Thursday, September 30, 2021

Temporal Patterns in Olfactory Perception

Temporality in olfactory perception is understudied. But as our ability to measure spike activity over small timescales improves, so will our understanding of olfaction, and human behavior in general.

On Time

Facebook knows what's up; they're making Time Cards for computers and networks so they can perform better, and integrate information better. They understand the mismatch between the size of today's clocks vs the speed of information. 

Today's clocks go down to the picosecond (trillionth of a second), and some things are being measured at the femtoscond (quadrillionth of a second). There's even some zepto-sensitive devices out there. The smaller the time-slice, the better your pattern recognition. Even back as far as Barabási's Bursts (2010) we knew that high resolution temporal patterns could be really informative of network behavior. More people in your study is also helpful, but networks like Facebook are running out of people* (but bots are infinite!), so they have to find another way of mining user data, hence an interest in temporal activity. 

If you think the fine-grained timing of patterns isn't that big a deal, why don't you ask the New York Stock Exchange, which is actually not located on Wall Street, but a few miles away in Carteret, New Jersey, because high frequency trading algorithms compete with each other at such high speeds (the speed of light) that they need the extra light-seconds provided by placing their servers a few miles closer to the international trunk connecting the Internet to the United States (it's called a latency advantage; and that trunk actually lands in Manasquan, a town on the Jersey Shore; still, closer to Carteret than New York).

The point here is that light travels fast, and if we want to understand it, then we will need to look at smaller and smaller slivers of the clock, and add this to the growing body of knowledge about how.

On Olfactory Timing

Think about it -- the brain is a network of billions of blinking neurons. Consciousness, or any neural activity, is an intelligent organization of these blinking neurons into meaningful patterns. But when you have billions of lights blinking on and off at the same time, you need to start slicing up the "time," so it's not all happening "at once." 

In the world of olfactory perception, a new look at the temporal side of things should supplement the intense interest we're seeing in this subject (check out the books Smellosophy or Nose Dive, and stutter at the thought of a $2 million grant in olfactory artifact research).

The author of Smellosophy, Barwich, actually gets into this aspect of olfaction. For her, it's a major distinction in the way we categorize olfactory information - between the historical approach to "mapping" the receptors of the two-dimensional olfactory bulb to "measuring" the timing of receptor activity, which includes the temporal dimension.

She argues that the measurement approach can reveal a key to the coding of the olfactory network. Olfaction is not just about identifying the different molecules present and their combinatorial patterns, but about when they appear and at what concentrations, and how these concentrations change over time. After all, olfaction is about detecting change, which implies time.

She says, "Rather than molecules, your brain depicts transient information patterns" (p246)
-Smellosophy: What the Nose Tells the Mind, A.S. Barwich, 2020, Harvard University Press

And here's a recent article on the topic:

Fast changing smells can teach mice about space
May 2021,
Mice can sense extremely fast and subtle changes in the structure of odors and use this to guide their behavior. The findings, published in Nature today, alter the current view on how odors are detected and processed in the mammalian brain.

via The Francis Crick Institute: Ackels, T., Erskine, A., Dasgupta, D. et al. Fast odour dynamics are encoded in the olfactory system and guide behaviour. Nature (2021).
Post Script:
Start with the 2014 article from Princeton (cited below) that said Facebook is losing its users like a susceptible-infected-recovered model of disease transmission, and that it would be done by 2018. Granted the article came from the unlikely Department of Mechanical and Aerospace Engineering in Princeton, and despite all the bad press, we can now fast forward to 2018 when Facebook is suspected to be more bots than people. Or is it that the people are acting more bot-like as they co-evolve with engagement algorithms in the artificial arena of natural selection. Bottom line is, social media networks, and all technologies adopted by individuals in a society, will follow a similar disease model. 

Not to mention, the bad press (possibly influenced by the same entity that took a full-page ad in the New York Times btw, and somewhere around 100K in case you were wondering) didn't age well.

But I'll let you be the judge of that:
"Facebook may be a massive drain on our attention that some people get sick of, but that doesn’t mean it actually operates like a virus." -TechCrunch, 2014
Epidemiological modeling of online social network dynamics, John Cannarell, Joshua A. Spechler. Department of Mechanical and Aerospace Engineering, Princeton University. arxiv:1401.4208v1 [cs.SI] 17 Jan 2014.

Post Post Script:
Zeptoseconds - New world record in short time measurement
Oct 2020,

Thursday, September 23, 2021

Olfacotry Camouflage

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

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.

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,

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

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?)