Entomology vs Etymology

image source

Personally I like words more than bugs, but I thought it would only be good form to give this guy some play…

Drosophila melanogaster, the lowly fruit fly, is the one creature whose olfactory system is the most extensively studied of any animal. Most of what we know about human olfaction was first studied via the fruit fly. Actually, a lot of what we know about human biology and genetics in general come from this, the most scientifically useful eukaryote there is. Caenorhabditis elegans (C. elegans, the lowly roundworm) is a close second for premier entomological fame, but their olfactory system is too different from ours (and I’m not really sure if worms are insects anyway).

On Allergies and Sensitization

Writing about smell will get you thinking about nuisance odors and about folks who think that smells are making them sick. A lot of this has to do with allergies, and allergies can be a tricky thing. There is no threshold for the amount of a thing that will elicit a reaction, and so allergies tend to be modulated by our own minds, at least to some extent. In other words, if you’re stressed, or if you’re thinking way too much about these allergies and their allergens and the environment where they come from, you may amplify the effects, and you may start sneezing or scratching at the most miniscule of exposures.

The way allergies work in the body is pretty damn confusing. There’s different kinds of allergies, some are hardwired, we might say, and some are ‘learned’ by the body. Some allergies can be deadly, like a shellfish allergy that closes your throat. Some can be just annoying, but won’t kill you or send you to the hospital (unless your body gets so hijacked by your own histamines that you smash your head into a wall).

All this being said, when I came across this short explanation on how allergies work, and I found it to be somewhat comprehendible, I thought I should repeat it here.

Most chemicals and their metabolic products are not sufficiently large enough to be recognized by the immune system as a foreign substance and thus must first combine with an endogenous protein [something that comes from inside the body not outside, endo- vs exo-] to form an antigen (or immunogen). Such a molecule is called a hapten. The hapten-protein complex (antigen) is then capable of eliciting the formation of antibodies. Subsequent exposure to the chemical results in an antingen-antibody interaction, which provokes the typical manifestations of allergy that range in severity from minor skin disturbance to fatal anaphylactic shock.

-Essentials of Toxicology, Casarett and Doull

Got all that? The “allergic reaction” is really an antigen-antibody reaction. It is your body fighting an intruder, and you are the collateral damage.

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Please take a look at another post called The Dangers of Smell and Perfumes in the Workplace but it’s based on this article: perfume in the workplace, which is an interesting look inside the work of an HR worker who has to deal with employees complaining about their smelly coworkers, and soothing the hypersensitive worker who thinks their coworker’s perfume is making them sick (it’s not; unfortunately, it’s your own mind doing that). 

On Very Large Databases

human metabolome database

The American Society for Biochemistry and Molecular Biology has this prescription for a periodic table of proteins, organizing protein complexes based on simple rules, tens of thousands of protein complexes each with their own 3-d structures, let us recall the hypothetical smell network of all possible smells as they occur to all people – the Lingua Anosmia.

There is a strong connection between olfaction and the growing databases of bioinformatics, because smells are organic entities themselves.

There is another database I envy, the human metabolome. It contains 40,000 entries, all the metabolites that exist within and among the human body. This one has even closer affinity with olfaction, because lots of metabolites smell; and if they don't smell, they are the molecules that eventually separate and combine to make something that does smell. Knowing the relationships among the molecules associated with smelly activity can help to organize the resulting smells of said metabolic activity. Your body odor does not come from your body - unless we consider our microbiome to be part of our body. Molecules that exit your body via sweat are deposited on the skin, a buffet plate for the colonies of bacteria that live with us. They eat your sweat and shit the body odor that you tend to consider yours. The smell of the beach is a secondary metabolite of seaweed, which means the same thing – sea bacteria eat the waste, or the metabolites, of seaweed.

Yes, that beautiful, intoxicating, deep and alluring scent of the seashore is to the ocean what body odor is to our bodies.

In conclusion, metabolites, and many things biological, and in their new supersized databasable format, are a step closer to the realization of the hypothetical smell network, the Lingua Anosmia.

I’d like to ask the driven and capable reader to hook-up this human metabolome with some smell data; I’d love to see it. Had I the time and expertise, I'd like to hook it up myself, but alas; it's on my list.

Post Script
Periodic Table of Proteins – University of Cambridge – Dec 2015

“We’re bringing a lot of order into the messy world of protein complexes”

-Sebastian Ahnert

Long form description of the Human Metabolomic Database:

The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. The database contains 41,993 metabolite entries including both water-soluble and lipid soluble metabolites as well as metabolites that would be regarded as either abundant (> 1 uM) or relatively rare (< 1 nM). Additionally, 5,701 protein sequences are linked to these metabolite entries. Each MetaboCard entry contains more than 110 data fields with 2/3 of the information being devoted to chemical/clinical data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (KEGG, PubChem, MetaCyc, ChEBI, PDB, UniProt, and GenBank) and a variety of structure and pathway viewing applets. The HMDB database supports extensive text, sequence, chemical structure and relational query searches. Four additional databases, DrugBank, T3DB, SMPDB andFooDB are also part of the HMDB suite of databases. DrugBank contains equivalent information on ~1600 drug and drug metabolites, T3DB contains information on ~3600 common toxins and environmental pollutants, SMPDB contains pathway diagrams for ~700 human metabolic and disease pathways, whileFooDB contains equivalent information on ~28,000 food components and food additives.

Citing the Human Metabolome Database:

1. Wishart DS, Tzur D, Knox C, et al., HMDB: the Human Metabolome Database. Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6. 17202168

2. Wishart DS, Knox C, Guo AC, et al., HMDB: a knowledgebase for the human metabolome.Nucleic Acids Res. 2009 37(Database issue):D603-610. 18953024

3. Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al., HMDB 3.0 — The Human Metabolome Database in 2013. Nucleic Acids Res. 2013. Jan 1;41(D1):D801-7. 23161693

Brainless Intelligence

Many-headed slime mold aka Physarum polycephalum, image via the French National Centre for Scientific Research, 2016 

Some folks made slime think. The lowly slime mold, a single-celled protist, shows evidence of learning. It remembers the particular route that avoids irritants placed in its path by tinkering scientists. Yup. Funny thing is, the organism investigated is commonly called the “many-headed slime.” This turns out to be an ironic name, for this organism, without a central nervous system, acts like it does in fact have a head, or a brain, and maybe more than that – many heads, and many brains.

This isn’t the first time slime mold has done amazing feats. It’s used to recreate roadmaps from ancient cultures, or Tokyo’s rail system, just based on topographical information. Who do these single-celled organisms think they are, acting like they have brains? This raises the following question: Where does intelligence come from? Does it need a brain?

In Hidden Scents, while talking about the evolution of the smelling organism, I suggest that the mind is first, and then comes the body. There is something thinking in the most primitive of organisms, deciding which molecules in its surrounding sea of life, and proto-life, should be taken into it, to become part of it, and which molecules should stay outside. To be alive, one of the most basic requirements is to have a boundary between the living thing and the outside. This defines the body. But how does this body, living in a sea of potential bodyparts, determine which parts to keep, and which ones to leave behind. The body comes from somewhere, doesn’t it? And isn’t a body - a living body - more than just a bunch of molecules? If so, what’s organizing those molecules? Who is running the show?

Chemosensation is the basis of this interface, and is the process by which human olfaction works. The initial decision-making algorithms to run with this chemosensation are also the base-algorithms of human thought. Rational thought is a much more complex affair, but at the base is the limbic system, and in smelling we have a model for the kind of thinking performed by a simple, multicellular organism. Or even a collection of single celled organisms, perhaps?

Our current mode for thinking about intelligence is undergoing a major reboot. In light of developments in artificial intelligence, the boundaries of human intelligence are already blurred – many of the things once considered human, rational thought are now programmed into an "artificial life form," i.e., a computer program.

But that’s ok, because current models of the brain follow the schematics of a computer in the same way the nervous system was initially thought of as a closed network of fluids and the brain a pressure-modulator. This was in the age of hydraulics, before we knew what electricity was. Now we know what a computer is, and so the brain is like a computer. Tomorrow, we may know what life is; will we then compare the brain to it?

Our ideas on thinking and intelligence necessitate a brain (whether it’s a computer or a water pump or a lifeform). It's very counter intuitive to hear that things without brains can think. Who knows, next it will be like “Things without bodies can think.” Does the temperature in a room think? Does it have a memory?

Notes:

Intelligent? Brainless slime can 'learn'

May 2016, phys.org

Slime Mold Grows Network Just Like Tokyo Rail System

Laura Sanders, Wired, via Science, 2010

Slime mould builds an ancient road network

Mar 2015, phys.org