Inside The Coffee Bean

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Coffea arabica Genome

We now know the genes of good coffee. The Coffea arabica (Arabica coffee) genome was released this month, announced at the annual Plant and Animal Genome conference XXV. Arabica coffee is consdiered better quality and is 70% of the world’s coffee. Several years ago, the simpler genome of Coffea canephora was sequenced (a.k.a. robusta), representing the other 30% of the world’s coffee supply.


Coffea arabica leaf. Photo by Ian Street

Coffea arabica is a natural hybrid of C. canephora and C. eugenioides and contains the genomes of both, the result of a rare hybridization event that returned viable seeds. Having two similar genomes can hamper sequencing efforts as highly repetitive sequencings can be hard to distinguish and assign to one genome or the other.

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Having a genome, as I said in my post on plant genomes sequenced in 2016, opens genetic possibilities. It is a reference for other individual coffee tree genomes and a start in mapping the diversity of a species as well as the genus. Mapping diversity or having targets to induce diversity by design (with CRISPR or other random chemical mutagenesis) can yield genes resistant to pests, more tolerant of a hotter world, and better suited to various locations – all issues coffee faces today.

Dissent and Innovation Fuel

Arabica has a long history in civilization. Coffee has its origins in what is now Ethiopia. The legend goes that a goat herder named Kaldi noticed his goats spring to life and furiously jumping around after eating the berries from a coffee tree. Somehow, coffee was turned into a drink for humans who noticed it kept them alert and awake and it spread from there, with coffee trees being planted where there was demand for the bitter beverage.

Kaldi’s Coffee is a Coffeeshop in St. Louis, MO. Photo by Ian Street.

The Islamic world was first to experience widespread coffee drinking with major cultural impact. In 1511, in Mecca, Khair Beg, a local enforcer of mroals and inspector of markets shut down all of the coffee shops as sites of immorality and possibly political dissent. As part of this, coffee was literally put on trial to determine if it was against Islam, an intoxicant akin to alcohol. Beg brought a vessel of coffee beans to the courtroom as several different representatives of Islam heard the evidence and enough clerics were persuaded that it was an intoxicant that it did end up briefly banned by Meccans. Though certainly a beverage with an effect, bans were hard because it clearly did not have the same effects as alcohol on the body.

As you write, work, learn, and engage people coffeehouses, think about the stories that have come out of coffee cups over centuries of consumption.

More objections to gatherings around coffee followed. A century after Khair Beg’s Mecca coffee trial, Sultan Murad IV banned coffee consumption in Istanbul. Murad would personally patrol the streets with a broadsword and decapitate those found in violation of the coffee ban. His successor only gave a beating on first offense, but on second offense, sewed you in a bag and tossed you in the river. It was observed that people in coffee shops drinking coffee could plan, and think, and intelligently stand against the government, unlike those drinking alcohol.

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Coffee’s spread has been met by skepticism and hostility by the rulers as it spread. An unconfirmed story from the dawn of the 16th century is that Catholic priests were skeptical of coffee, thought it was the devil’s drink, until Pope Clement VIII gave it a Papal blessing.

In 1675, King Charles II of England put in place a coffeehouse shutdown that only lasted 11 days because they were seen as places of dissent against The King. Public backlash made Charles reverse course. People loved their coffee and coffee shops. It fueled not just political ideas, but intellectual developments in science and math as well.

Arguably, coffee tracked the intellectual centers in the Middle East and the West as they developed. Coffee’s domestication date in Ethiopia isn’t known. It spread from Ethiopia into the intellectual culture of the Middle-Ages Middle East, and was there relatively early during Europe’s Enlightenment era. Coffee remains popular, of course, but it is also facing challenges from climate change, coffee rust, and insect pests able to get around the caffeine that is part of a coffee tree’s chemical defenses.

Coffee and Animal Crackers. Photo by Ian Street.

The next time you are in a local coffee shop, even a Starbucks, think about the legacy of coffee as you talk with friends, or maybe even a stranger. As you write, work, learn, and engage people at modern coffeehouses, think about the stories that have come out of coffee cups over centuries of consumption. Think  how it’s been a long symbol of intelligent dissent by the people against those in power.

I got inspired to write this post by this episode of The Futility Closet Podcast. If you like quirky and wild stories from history, it’s well worth a listen.

03/01/2017 – This post has been updated to correct typos and clarify sentences.

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