Thursday, July 14, 2016

Beer Made With 45 Million Year Old Yeast?

The other day I came across a Reddit post entitled: “Beer Made With 45 Million-Year-Old Yeast Found in Amber.”

And I was intrigued.

The link led to an Indiegogo campaign from the Fossil Fuels Brewing Co. aiming to raise money to further their production of beer made with ancient yeast. As the story goes, the idea was born after the “chance discovery of a beautiful amber stone, replete with a 45 million year old leaf, and a single yeast spore – still alive and itching to make beer.”

Immediately, I thought, This sounds like BS. I distinctly recall recent studies showing DNA doesn't last that long, especially in amber. Thousands of years? Sure. But 45 million? No way cells live that long. 

But mid-scoff, I noticed two of the brewery team-members are published microbiologists, one of whom – Dr. Raul Cano – is allegedly the “first scientist to isolate viable DNA from an amber crystal.” Plus I remembered recently coming across a paper in Nature(!) claiming to have revived 250-million-year-old bacteria. Perhaps my initial reaction was wrong. 

My skeptic senses were tingling, but my scientist's trusty maybe-I'm-mistaken alarm was buzzing as well. So I did some investigating. 

Here's what I found.

Long-slumbering spores

Dr. Cano did indeed make headlines for a 1995 Science paper describing the discovery of dormant, still-living bacterial spores from the gut of a fossil bee preserved in 25- to 40-million-year-old Dominican amber. He and his co-author even claimed to have revived and cultured these microbes, which were similar to modern Bacillus bacteria. They explained the measures they took to confirm these bacteria weren’t lab contaminants, but in fact ancient, tens-of-millions-of-years-old prehistoric survivors.

Amber from the Dominican is famous for containing ancient insects.
This is a bee, not unlike the bee in whose gut Dr. Cano supposedly
discovered spores.
Image by Michael S. Engel via Wikipedia.
This wasn’t the only such report. Actually, the 90s to early 2000s were somewhat of a heyday for super-ancient DNA and microbes. Cano and other researchers published several reports of DNA extracted from bones, plants, and insects at tens or even hundreds of millions of years old, plus the resurrection of other ancient bacteria, including Staphylococcus from Dominican amber and Micrococcus from Israeli amber as old as 120 million years.

(Interestingly, it doesn’t look like Dr. Cano has ever published on the yeast supposedly used for this beer.)

The study that took the cake, however, was the October 2000 report I mentioned earlier, of Bacillus bacteria preserved not in amber, but in a salt crystal 250 million years old. If true, those individual cells would be older than the first dinosaurs. Some researchers also pointed out the noteworthy implications for inter-planetary transport of dormant microbes. The age of ancient DNA and fossil microbe resurrection seemed upon us.

Problem was, well, there were problems.

Problems

As you’d expect, these studies inspired some controversy. As they say, extraordinary claims require extraordinary evidence, and not everyone was convinced the evidence was sufficient. For starters, scientific understanding indicated that DNA shouldn't last that long in fossils. Critics also pointed out that many of these supposedly ancient DNA sequences were suspiciously similar to the sort of modern-day species you'd expect to find as lab contaminants. Understandably, many researchers questioned the procedures used in these extraordinary discoveries.

But of all the issues, perhaps the biggest was reproducibility. It is generally accepted that DNA, and even spores, can survive in fossils thousands of years old, but only after numerous repeated experiments removed all doubt. But no such repetition was presented for these millions-of-years-old examples. A number of other scientists in other labs tried to extract DNA from their own ancient amber samples, and repeatedly failed. On top of that, it seems the original researchers were unable to replicate their own experiments.

In order to rule out the possibility that lab contamination was responsible for these supposedly ancient samples, researchers would be expected to replicate their extractions in separate laboratories. Finding the same result in two labs would be a big clue that this was no mistake. But as a 2005 critique stated: “Intriguingly, no claims of geologically ancient cultures or DNA sequences published to date (i.e., claims >1 [million years]) have followed this simple criterion of authentication.”

Extracting DNA and microbes from fossils is a very delicate process.
As you can imagine, contamination by modern microbes is VERY likely,
so careful procedures are followed to avoid it.
Image from University of Copenhagen.
For those reasons, these claims remained controversial and unproven for several years. And then a few years ago two more important studies came out. I've already alluded to them at the beginning of this post; they were the first studies that came to my mind when I read that dubious headline.

In 2012, a team of scientists put their minds to answering the question: Just how long does DNA last in fossils anyway? They studied DNA preserved in a series of fossils of different ages, and used the data to estimate the rate of DNA decay. Even under ideal conditions, their calculations indicate that DNA would degrade into illegibility in perhaps 1.5 million years, a far cry from 250, 120, or even 45 million.

And in 2013, the question of DNA survivability in amber was answered dramatically. Researchers attempted to extract DNA from insects trapped in two specimens of copal (that is, partially-fossilized tree resin before it becomes amber), one dated to around 10,600 years old, the other younger than 60 years old. And they found no ancient DNA. In either sample. Turns out amber is really really bad at preserving DNA.

These two studies supported the implications of earlier findings: DNA simply does not last very long in fossils. And with no known mechanism for cells to preserve their own DNA for millions of years, these results cast some serious doubt on these ancient microbes.

So, 45 Million Year-Old Yeast?

In science, it's always hard to justify a definitive 'no.' But, no. 

To date, claims of living microbes from fossils millions of years old are plagued with uncertainty, and none have been replicated, including apparently Dr. Cano's own bacteria and yeast. What's more, studies have repeatedly shown that millions of years is too long for the survival of DNA, let alone living cells. Especially in amber. 

Apparently critics say this beer is unusual but tasty. I'm certainly in no position to dispute that claim. But more than likely that yeast came from someone's hands or clothes, not from the Eocene.

References:
Cano & Borucki 1995. Revival and Identification of Bacterial Spores in 25- to 40-Million-Year-Old Dominican Amber. [PDF]

Greenblatt et al. 2004. Micrococcus luteus – Survival in Amber. [PDF]

Austin et al. 1997. Problems of reproducibility – does geologically ancient DNA survive in amber-preserved insects? [PDF]

Walden & Robertson 1997. Ancient DNA from Amber Fossil Bees? [PDF]

Maughan et al. 2002. The Paradox of the “Ancient” Bacterium Which Contains “Modern” Protein-Coding Genes. [Full Text]

Willerslev & Hebsgaard 2005. Comment on Satterfield et al. (2005). New evidence for 250 Ma age of halotolerant bacterium from a Permian salt crystal. [PDF]

Allentoft et al. 2012. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. [Full Text]

Penney et al. 2013. Absence of Ancient DNA in Sub-Fossil Insect Inclusions Preserved in ‘Anthropocene’ Colombian Copal. [PDF]

Sunday, June 12, 2016

Tracking the Mighty Sabertooths

This is a modern Tiger print.
By Aiwok, via Wikipedia.
Did you hear about those newly-discovered saber-toothed cat footprints? If not, check it out over at Science (there’s an awesome picture). The tracks are apparently up to 19cm across – bigger than a Bengal tiger’s! They were discovered in Argentina (because some countries have all the luck these days), and presented at a conference in May. These tracks probably belonged to a species of Smilodon, the most famous saber-toothed cats of them all.

Sabertooth tracks are rare, but these aren’t the first. I’ll get more into that later, but first: what exactly is a saber-toothed cat? Are they really cats anyway? 

Saturday, June 11, 2016

Island of the Tiny People

In 2003, the field of human evolution was rocked by the discovery of “hobbits,” an ancient species of human relatives who stood barely more than a meter tall. Named Homo floresiensis, they lived on the Indonesian island of Flores, and for years researchers argued over whether they represented the first-known human case of “island dwarfism” or if these ancient individuals had some sort of disease causing their short stature. If they were diseased, what disease did they have? If they were a legitimate species, where did they come from?

The disease hypothesis has mostly fallen out of favor. Numerous studies have countered suggestions that H. floresiensis had microcephaly or hypothyroidism or other proposed conditions. On Wednesday, a new study provided evidence against Down Syndrome being responsible for the fossils’ appearance. So it seems the “hobbits” were their own species, but that leaves still many questions.

Friday, June 10, 2016

The Earth's Deepest Scars

No matter how thoroughly researched and well-understood a scientific theory is, there’s always room for improvement, always something we missed. Plate tectonics is one of the most powerful and comprehensive theories in modern science, but according to a new study out today, we may have missed an important piece of the geologic puzzle. According to this research, tectonic activity may be controlled by forces deeper below the surface than we’ve realized.

Plate tectonics theory explains how the Earth’s crust moves and changes. The crust isn’t a solid shell over the Earth, it’s broken into fragments: plates. Each plate butts right up against all the surrounding plates, so there’s no space in between, but they can rotate in place, or shift like conveyor belts, sliding and grinding past each other, into each other, or underneath each other. Boundaries between plates are areas of massive geologic activity. Where plates move together, they form massive mountains or deep trenches; where plates pull apart, volcanic activity creates new crust. The surface of the Earth is constantly shaking, shifting, and deforming, mostly at these boundaries.

This is a map of the major tectonic plates of the Earth.
Notice the places where the plates meet - those are the very active plate boundaries.
Image from Wikipedia.

Thursday, June 9, 2016

"Saurian" is Already the Best Dinosaur Video Game of All Time

As popular as dinosaurs are, they’ve been surprisingly under-developed in video games. Most “dinosaur video games” – Primal Carnage, Turok, ARK, etc. – fun as they may be, feature re-hashed versions of misinformed prehistoric beasts being hunted and/or fought and/or ridden by humans. And just as the same-y anachronistic lizard-monsters of Jurassic World didn’t cut it for a lot of dino-fans, the ancient beasts of those video games similarly fail to impress. They just don’t feel like real dinosaurs.

And then there's Saurian. Watch this video:

Dinosaurs don't get realer than that.