The Languages of Chemistry: A Review

We live in a chemical world. How are we currently describing it?

10 min readSep 11, 2017

As the drum of science and technology charges forward, we’re discovering more ways to modify the world around us, including our own health. Unfortunately, our collective ability to understand and make sense of these developments seems to have, at best, flatlined.

Every day, we face chemicals as utilities: Rubbing alcohol, cleaning products, gasoline, propane, batteries, plastics, and so on. There are chemicals we consume: Alcohol, fats, vinegars, sugars, water, vitamins, nootropics, caffeine, pectin, to name a few. Finally, there are the chemical codes of life: DNA, proteins, amino acids.

Each time we’re confronted with a chemical, we’re faced with a decision: Do we seek to understand it, or do we just accept it? Do we trust it, or do we not? To this end, even a basic understanding of chemistry can lead people to make more rational decisions regarding the chemical world around them.

So, how might everyday people become better equipped to understand our chemical world?

Approaches

Approach 1: Artificial Intelligence

At the moment, our tendency is to put our faith in artificial intelligence — to first process and then communicate information back to us.

This is helpful, but there are a couple of problems with that (designers take note!): Unlike our own rational thinking, AI takes in many inputs and processes it in ways it can’t itself always articulate. There is risk in a lack of algorithmic transparency.

It also increases the asymmetrical power between AI and humans: By banking even more on AI, we lower our incentives to take in such results critically and feed the pursuit of human curiosity. In its extreme, this could lead to a devaluation of education for the masses.

An example? Google doesn’t just give search results anymore —increasingly, it answers questions.

Approach 2: Education

Human education is the counterbalance to AI. If everyone is able to learn chemistry and make decisions on their own, then the result is more individual autonomy.

The downside of focusing on education is that it’s dependent on forces at the Municipal, State and Federal levels. Another downside is that it requires a large time investment from the recipient of the information, which is exactly what we’re trying to make easier here. Which leads to the final approach…

Approach 3: Language

A third solution is to improve the way that chemical systems are communicated.

Chemistry is information, and information is often transmitted through language. The current language of chemistry is restricted to terms and symbols that are technically detailed, thus requiring a substantial knowledge investment on both the provider and the recipient. There are few methods for communicating chemical systems in terms that are both intuitive and relatable.

My hypothesis here is that if the language of chemistry can be improved, then everyday people can increase their comprehension of chemistry.

Furthermore, this solution is within easy reach of anyone who attempts to improve the problem.

A Review of Chemical Languages

My purpose with this essay is to serve as a living, breathing collection of the vocabulary used to communicate chemicals and interactions. Many methods are being tried, in textbooks, on the web, and in research papers, yet there’s little consistency.

So this is a good thing! It means we can learn from the various methods tried. Drawing on this review, we’ll be able to extract a collection of best practices towards a more effective chemical language.

Traditionally, chemists use their own method of categorizing the different sizes and types of molecules. But my goal is to translate the chemical world into one that’s intuitive and relatable, and chemists (sorry folks) rarely speak Chemistry to non-chemists. To narrow down the focus, I’m going to focus here on organic chemistry, rather than material chemistry, as it’s what I’m personally most familiar with.

My unit definitions are vague to start, so I’m sure this will tickle chemists the wrong way. But that’s the whole point. So let’s begin.

Level 1: Materials

What I call Materials are the building blocks and most common elements found in chemical systems.

Rather than restricting this category to only atoms, it’s helpful to expand it to common, basic compounds such as water, CO2, O2, and methanol. Certain elements play significantly more important roles than other ones – like hydrogen. It may be useful for any chemical language to take this differential into account, in some way.

Due to the fundamental level of Basic Units, their communication takes place in the context of larger units. Which brings us to Level 2.

Level 2: Components

Alcohols, vinegars, fats, sugars. We can think of these as the cogs, transistors, and the batteries in a system. These are small chemical units that serve very common roles and piece together to build larger machines. Let’s take a look at two examples.

Palmitic Acid

Palmitic acid is a common saturated fat. In the language of chemistry, here’s what it looks like:

In design, we often use scenarios and stories as the starting point. For organic chemistry, this often involves some sort of pathway — how is this chemical created, and then how is it used? Here’s what it looks like in a story:

Sucrose

I overheard a stranger at the gym trying to describe why sugar and sugar alcohols are important to his diet: So let’s use a common sugar, sucrose, as our next example. Sucrose is interesting because it’s a compound made up of two smaller sugars, fructose and glucose. Let’s see what it looks like:

What about showing this molecule in action – being created (during photosynthesis), and then being used (becoming cellulose in the cell walls)? (In industry jargon, this is called the metabolic pathway.)

Ok, it’s glucose not sucrose – but worth including here.

Amino acids and more!

I want to throw in a final mention here, which caught a lot of traction on Twitter recently. Let Jacob Tennessen speak for himself:

To which someone replied:

Clearly other heads see the potential of a new language.

Level 3: Machines

Collections of components form a class consisting of the engines, vehicles, and robots.

ATP Synthase

A favorite of many biologists is ATP Synthase, a protein that’s responsible for powering the cellular powerplants known as mitochondria:

ATP Synthase is one of the more complex proteins that we know of, and stands as one of the most magnificent proteins powering life on Earth.

Insulin

Let’s look at a much smaller gizmo that also plays an important role in biology, insulin (we’ll use the human version). An understanding of insulin is important for respecting the need for limiting sugar in one’s diet — not just for diabetics, but for everyone.

Level 4: Factories

Factories are huge. Here, we come upon the dragons of the molecular world, the genes we so frequently discuss in everyday life. Where much of the magic is currently taking place in science today.

The human genome itself is about 700Mb in size, containing hundreds of thousands of genes, bundled up into only 23 compounds called chromosomes. Yet the blueprint itself isn’t of use without the factory itself… metaphorically meaning, raw DNA isn’t as valuable as the genes it codes for.

And right off the bat, this seems to be a key takeaway for Factories. So much genomics software focuses on the blueprint, rather than the factory and its machinery.

Given these examples, it appears that genomic languages tend to resemble data analytics rather than a language. This is worth exploring further.

Intermediaries, Interactions, and Measurements

You might remember equations like this from chemistry class:

If only chemistry were that simple! Yet as simple as this depiction is, it fails to communicate what’s actually going on, without a deep understanding of each individual atom.

If a langauge is to reflect the reality of chemistry, it must sufficiently reflect interactions between chemicals in various quantities. And here too, we find that the current language of chemistry is significantly flawed.

Nearly all metabolic pathways involve “intermediary” molecules: Molecules that serve no function but are merely “tweens” towards the next functional state.

Furthermore, these intermediaries are aided by helper molecules at each step! Molecules that exist only to help other molecules transform. These often produce byproducts themselves. And the complexity here has virtually no limit.

Takeaways

Analogous Functions

As I wrote the above, and edited it to clarify my words, it quickly became clear that my own language tended towards a functional and analogous approach towards describing chemistry. This seems significant.

Taking this further, did you notice what happened as we jumped from one level to the next? Each level became more analogous! We can now loosely presume that the more complex a molecule becomes, the more specialized its function, thus easier to describe succinctly and at a higher level of abstraction.

Context

The context was important for determining what properties to highlight about a molecule or interaction. Furthermore, a storyboarding approach seemed to effective for molecular pathways — treating compounds as central characters that evolve throughout a narrative.

Quantity

This was notably lacking in nearly all of the examples, yet is core to all chemistry. Ratios, absolute quantities, and orders of magnitude are different aspects of quantity that could all be important depending on the context.

Color and Shape

Most immediately identifiable by the human eye, yet these are currently used in ways that are most often unhelpful.

Abstraction

Molecule names and codes aren’t always helpful for visually communicating their functions within a larger metabolic system, and attempts at visualizing them contain too many details, resulting in information noise. Given the levels we’ve defined, more methods of abstraction should be explored.

Time Progression

Metabolic systems don’t happen all at once, like they appear in charts — they are an ongoing fluctuating evolution of multiple side characters and main characters, balancing out in an equilibrium. To truly understand a chemical system is to understand this.

Time progression builds a case for an explorable and interactive language, not one confined to a static printed journal or textbook page.

Scope

The scope of a metabolic pathway can extend very far, but how far is necessary? Given a single molecule, you can work backwards from its origin of synthesis or forwards into some future evolutionary form, but rarely is the entire scope important.

Importance

A metabolic pathway is exactly that — a pathway that molecules take. But along the way they encounter other molecules, create new ones, and diverge down multiple paths. In highlighting any system, separating the key characters from the noise is important.

Glanceability

Currently, glanceability of metabolic pathways is dependent upon a very thorough and refined vocabulary.

Progressive Disclosure

Not all properties and levels of heirarchy are important all the time. Through an interactive language we can leverage this using the principle of progressive disclosure.

Conclusion

Much more remains to be tried, but I’m ever more convinced that a new language is needed if chemistry is to be made more accessible to non-chemists. Various other notable attempts are already being made at this, such as the Khan Academy and the NOVA Elements app, to name a couple.

But the next level requires adequately addressing each of the takeaways above, which I’ve yet to see done successfully.

Testing for Success

What might a successful language be able to do? Here are some ideas:

Test A: Understanding pH
Test B: Understanding ATP Synthase
Test C: Understanding Proton Gradients

More examples?

If you have other examples, please tweet them over to me (Eric Wittke) or share them here in the comments.

To be continued…

Sources

Ping me if you’re curious about any additional sources, or just search Google.