Don't tell me they found Tyrannosaurus rex meat again!

It seems that some scientists are still claiming they can find bits of dinosaur meat clinging to the fossilized bones of ancient dinosaurs. Don’t sharpen your dinner knives yet.

I thought this story, which first appeared in 2007, had died long ago, but it has just reappeared. Before I get to that, though, let me explain the original claims. Back in the late 2000’s, a couple of paleontologists managed to publish two articles in the journal Science claiming they had found traces of original dinosaur proteins in 68-million-year-old Tyrannosaurus rex fossils, and in an even older 80-million-year-old fossil from another dinosaur, a hadrosaur.

This would have been shocking news if it was true, but alas, it wasn’t (even if Jurassic Park fans wished otherwise). Organic material survives only a very short time after an animal dies, usually just a few years. Bones and teeth can last far longer, though. Scientists have extracted DNA from the bones of Neandertals and cave bears that are over 50,000 years old, which is pretty extraordinary.

But 68 million years is far, far longer than 50,000 years. Those fossils are one thousand times older than bones from Neandertals.

But maybe proteins can last longer than DNA? Well, perhaps, but not that long. The oldest known protein fragment, which was preserved in an exceptionally cold environment, is about 3 million years old. The T. rex fossils studied in the Science paper were found in a warm climate, where any proteins must have degraded far more quickly.

I wrote about this way back in 2008, expressing my disappointment with the journal and explaining some of the problems. Nature ran a news story about the controversy as well.

But wait, you’re probably thinking, that T. rex study was published in a prestigious journal, so how can it be wrong? Well, what seemed to happen was this: one of the editors at Science back in 2007 simply believed the study, or maybe he just wanted to believe it, so he ignored the reviewers. How do I know this? Well, when the first paper appeared, in 2007, two of the scientific reviewers, both experts in the field, contacted me to tell me that they had both recommended rejecting the paper, but the editor went ahead with publication anyway. (They contacted me because I had published papers in Science before, and they wanted my advice on what they could do.)

My guess is that the Science editor wanted to get headlines along the lines of “T. rex tasted like chicken.” (To explain: the tiny fragments of protein that the first paper found appeared to be similar to proteins from birds.) The editor got exactly that, in stories that ran in the Washington Post, the New York Times, Smithsonian Mazazine, and elsewhere back in 2007 and 2008.

After the original T. rex paper appeared, at least two letters were sent to Science explaining why it was wrong. Science published them as a “technical comments,” which weren’t nearly as prominent as the original paper.

That letters gave far more plausible explanations for the data from the paper: first, one letter explained that it was very likely that the tiny, tiny trace of chicken-like protein was simply contamination from a modern bird, maybe as benign as someone’s turkey sandwich. That letter also pointed out that the supposed T. rex protein appeared to be modern in origin, because it lacked the signs of aging that an ancient protein fragment should have. (The details are very technical; follow the link if you want to learn more.) The other letter pointed out errors in the statistical analysis, pointing out that the result could easily be a statistical artifact.

A later paper, published independently, re-analyzed the T. rex data itself and found that the sample appeared to contain “common laboratory contaminants, soil bacteria, and bird-like hemoglobin and collagen.” In other words, no ancient proteins at all.

I should note that the experiments used to detect the dinosaur proteins, using a technology called mass spectrometry, are notoriously plagued by contaminants. Even a tiny trace of a modern bird in the mass spectrometry lab (e.g., someone eating a turkey sandwich) is liable to produce a few protein fragments that show up in the experiment. Scientists at the time pointed out that the very same lab had done experiments using ostrich bones around the same time as the dinosaur fossils.

And if that wasn’t enough, yet another published paper argued that the “soft matter” found in some fossils by the paleontologists was likely to be a bacterial biofilm. Fossils, I should explain, are highly porous, and it’s easy to imagine how bacterial could infiltrate them over the millenia.

In fact, you don’t have to imagine that at all: another scientific paper from 2019, published in the journal eLife, described finding “an abundant microbial community” in dinosaur fossils.

All of this skepticism did not deter the original scientists. It was less than two years before they’d published a second report (also in Science, with the same editor) claiming that they’d found similar proteins in another, even older dinosaur fossil, an 80-million-year-old hadrosaur.

And yes, the paleontologists continued to insist that they found “soft matter” that must have originated from the original dinosaurs. Dinosaur meat! The highly regarded CBS news program 60 Minutes was so impressed that they aired an entire segment on this finding:

Alas, there’s just no way that fossils contain any soft matter from 62 million years ago. It was likely just bacteria. But we can’t let that get in the way of a good story.

So how long can animal proteins survive? In temperate regions (such as those where the T. rex fossils were found), most organic matter decays in a few decades. If the animal happens to die in a very cold place, and its body is encased in ice, it seems that some organic material can survive up to one million years, and possibly even longer. Cool! (Pun intended.)

But the T. rex fossils from the original Science study were found in temperate climates. They were not frozen in deep permafrost or ice, and the original organic material was almost certainly long gone many millions of years ago.

I thought this story was dead, but apparently I was wrong: a small cadre of scientists continues to believe that dinosaur fossils–which are made entirely of stone, not bones–contain detectable traces of the original dinosaur proteins. Unbeknownst to me (because I wasn’t following it), another paper appeared in 2017 that claimed to find signs of dinosaur proteins in a 195-million-year-old fossil, more than twice as old as the previously reported claims.

Astounding, if true. And just this month, a chemistry professor at MIT reported that he has the explanation for how these proteins survived so long. This finding, though, is more about how the chemical bonds in collagen–the protein that bones are built upon–are exceptionally stable. That’s interesting, but it doesn’t at all prove that collagen can last for nearly 200 million years.

So count me as deeply skeptical. The science of dinosaur “meat” has from the beginning been fraught with wishful thinking. Multiple papers appeared refuting the original claims, and none of those were effectively rebutted; it seems they were just ignored by scientists who preferred a more fanciful story. I wish it were otherwise, but fossilized bones from Tyrannosaurus rex and other dinosaurs lost any traces of the original organic material eons ago.

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.)

Let's speak up for research that saves lives

In this week’s Science magazine, former Republican Congressman John Porter calls on scientists to “speak up for research.” Well, I’m all in.

We’re in the midst of a remarkable stream of scientific and medical advances, spurred by dramatic advances in biotechnology, computing, and miniaturization. Our knowledge of biology has led to amazing leaps in our understanding of aging, immune responses, inherited diseases,  and brain function, to name but a few. And yet we're cutting science funding, year after year. As Porter writes,

“the general public, and in particular elected officials, have failed to embrace the promise of cutting-edge science as a means to improve health and the economy.” 

Somehow we found (or borrowed) $2 trillion dollars to spend on wars in far-off countries whose citizens don’t like us - a cost that will at least double before we’re done paying the bills. And some politicians this past week were demanding that we invest billions more in Iraq, money that we don’t have. It's touching how concerned they are for the citizens of Iraq.

Meanwhile, eight of the top 10 causes of death in the U.S. are diseases that we might cure through better research, including heart disease (#1), cancer (#2), Alzheimer’s, diabetes, and kidney disease. We already have far better treatments for these diseases than we had a few decades ago, thanks to our past investments in biomedical research.

In this column over the past few years, I’ve highlighted just a tiny sample of the remarkable advances coming out of the scientific world, such as

• a breakthrough cure for some forms of leukemia; 
• a new, less invasive prenatal test for Down Syndrome and other chromosomal abnormalities; 
• stem cell treatments that can repair damaged hearts; 
• a promising breakthrough in Alzheimer’s treatment; and
• stem cells to treat blindness. 

Curing these diseases will not only save lives - it will also save money. A nonpartisan study revealed that publicly-funded research generates returns of 25 to 40 percent a year. And former Congressman Porter explains,

“If a treatment became available in 2015 that delayed the onset of Alzheimer's disease by 5 years annual Medicare and Medicaid spending would be $42 billion less by 2020.”

Without investment in research, though, these treatments will never arrive. Meanwhile, we’re spending $400 billion (13 times the entire annual NIH budget) on a new fighter plane that won’t even be ready to fly for another 5 years, after which the Pentagon says it will cost $850 billion to keep it going. We’re spending billions more on military equipment that even the Pentagon doesn’t want, such as the Global Hawk drone program, which Congress is forcing the Air Force to keep.

Obviously, the military-industrial complex has better lobbyists than we in the biomedical research world have.

We don’t invest in research just to make money, though. Make no mistake: biomedical research saves lives. We’ve effectively cured many types of childhood cancer such as retinoblastoma and Hodgkins lymphoma, but there are over 200 types of cancer, most of them still needing far more research.

We need elected leaders with the vision to re-examine our priorities and invest in the future. The U.S. scientific research enterprise remains the envy of the world, but it won’t stay that way long if we keep cutting it as we have been.

How much should we invest in biomedical research? Let me put some numbers on the table - not that we can get there overnight, but we could set these as goals and and then figure out how to get there.  How about allocating 2% of our total budget - $75 billion - for all of our biomedical (NIH) and basic science (NSF) research?  NIH’s budget is currently about 4 times the size of NSF; if we keep that ratio then NSF would get $15B and NIH $60B. That’s about twice what we spend now. We've done this before: Congressman Porter and his colleagues advocated a doubling of the NIH budget between 1998 and 2003, and we could do it again.

Congressman Porter wants us to speak up for research. Let’s start now.