The loneliest word, and the extinction crisis

We're in the midst of an extinction crisis. Just two months ago, an international committee known as IPBES released a report, compiled over 3 years by 145 experts from 50 countries, that said 1,000,000 plant and animal species are threatened with extinction, many within the next few decades.

Martha, the very last passenger
pigeon, shown when she was
still alive.

Before getting to that report, I want to introduce a word that I only just learned: endling. An endling (the word was coined in 1996) is the last surviving member of a species. One example was Martha, the very last passenger pigeon, who died in the Cinncinnati Zoo in 1914. Passenger pigeons numbered in the billions in the 19th century, but humans wiped them out.

In 2012 we lost another endling, Lonesome George–the very last Pinto Island tortoise from the Galapagos Islands–who died at around age 100.

If you want to see a particularly poignant example of an endling, watch this rare and heartbreaking video of Benjamin, the very last Tasmanian tiger (or thylacine), pacing around his cramped enclosure in Hobart, Tasmania. This film from 1933 is the last known motion picture of a living thylacine. Benjamin died in 1936.

Two Tasmanian tigers in the Washington, D.C. zoo, in a photo
taken around 1904. Photo credit: Baker; E.J. Keller. from the
Smithsonian Institution archives

We have records of other endlings too: the last Caspian tiger was killed in the 1950s in Uzbekistan, and the last great auks were killed for specimen collectors in 1844.

Unfortunately, we're likely to see more and more endlings in the years to come. The causes of extinction are varied, and many of them are related to human activities. The IPBES ranked the culprits, in descending order, as:

1. changes in land and sea use,
2. direct exploitation of organisms,
3. climate change,
4. pollution, and
5. invasive alien species.

In response to the IPBES report, the House of Representatives held a hearing in May to discuss the findings. Republicans on the committee took the opportunity to display a new form of denialism: extinction denialism. As reported in The Guardian, Representatives Tom McClintock and Rob Bishop used their time to attack the reputations of the report's authors, rather than addressing the very serious consequences of large-scale extinction. They called two climate-change deniers as witnesses, who also used their time to attack the authors.

This is a classic strategy used by deniers: attack the messenger, rather than dealing with the substance of the report. Let's consider just a few of the report's main findings (see much more here):

• Across the planet, 75% of the land and about 66% of the marine environments have been significantly altered by human actions.
• Up to $577 billion in annual global crops are at risk from pollinator loss (bees and other insects)
• In 2015, 33% of marine fish stocks were being harvested at unsustainable levels; 60% were maximally sustainably fished.
• Plastic pollution has increased tenfold since 1980, 300-400 million tons of heavy metals, solvents, toxic sludge and other wastes from industrial facilities are dumped annually into the world’s waters, and fertilizers entering coastal ecosystems have produced more than 400 ocean ‘dead zones’, covering a combined area greater than that of the United Kingdom.

The report is a call to action. It explains that transformative change is needed to protect and restore nature, and collective action is needed to overcome special interests such as the fossil fuel industry, which donates heavily to politicians. The Congressional hearing was a vivid demonstration of how effective the anti-environmental lobbyists have been.

Endling is the saddest word in any language. If we humans continue to treat nature as we've done in the past, we're going to see many more videos like the one of Benjamin, the last Tasmanian tiger. Let's hope we can do better.

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.)

Jurassic World fact check: can we clone dinosaurs?

One of this summer’s biggest hits was the movie Jurassic World, which earned a record $209 million on its opening weekend back in June. It's so popular that it’s still showing in theaters now, more than two months later.

Like its predecessors, the fourth movie in the Jurassic Park series features a theme park filled with dinosaurs that were created by cloning dinosaur DNA. In the movie, the dino DNA was collected from mosquitos preserved in amber, which (in the fictional movie world) had sucked the blood of dinosaurs 65 million years ago.

The success of the movie spurred YouGov.com to conduct a poll, asking Americans if they believed it was currently possible to create dinosaurs from DNA found in fossils. 28% said yes.

It makes for a fun story, but is there any science behind it? Well, yes and no.

Can we clone a living organism entirely from scratch, just from its DNA sequence alone? Yes! Not only can we do it, but it has already been done. Genome scientists Craig Venter and Hamilton Smith, both former colleagues of mine, achieved this at least twice, creating bacteria by synthesizing the necessary DNA and then “booting up” a new bacterial cell, which went on to replicate itself and grow into colonies of brand-new bacteria. Very impressive work, although bacterial genomes are quite small, only a few million nucleotides long.

Moving up a step, just last year, Hopkins scientist Jef Boeke (who is now at NYU) and his team synthesized an entire yeast chromosome. Yeast are single-celled like bacteria, but they're eukaryotes, evolutionarily closer to humans and dinosaurs than bacteria. Eukaryotes keep their DNA sequestered inside a nucleus, which in turn makes them way harder to clone from scratch. Synthesis of the remaining yeast chromosomes is under way, and it’s entirely feasible that we’ll have artificial yeast in just a year or two.

As of today, though, no one has even come close to synthesizing a multi-cellular creature like a dinosaur–or a chicken, or a frog, or a human. But in principal, it is possible to create a living animal just from its DNA, though it might take a few more decades to do it.

So yes, we might someday create animals from DNA. But dinosaurs? Alas, this half of the Jurassic World question gets a big “no.”

The problem is, despite the compelling story in the movie, there is no dinosaur DNA left on the planet. None at all, despite what you might have read. Dinosaurs went extinct about 65 million years ago, mostly likely because of a massive asteroid impact in the Yucatan peninsula, and DNA simply doesn’t last that long.

But wait, you might ask: what about all these stories about Neandertal DNA, or woolly mammoth DNA, or other ancient species? These studies are true and are very exciting. Scientists have reconstructed the genome of our Neanderal relatives from very old bones, around 30,000-40,000 years old. We can extract DNA from bones that old, although the DNA is badly degraded. I worked on an ancient DNA project myself, using an 11,000 year old mammoth thigh bone to reconstruct part of its genome. We were able to recover quite a lot of mammoth DNA from that bone.

Other work on ancient samples has demonstrated that in the most extreme conditions, where the bones have been continuously frozen in the Greenland ice sheet, DNA may survive as long as 1 million years. However, dinosaurs lived in temperate climates where DNA degrades far more quickly, and virtually all dinosaur DNA was probably gone within a few thousand years after the dinosaurs became extinct.

(By the way, that same YouGov poll that asked about cloning dinosaurs also asked "Do you believe that dinosaurs and humans once lived on the planet at the same time?" 40% of Americans said yes, demonstrating once again that Americans are woefully misinformed about evolution and the history of the planet.)

So alas, a mosquito that sucked the blood of a Tyrannosaurus rex, and then got swallowed and preserved in tree sap, would not yield any T. rex DNA for present-day cloning experiments.

This doesn’t mean we’ll never have a Jurassic Park, but if we do, we’ll have to guess at what that dino DNA looked like, perhaps using the DNA of birds. Perhaps, though, we should focus on saving the species we have left, which we are rapidly wiping out, before worrying about reviving long-lost dinosaurs.