Relish that coffee now. It might be extinct in 20 years.

Most people think there are two major kinds of coffee, arabica and robusta. (No doubt some people think the two kinds of coffee are regular and decaf, but I digress.) And it's true that almost all the coffee that you can find in the market, or at your local coffee shop, is made from one of these beans or from a blend of both.

Actually, there are 124 species of coffee. Unfortunately, as we learned in a new paper published last week in the journal Science, 60% of them are currently in danger of going extinct. The primary threats are habitat loss (caused by humans) and climate changes (also caused by humans).

Even though the term "endangered species" is more often used to refer to animals, we humans have already wiped out countless plant species, primarily through deforestation, and many more are going extinct each year. We will never know how many species have already been lost as we've chopped down rich rainforests to create grazing lands for cattle or monoculture plantations, but we do know that it's still going on.

Of the two major beans that we use for coffee, the better-tasting bean, arabica, is already endangered, according to the new study. Robusta coffees aren't bad, but as the new paper explains:

"Although robusta has some negative sensory qualities (e.g., tasting notes of wood and tobacco), it is favored in some instances for its taste, high caffeine content, and ability to add body to espresso and espresso-based coffees; it is now the species of choice for instant coffee."

If we don't do something to protect wild coffee species, we might soon be drinking nothing but robusta coffee.

If that seems implausible, recall that this already happened to the banana. In the mid-1900s, the entire worldwide production of bananas was basically wiped out by Panama disease, caused by a fungus. Before then, a tasty variety called Gros Michel was the dominant species, but thanks to the fungus:

"By 1960, the Gros Michel was essentially extinct and the banana industry nearly bankrupt. It was saved at the last minute by the Cavendish, a Chinese variety that had been considered something close to junk." (Source: NYTimes)

Now, the robusta bean is far better than "junk," but I for one prefer my arabica coffee.

The main threats to arabica (and robusta) are outbreaks of mold and fungal infections, not unlike the disease that wiped out bananas. Those 122 wild species–of which 60% are now endangered–are often resistant, allowing plant scientists to inter-breed the wild and domesticated varieties to create new strains that resist disease and taste just as good as the original. This wild "reservoir" of coffee is critical to saving coffee as we know and love it today.

You're probably accustomed to seeing coffee labelled by the region it's grown in, rather than the type of bean. This is similar to how we label wines as being from France, California, Australia, etc. Coffee is grown in many temperate regions, including Central and South America, Indonesia, central Africa, and Hawaii. Just as with wine, the climate makes a difference, but the bean itself is an even bigger factor. Consider the difference between cabernet, pinot noir, or sauvignon grapes for wine–in the same way, arabica bean coffees tastes quite different from robusta coffee.

If we don't pay attention to the threat to coffee, we might all be drinking a less-tasty brew in the years to come.

(Aside: I've been working for several years on a project to sequence Coffea arabica, the tetraploid genome of arabica coffee, and our results will likely be published soon. We're hoping that the genome will assist coffee scientists who are trying to breed new, disease-resistant varieties.)

World Health Organization endorses TCM. Expect deaths to rise.

Mother and young rhinoceros killed for their horns.

Image credit: Wikipedia

A few days ago, a news story in the journal Nature reported that the World Health Organization, which is supposed to be devoted to improving the health and medical care of people around the globe, will for the first time endorse a belief system called "traditional Chinese medicine." I'm labeling TCM a belief system because that's what it is–but the WHO will be endorsing it as a set of medical practices.

The Nature writer, David Cyranoski, presents this news in a classic two-sides-of-the-story format, describing the "endless hours" that TCM proponents spent on such important topics as the "correct location of acupuncture points and less commonly known concepts such as ‘triple energizer meridian’ syndrome." Later in the article (but much later), he points out that scientists have argued that qi and meridians simply don't exist.

Cyranoski also falls into the trap of using the phrase "Western medicine" as if it were just an alternative point of view. An apt response is this comment from a biology Ph.D. student, who goes by @astrelaps on Twitter:

"What a weak, equivocal article from the world's preeminent scientific journal. "For those steeped in Western medicine..." is like writing "For those steeped in climate science" or "For those steeped in evolutionary biology" when reporting on climate change denial or creationism."

Well put. On the other hand, Cyranoski does point out that the major motivation for TCM is money:

"[China] has been aggressively promoting TCM on the international stage both for expanding its global influence and for a share of the estimated US$50-billion global market."

Were you thinking this was about health care? Afraid not. Cyranoski goes on to point out some serious problems with TCM, for example:

"Critics view TCM practices as unscientific, unsupported by clinical trials, and sometimes dangerous: China’s drug regulator gets more than 230,000 reports of adverse effects from TCM each year."

Actually, it's much worse than this.  Here's what TCM really looks like: the horrific slaughter of the last remaining rhinoceroses in Africa in order to hack off their horns, which are sold to become part of elixirs that some people mistakenly think confer strength or virility. Last year, National Geographic ran a heart-wrenching photo essay showing some of the awful results of rhinoceros poaching in Africa; take a look at these photos here.

TCM also looks like this: black bears kept in grotesquely cruel "farms" with a permanent tube inserted into their abdomens so that their bile can be harvested. Despite a growing movement to end this inhumane practice (see this NY Times story), it persists today, with thousands of bears kept in cages so small they can barely move. No one can view photos such as these and say that TCM is a good thing.

And TCM is behind the slaughter of the last remaining wild tigers, which are virtually extinct now in Asia, so that men can foolishly eat their bones, claws, and genitals in the mistaken belief that tiger parts will make them virile. Here too, National Geographic has details and photographs that are almost too painful to look at.

And don't get me started on pangolins, the beautiful, peaceful mammal that's now perilously endangered because TCM practitioners think its scales have some sort of medicinal value. (They don't.) For more on these gentle creatures, see the article I wrote last year.

I can almost hear the counter argument: but what about artemisinin? That's a plant extract derived from Artimisia annua, an herb that was traditionally used in China to treat malaria. Turns out that it really works, and artemisinin is now the basis of a number of modern malaria treatments.

Well, great. If an herb has the potential to treat disease, we should (and can, and do) study it, figure out what the active ingredient is, develop a controlled process for delivering effective doses, and use it. That's what happened with artemisia, and it also happened with taxol, an effective cancer chemotherapy derived from the Pacific yew tree, and common aspirin, derived from the willow tree.

But one success doesn't excuse hundreds of bogus claims that are based on little more than magical thinking.

There's no legitimate reason to use terms such as "Chinese" medicine, or American, Italian, Spanish, Indian, or [insert your favorite nationality] medicine. There's just medicine–if a treatment works, then it's medicine. If something doesn't work, then it's not medicine and we shouldn't sell it to people with false claims. The same is true for alternative, holistic, integrative, and functional medicine: these are all just marketing terms, with no scientific meaning. They merely serve to disguise sloppy, unscientific thinking at best, and in a less charitable interpretation, outright fraud.

As the Nature article points out, TCM has been a scam for decades: it was revived and heavily promoted in China by former dictator Mao Zedong, who didn't believe in it himself, but pushed it as a cheap alternative to real medicine. I won't go over that again here, but see these stories from Alan Levinovitz in Slate and David Gorski at Science-based Medicine.

Finally, why would the World Health Organization start pushing a set of unscientific practices that are likely to harm people's health? Support for TCM grew during the tenure of former WHO director Margaret Chan, who ran the WHO until 2017 and who had close ties to China. When Nature tried to contact Dr. Chan, the WHO responded that Chan "is not answering questions on matters related to the WHO."

By endorsing TCM, the WHO is taking a big step backwards. Let's hope that the current leaders of the WHO will realize that this step undermines their core mission. The WHO should not advocate treatments that not only have no evidence to support them and that can cause real harm to patients, but also are the primary reason that humans are hunting rhinoceroses, tigers, pangolins, and other animals to extinction.

World's cutest mammal critically endangered because of Traditional Chinese Medicine

A pangolin. Photo (c) Christian Boix.

Pangolins, timid little anteaters that are covered with scales, are being hunted to extinction. Why? Because some humans think their scales can be used as medicine. Pangolin scales are made of keratin, the same stuff that makes fingernails and claws, and they have no more medicinal value than any other fingernails–which is to say, none at all.

Pangolins are gentle, toothless mammals that eat ants with their long, sticky tongues. They are covered with scales (sort of like a walking artichoke) which protect them from predators but not from humans, who simply pick them up to harvest them. Baby pangolins ride, adorably on their mothers' tails or backs, as shown in the picture here.

Photo by Firdia Lisnawati.

How could someone look at these creatures and want to kill them? And yet pangolins are being slaughtered in large numbers because some practitioners of traditional Chinese medicine (TCM) think (wrongly!) that pangolin scales can treat nervousness or palsy. They are also being killed for meat: regrettably, pangolin meat and fetuses are considered a delicacy by some people in China.

Just a few months ago, the CITES organization (Convention on International Trade in Endangered Species) banned trade in all eight species of pangolins. We can only hope that this blanket ban is not too late. Previously CITES had declared that Asian pangolins were endangered, but had allowed trade in African pangolins, but because the meat is indistinguishable, the limited ban did little to stop the widespread killing of Asian pangolins. Just before the CITES meeting, Annamiticus (@annamiticus) reported that in the first nine months of 2016, 18,670 tons of pangolin scales from 19 countries had been seized from smugglers, mostly in Hong Kong. And that's just the amount that was stopped; many more tons doubtless slipped through.

Despite the new CITES restrictions, trade in pangolins continues. In December, customs officials in Shanghai arrested 3 people who were attempting to smuggle over 3 tons of pangolin scales into China. That shipment alone represents 5,000 to 7,500 pangolins that were killed for their scales.

Next Saturday (18 February) is World Pangolin Day. Let's hope that the new CITES restrictions, and greater public awareness of the endangered pangolin, can save these gentle animals from extinction.

*note: perhaps it's not the "world's cutest mammal," but the pangolin is still worth saving.