The exciting finding by Piloto and colleagues is that a deep-learning AI system modeled on what babies do, outperforms a system that begins with a blank slate and tries to learn based on experience alone.

via Princeton University: Luis S. Piloto et al, Intuitive physics learning in a deep-learning model inspired by developmental psychology, Nature Human Behaviour (2022). DOI: 10.1038/s41562-022-01394-8

Image credit: AI Art - Fragrance Advert by Magritte - 2022: portrait fragrance advertising campaign by magritte [link]

Engineers build a robot that learns to understand itself, rather than the world around it
Jul 2022,

Robot able to learn a model of its entire body from scratch, without any human assistance by creating a kinematic model of itself, and then using its self-model to plan motion, reach goals, and avoid obstacles in a variety of situations. It even automatically recognized and then compensated for damage to its body.

The researchers placed a robotic arm inside a circle of five streaming video cameras. The robot watched itself through the cameras as it undulated freely. After about three hours, the robot stopped. Its internal deep neural network had finished learning the relationship between the robot's motor actions and the volume it occupied in its environment.

Yeah I'm creeped out.

via Columbia University School of Engineering and Applied Science: Boyuan Chen, Fully body visual self-modeling of robot morphologies, Science Robotics (2022). DOI: 10.1126/scirobotics.abn1944.

Thursday, October 13, 2022

Headlines in the Smell World

Scientists thought they knew how the nose 'knows,' but new research suggests otherwise
Aug 2022,

I'm not doing a great job following this development, a reversal rather -- there's apparently some reconsideration that needs to be given to the way odorous molecules activate their respective olfactory receptors. Smell is the most understudied of all our senses, so it should be less of a surprise that one of the foundationary hypotheses of olfactory science needs some fine-tuning: 

G protein signal amplification is actually very low—so low that the probability of an odorant receptor activating just one G protein would be perhaps only 1 in 10,000. Yau said that, as such, the activation level "is very weak."

On a sidenote, what really stands out to me from this article is that the rhodopsin in the photosensitive cells on your retina (and all over your body in fact) are so sensitive they can detect a single photon of light. One single photon. And I thought our nose was sensitive. (It is, but for chemicals; the eye, and the photoreceptors in it, are for detecting the electromagnetic radiation beaming through our solar system.)

via Johns Hopkins University School of Medicine: Rong-Chang Li et al, Low signaling efficiency from receptor to effector in olfactory transduction: A quantified ligand-triggered GPCR pathway, Proceedings of the National Academy of Sciences (2022). DOI: 10.1073/pnas.2121225119

Friends at first sniff: People drawn to others who smell like them
Jun 2022,

The researchers found that the odor signatures of "click friends" were statistically more closely matched than odors between non-friends.
This study was done using the T-shirt test, an old trusty in smell science. 

I can't figure out which is more interesting here. The word "click friends" is pretty cool, never heard it. But this one is good: "Nonhuman terrestrial mammals constantly sniff themselves and each other and, based on this, decide who is friend or foe," wrote a group of researchers led by Inbal Ravreby at Weizmann Institute of Science in Israel.

"I don't sniff myself; I am not an animal; gross" as you completely obliviously brush your hair away from your face, or scratch your temple. The study that proved our absolute inability to avoid smelling our own hands (and the hands of everyone we meet, by way of our own hands that shook theirs) found that BEFORE the study even started, while people were still in the waiting room, they had their hand ready next to their nose 22% of the time! (see older post and the article itself). Filthy animals!

via Weizmann Institute of Science in Israel: Inbal Ravreby et al, There is chemistry in social chemistry, Science Advances (2022). DOI: 10.1126/sciadv.abn0154

People who consider olfaction important and actively sniff other's odors have stronger sexual desire
Aug 2022,

This study is based on questionnaires given to Chinese college students, and recall that there is a general understanding in the smell world that Asian people tend to not have the same scent-emitting glands as non-Asians; in other words, the deodorant market doesn't work very well in China. After their initial findings however, they started over and sent the same questionnaires to college students in both the U.S. and in India, and after all that:

  • Students who reported giving high value to olfaction or who actively sniffed other people also reported having a stronger sexual desire than others who responded.
  • Women tended to place more emphasis on smell than men, and reported lower levels of sexual desire in general.
  • Men in India reported stronger sexual desire than those in China and the U.S., and they also reported placing more importance on olfaction.  

A final thought -- culture in some ways can be a stronger mediator for olfactory perception than biology or genetics. Science like this is great, but it's only s very small piece of the full picture. I'm thinking of how the Marshmallow Test fell apart in a recent study because they considered that Japanese kids are conditioned to wait for everyone to be ready to eat at the dinnertable, and U.S. kids are not. 

via Southern Medical University in China and Technische Universität Dresden in Germany: Zi-lin Li et al, Sniffing of Body Odors and Individual Significance of Olfaction Are Associated with Sexual Desire: A Cross-Cultural Study in China, India, and the USA, Archives of Sexual Behavior (2022). DOI: 10.1007/s10508-022-02398-1

Rapid loss of smell predicts dementia and smaller brain areas linked to Alzheimer's
Jul 2022,
(But how about their sexual desire??)

via University of Chicago Medicine: Rapid olfactory decline during aging predicts dementia and GMV loss in AD brain regions, Alzheimer s & Dementia (2022). DOI: 10.1002/alz.12717

New study reveals where memory fragments are stored
Jul 2022,

This is about memory recall, the way we access memories stored in our brains, and it certainly does change the olfactory science, since we tend to consider olfaction as being deeply connected to our autobiographical memory via the hippocampus, which it is, but this suggests there are more olfactory details being stored in the prefrontal cortex than we thought:

While the overall experience is stored in the hippocampus, the brain structure long considered the seat of memory, the individual details are parsed and stored elsewhere, in the prefrontal cortex. This separation ensures that, in the future, exposure to any individual cue is sufficient to activate the prefrontal cortex, which then accesses the hippocampus for recall of the whole memory.

via Laboratory of Neural Dynamics and Cognition at Rockefeller University and Weill Cornell Medicine: Priyamvada Rajasethupathy, Prefrontal feature representations drive memory recall, Nature (2022). DOI: 10.1038/s41586-022-04936-2