10,000 Years of Solitude

Coffee is in danger of extinction. Here’s how science aims to save it.

Today, coffee can be easily confused with a smoothie or even a nice glass of wine. Every type boasts notes of flavor ranging from the fruity (raspberries) to the sweet (chocolate) to the earthy (oak) to the odd (taco-flavored coffee?). Countries all over the world have their own mix, each with farmers who cultivate and gather coffee beans that carry the aforementioned flavors and then some. Each mix is then shipped around the world for people to grind up and consume for their caffeine fix, be it an espresso shot or a Frappuccino or a cup of cold brew. The monolithic infrastructure behind our daily dose of caffeine may be ubiquitous, but to think -- a few years ago, this behemoth was on the brink of extinction.

Coffee would have quietly slipped off the face of the earth if it had not been for a couple of people dipping their fingers into coffee’s genetics to correct the longest running case of inbreeding, rivaled only by midcentury monarchies.

This is a story about how people really messed up, and then had to fix it.

Chapter 1: The Messed-Up Family Tree

Let’s talk about how messed up coffee is.

Coffee is actually a genus (aptly named Coffea) with over 100 species to its name. Did you know that out of all those species, we mostly drink one? Coffea arabica, otherwise known as Arabica.

L to R: Maxwell House Original: switched to 100% Arabica in 2007, Illy Instant Coffee: boasts “100% Arabica dark roast”, Nescafé Taster’s Choice: made from “the finest Arabica beans from the lush, mountainous regions of Colombia”, Starbucks Espresso Roast: which uses “high-quality Arabica coffee with its diversity of flavors”, Folgers: which uses primarily Arabica beans in its flagship roast.

If you enter a typical American home and open up its typical American cupboard, you will find Folgers instant coffee, which is made from Arabica beans. Starbucks boasts that the heart of their business lies in “high-quality Arabica coffee with its diversity of flavors”. They’re not alone; well-known coffee giants from Dunkin’ Donuts to Juan Valdez to Tim Horton’s pride themselves on their 100% Arabica beans. All of these names source Arabica beans from Central America, Asia, the Caribbean, Mexico, but most importantly: Ethiopia, where Arabica originated.

So out of all the 100-plus species, why does Arabica make up such a disproportionate amount of coffee consumption?

Above: A composite of the 124 species that make up the Coffea genus. Beans that are clearly defined represent the species used in today’s coffee consumption, whereas the beans that are blurred out represent the 121 other species that we do not consume. (L to R: C. arabica -- 75-80% of all coffee consumption, C. robusta -- ~20% of all coffee consumption, C. liberica -- 2%)

It’s all about the taste. Arabica has a delicate, more complex flavor profile than other coffee species. Its competitor, Robusta (which makes up 20% of coffee consumption as opposed to Arabica’s 80%), is harsher, more bitter. Arabica’s flavor is attributed to growing in the cooler temperature of the highlands, while Robusta grows in direct sunlight.

Name: Arabica
Tastes like: Sugar, fruit, berries
Adjectives: Sweet, soft
Caffeine level: 75-130 mg / cup
Maturation: 5-7 years
Altitude: 1300-2200 m
Temperature: 59-72˚F

Name: Robusta
Tastes like: Grains, peanuts
Adjectives: Strong, harsh, good crema
Caffeine level: 140-200 mg / cup
Maturation: 2-3 years
Altitude: 0-800 m
Temperature: 64-96˚F

Arabica, unlike Robusta and most other coffee species, is self-pollinating, and does not need other species in order to reproduce. Arabica can only breed with itself because it has to grow in it’s specific, sheltered, environment. So throughout its 10,000-year-long lifespan, Arabica has become an inbred species, constantly remixing and rematching its own genetics. While Arabica can spawn several different varieties, like Bourbon, the previous centuries of self-pollinated inbreeding have created an extremely limited set of genetics with incredible problems. Much like how the human royal monarchy suffered from hemophilia when their genetics didn’t have enough blood clotting factors, Arabica has a reduced immune system from not having enough caffeine.  

A really messy family tree

Turns out that caffeine is a natural fungus and bug repellent, and when it goes away, the fungus and bugs come in full force.

Chapter 2: The Bad Bug Cometh

Coffee plants have two natural enemies: coffee rust and the borer beetle.

When a species has low levels of caffeine, then these two are free to attack the plant. Coffee rust is a fungus that comes in two strains: one of which is found all over the world, and the other, unfortunately for Arabica, is found in the African highlands. The fungus is simple but effective, and can completely eradicate a tree in just a few weeks. To safely get rid of the fungus, a farmer must destroy the tree, and anything else within 30 yards. A mature coffee plant can ward against the fungus, but Arabica’s relatively long maturation period (5 years!) is too slow to create the proper defenses to ward off coffee rust.

L to R: Healthy coffee beans are often green, with tints of red and yellow (Creative Commons License at CIDSE), whereas coffee rust causes coffee beans to darken and wither away. The second photo (AFP PHOTO/Orlando Sierra) depicts coffee beans that have “rusted”, rendering them undrinkable.

Fungus is not the only threat to coffee.

Above: Borer beetles, being the only animal that can solely feed on coffee, can destroy whole coffee crops simply by laying their eggs inside the coffee beans. Their small size allows them to crawl through the cracks of the beans and infest them.

Over the years, the climate has been getting warmer, which creates the perfect conditions for the borer beetle to propagate. Arabica, already under threat from global warming, doesn’t have adequate caffeine levels to ward off the beetles. Though the borer beetle’s origins aren’t entirely known, the pest has spread to nearly every coffee-producing country since the year 2000 and all altitudes in which coffee is grown. The borer beetle infests a coffee tree, and if the seeds are low in caffeine, uses them as little nurseries for its eggs. Borer beetles eat away at the Arabica trees at incredible rates, destroying an estimated $500 million worth of coffee per year.

With Arabica under attack from coffee rust and borer beetles, the future of coffee faces almost inevitable extinction by 2080. 

Above: The areas where Arabica is grown are being eaten away. The Bean Belt (in dark brown) is where all coffee is grown now. Borer beetles eat about 16% of this land, and this figure is risisng, so coffee can grow only in the grey region. Coffee rust caused by fungus infects 28% of crops globally on average, which shrinks the land that can sustain coffee into the lime-green region. By 2050, only 50% of today’s Bean Belt will be able to grow Arabica (orange). 

Chapter 2.5: Another One Bites the Dust

Food extinction, unfortunately, is not a new story, even in our lifetimes. Have you ever wondered why banana-flavored candies don’t actually taste like bananas? Turns out bananas faced a fate similar to coffee, but they didn’t make it out too well.

Above: Could you actually imagine real bananas tasting like banana candy? (Real Clear Science)

Up until the mid-20th century, the bananas we ate and bought were from the Gros Michel cultivar. This banana was originally cultivated to be perfect: It was sturdy enough to not be easily damaged during transport, grows in large dense bunches, and has a great, “amplified”, “sweeter” taste. By 1950, a lot of candy was engineered to have the same taste as the Gros Michel.

But the Gros Michel had a flaw: it was an inbred monoculture. In the 1950s, the fungal-based Panama disease completely wiped out the bananas, which did not have the genetic resistance needed to withstand the infection. Exporters were forced to cultivate a new kind of banana that could withstand the fungus.

L to R: The Gros Michel banana (credit: Alex Zhang), the Cavendish banana -- the bananas we eat today (Granini)

Thus, the bananas we eat today are Cavendish, which is a separate species that was cross pollinated with many different plants. While Cavendish is engineered to resist fungus and various diseases, the Gros Michel banana taste is lost. Today, finding a Gros Michel banana is nearly impossible, even though it was few decades ago.

Chapter 3: The Turnaround

The future looks bleak for Arabica.

Humans had created a staple resource from a crop that was completely unsustainable, so it is about time we took responsibility for our actions. However, despite the grim prognosis for Arabica, not all hope is lost for coffee.

For one, scientists are starting to examine Robusta in a new light. While the standalone taste of Robusta has long been scorned as inferior or harsher than that of Arabica, Robusta can be crossed with Arabica to create hybridized non-Arabica based species, like Tim Tim, a Timor Hybrid.

A much more natural looking family tree

Rather than breeding for taste, people can control the genetics of the plants to create cultivars that have Robusta’s resistance to borer beetles and coffee rust and have Arabica’s great taste. With these new cultivars, we can start changing the genetic markup of coffee and create varieties that have the best qualities: complex flavors, strong defenses, and the ability to grow in new locations.

Instead of the old approach of creating big monolithic, and ultimately flawed giants, we have begun creating species that are diverse and local to strengthen the ecosystem of coffee. Caffeine increases, and so does the varieties in tastes as trees are grown in new regions, and in new soil.

Above: The areas where Arabica will be able to grow are diminishing. By 2050, the current “Bean Belt” will have shrunk to the red area. However, by cross-breeding Arabica with other species to form coffee hybrids, coffee growth can expand to new pastures (green).

Now that coffee is grown in a sustainable and diverse way, plenty more good is happening. The new trees are becoming homes to new birds, and the soil attracts new bugs and wildlife. Diverse pastures practically double the diversity of the ecosystems of the older generation coffee farms. The new wildlife also feed on borer beetles; hybridized pastures have 70% fewer borer beetles than before.

Coffee is now on a fresh -- and positive -- path. ☕

The industry booms because now people can have a choice and develop preferences between species and cultivars of coffee. As a food staple, coffee is less threatened and more global. It is easier now to ship globally and to share the particular varieties developed from around the world. Coffee is a story of GMOs, but of the small-scale, precious kind, rather than the industrial, monoculture kind. GMOs are the key to creating biodiversity, and allow us to preserve endangered species for the future.


1. A report from the Climate Insitute of Australia on the impact of climate change, and the future of coffee. 
2. Professionals Guide on statistics about coffee rust and how to deal with it from the Roya Recovery Project. 
3. A published paper on trends in global coffee production and the impact of pests. 
4. A review of work analyzing the effects that diversified farms and farming techniques have on improving the sorrounding wildlife ecosystem. 
5. Shoutout to everyone who helped us and donated a selfie with some coffee. Thanks! ☕