Thursday, March 31, 2022

Skunk Notes

Why cannabis smells skunky
Dec 2021,

Finally, move over terpenes, the real smell of cannabis is here -- a new family of prenylated volatile sulfur compounds (VSCs), aka "skunk" is found in dank buds. 

Of the VSC varieties, 3-methyl-2-butene-1-thiol (VSC3) was the skunkiest. And of the 13 strains of cannabis tested, Bacio Gelato was the skunkiest.

via American Chemical Society: Iain W. H. Oswald et al, Identification of a New Family of Prenylated Volatile Sulfur Compounds in Cannabis Revealed by Comprehensive Two-Dimensional Gas Chromatography, ACS Omega (2021). DOI: 10.1021/acsomega.1c04196

Post Script:
Don't forget that dank smells does not mean potent pot, yet people associate citrusy-sweet-sour aroma with more THC:
Gilbert AN, DiVerdi JA (2018) Consumer perceptions of strain differences in Cannabis aroma. PLoS ONE 13(2): e0192247.

And, from a separate study, it was noticed that the genetic, terpinoid and cannabinoid profiles of selected strains didn't match their descriptions as either Sativa or Indica. Instead, it looks like people just name them whatever they smell like, sweet for Sativa and earthy for Indica:
S. Watts et al, Cannabis labelling is associated with genetic variation in terpene synthase genes, Nature Plants (2021) DOI: 10.1038/s41477-021-01003-y

Can't leave without this; why does natural gas smell somewhat skunky? It's been odorized on purpose since a big explosion that killed almost 300 people in the 1930's:
49 CFR, Part 192:Transportation of Natural and Other Gas by Pipeline: Minimum Federal Safety Standard, Subpart L: Operations, 192.625 - "Odorization of Gas"

Are Terpenes the New Antioxidants, 2018

Monday, March 28, 2022

Simulated Oversight

'Virtual nose' may reduce simulator sickness in video games
Purdue University News, Mar 2015  

Yes, you can relieve motion sickness in virtual reality by coding a nose overlay into the frame as a visual guide.

I sure didn't realize it until I read this, but you're looking at your nose all day; you're looking at it right now. Well, maybe you're not looking at it, but it's there. Maybe now you're looking at it, since we're talking about it. Anyway, it's there all day. If your eyes are open, your nose is in your field of vision. And when it's not, you're disoriented.

I'm pretty sure this is not what they mean when they say "right under your nose" or "right in front of your face," but it sure works in this case. Throw that onto the heaping pile of other things we don't notice about our nose or what it does for us. And add that to the other pile of things that we could improve if we looked to the nose and olfaction in general as a source of biomimetic supremacy.

via Purdue University: Whittinghill, D.M. et al. Nasum virtualis: A simple technique for reducing simulator sickness. In Proceedings of the Games Developers Conference (GDC), San Francisco, CA, USA, 2–6 March 2015; p. 74.

via University of Wuerzburg: A Virtual Nose as a Rest-Frame - The Impact on Simulator Sickness and Game Experience. Carolin Wienrich et al, 10th International Conference on Virtual Worlds and Games for Serious Applications, Sep 2018. DOI:10.1109/VS-Games.2018.8493408

via the BioComputing Lab at Korea University of Technology and Education: A Study on Visually Induced VR Reduction Method for Virtual Reality Sickness. Ju-hye Won and Yoon Sang Kim. Appl. Sci. 2021, 11(14), 6339;

Thursday, March 17, 2022

Flipping the Switch

The 'surprisingly simple' arithmetic of smell
Jan 2022,

The age of artificial olfaction is upon us.

This is now the second report in the last few months that presents a computational model for the olfactory bulb, which is the biological supercomputer on your face that crushes gigtons of databytes per attosecond (slight exaggeration).

The last paper came from a physicist working on information theory (Tavoni et al at Penn State). Another paper the month prior, which came from none other than the lab that discovered olfactory receptors, found, again, a computational model, discovered via machine learning, that compresses the n-dimensionality of odorant sensory data. 

But again, this new paper comes primarily from a department of electrical and systems engineering, in collaboration with the biomedical engineering department. I don't know everything that's going on, I only read the papers on the weekends, but that's a lot of papers about computing in olfaction, and from people who do not study olfaction exclusively.

And this is at the level of the bulb. We're not talking about the DREAM project, where big-data's worth of words and molecules are processed by GPT-3 to predict the names of smells. This is about looking at the hardware. How in the world does that bulb, which compresses thousands of receptors, themselves receiving information from un-countable stimuli, into dozens of signals that go on to control the entire enormity of a mammalian body via its limbic system. The bulb is the choke point for this system, and it's using magic that we are only now beginning to understand to the point of copying it. 

I doubt this is the earliest example, but as far back as 1991, scientists were talking about olfaction as a model system for computational neuroscience. These were neuroscientists and psychologists writing about this. But they could see the significance -- it's literally wired like the deep learning neural networks you hear about in the news (you know, powering the AI in your toaster, your tissue box and your alarm clock). 

It really looks like we're getting the hang of this. They started with a simple question -- how come things smell the same to us, even in different contexts or environments? Like how a plaid shirt looks okay in your sunlit bedroom, but later looks like a shit sandwich in the fluorescent lights of your office (or remember the black-and-gold dress? maybe you're trying to forget). 

If smells come from evaporating molecules, which are literally volatile, changing all the time based on environmental conditions, how come they always smell the same to us? Maybe olfaction would be a good model to investigate. 

So they did, by pairing locusts with a training smell, under all kinds of different conditions, hungry, full, hot, cold, humid, dry. Every time, the locust recognized the training smell (with the locust equivalent of a salivating dog). Yet, "The neural responses were highly variable," one of the researchers said. Same molecule, same response, but completely different receptor patterns, every time. It just doesn't make sense.

Deep learning to the rescue (obviously). The algorithm found that it's the interaction of activating and inhibiting neurons; I'll copy the copy directly:

Finding the features you want is similar to the information conveyed by the ON neurons. Absence of deal breakers is similar to silencing of the OFF neurons. As long as enough ON neurons that are typically activated by an odorant have fired—and most OFF neurons have not—it would be a safe bet to predict that the locust will open its palps in anticipation of a grassy treat.

via the Department of Electrical and Systems Engineering and the Department of Biomedical Engineering, Washington University in St. Louis: Srinath Nizampatnam et al, Invariant odor recognition with ON–OFF neural ensembles, Proceedings of the National Academy of Sciences (2022). DOI: 10.1073/pnas.2023340118

And further reading:
via University of Pennsylvania: Gaia Tavoni et al, Cortical feedback and gating in odor discrimination and generalization, PLOS Computational Biology (2021). DOI: 10.1371/journal.pcbi.1009479

via Massachusetts Institute of Technology's McGovern Institute for Brain Research: Peter Y. Wang et al, Evolving the olfactory system with machine learning, Neuron (2021). DOI: 10.1016/j.neuron.2021.09.010.

via MIT: Davis J L & Eichenbaum H, eds. (1991). Olfaction: A Model System for Computational Neuroscience. Boston: Bradford Books/MIT Press.

Deep Nose, 2022
Signal to Noise for the Win, 2021
Olfatory Overload, 2021

Image credit: Inhibitory Synapse - TAO Changlu, LIU Yuntao, and BI Guoqiang; Image design: WANG Guoyan, MA Yanbing - 2021

Friday, March 11, 2022

Somatic Semantics

The above image was illustrated by Joe Scordo for Hidden Scents circa 2014, and based on the 1950's illustrations credited to Penfield and Rasmussen, which is need of an update, no?

Brain computer interface turns mental handwriting into text on screen
May 2021,

My rudimentary understanding of the brain says that the patterns coming from you head when you use any form of motor control would be much easier to see that patterns from simply visualizing letterforms. Something about the somatosensory cortex anatomical map.

For the first time, researchers have deciphered the brain activity associated with trying to write letters by hand. Working with a participant with paralysis who has sensors implanted in his brain, the team used an algorithm to identify letters as he attempted to write them. Then, the system displayed the text on a screen—in real time.

via Howard Hughes Medical Institute: High-performance brain-to-text communication via handwriting, Nature (2021). DOI: 10.1038/s41586-021-03506-2

Post Script:

'Rough' words feature a trill sound in languages around the globe
Jan 2022,

"They demonstrate a deep-rooted and widespread association between the sounds of speech and our sense of touch."" -Mark Dingemanse, Co-author and Associate Professor in Language and Communication at Radboud University

Also, kiki bouba.

via Radboud University, home of the Limbic Signal patron saint Asifa Majid: Bodo Winter et al, Trilled /r/ is associated with roughness, linking sound and touch across spoken languages, Scientific Reports (2022). DOI: 10.1038/s41598-021-04311-7

Why writing by hand makes kids smarter
Oct 2020,

"The use of pen and paper gives the brain more 'hooks' to hang your memories on. Writing by hand creates much more activity in the sensorimotor parts of the brain. A lot of senses are activated by pressing the pen on paper, seeing the letters you write and hearing the sound you make while writing. These sense experiences create contact between different parts of the brain and open the brain up for learning. We both learn better and remember better," says Van der Meer.

via Norwegian University of Science and Technology: Eva Ose Askvik et al. The Importance of Cursive Handwriting Over Typewriting for Learning in the Classroom: A High-Density EEG Study of 12-Year-Old Children and Young Adults, Frontiers in Psychology (2020). DOI: 10.3389/fpsyg.2020.01810


Mechanism behind loss of smell with COVID-19 revealed
Feb 2022,

  • For more than 12 percent of COVID-19 patients, olfactory dysfunction persists 
  • SARS-CoV-2, indirectly dials down the action of olfactory receptors
  • The new study may also shed light on the effects of COVID-19 on other types of brain cells, and on other lingering neurological effects of COVID-19 like "brain fog," headaches, and depression
  • Presence of the virus near nerve cells in olfactory tissue brought an inrushing of immune cells, microglia, T cells, and cytokines that changed the genetic activity of olfactory nerve cells
  • They used infected golden hamsters and olfactory tissue from 23 human autopsies [hamsters are more susceptible to nasal cavity infections]

Reminder of why it's such a big deal when you start messing with smell:
"Other work posted by these authors suggests that olfactory neurons are wired into sensitive brain regions, and that ongoing immune cell reactions in the nasal cavity could influence emotions, and the ability to think clearly (cognition), consistent with long COVID."

The talk on gene behavior and downregulation of receptor building is lost on me (not a geneticist, not a neurologist), but one of the main points I am reminded of when reading this is -- for those who experienced a change in taste or smell, for any reason, but especially after a COVID infection, long-term brain damage is possibly ongoing, but it's the kind to go undetected for another 20-30 years, depending on how old you are, of course. 

They also seem to suggest that this is an explanation for why people experience brain fog, and even emotional disturbance, all of which makes a lot of sense, because your sense of smell is connected to the all those brain areas -- the hippocampus for memory and the amygdala for emotion, both integral parts of the limbic system. 

via NYU Langone Health Department of Microbiology, NYU Grossman School of Medicine and Columbia University: Marianna Zazhytska et al, Non-cell autonomous disruption of nuclear architecture as a potential cause of COVID-19 induced anosmia, Cell (2022). DOI: 10.1016/j.cell.2022.01.024


Monell Anosmia Project - US Organization studying smell and taste

AbScent - UK Organization raising public awareness of smell loss

National Institute on Deafness and Other Communicable Disorders (NIDC) - Smell Disorders

ENT UK - Loss of Smell as Marker of Covid-19 Infection

Post Script:

Thursday, March 3, 2022

Organoids of the Nasal Persuasion

Model of the human nose reveals first steps of SARS-CoV-2 and RSV infection
Feb 2022,

I used to think it was a big deal that we knew how to grow diamonds in a laboratory. But then we started to grow organs. Intestines, kidneys, lungs,  brains (pictured above) and now noses.

They made a nose from scratch, using nose epithelial cells swabbed from somebody's nose, and placed on a substrate designed to enable them to interact as they normally would with the environment. (For this study, they were adding to that environment SARS-CoV-2 and RSV virions.) We could then call this an artificial nose, although that might be misleading. It's not full-blown olfaction, but it's a step. 

via Baylor College of Medicine: Anubama Rajan et al, The Human Nose Organoid Respiratory Virus Model: an Ex Vivo Human Challenge Model To Study Respiratory Syncytial Virus (RSV) and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Pathogenesis and Evaluate Therapeutics, mBio (2022). DOI: 10.1128/mbio.03511-21

Image credit: This is a human brain organoid, from the National Institutes of Health, circa 2021.