Back in 2003, a strange skeleton was discovered in a deserted Chilean town in the Atacama Desert. Featuring an elongated skull, sunken eye sockets, and an impossibly tiny body, some suggested it was of extraterrestrial origin. An updated genetic analysis confirms the skeleton as being human — but with an unprecedented variety of mutations.
Preserved by dry desert conditions, “Ata,” as the mummified skeleton is called, is undeniably weird. It’s only about six inches long, it’s missing a pair of ribs, and it has a highly deformed head and face. Though discovered 15 years ago, the specimen dates back about 40 years, so it’s not ancient. Soon after its discovery, short documentary.
Photo: Dr. Emery Smith
Intrigued, Garry Nolan, a Stanford University School of Medicine microbiologist and immunologist, decided to take a closer look. His 2013 study concluded that Ata was indeed human, and that the skeleton’s bones gave the impression that it was between the age of six and eight years old when it died — a very strange observation given the skeleton’s diminutive proportions. But many questions remained, such as Ata’s gender and why it featured such strange physical characteristics, such as the elongated skull, sunken and slanted eye sockets, undeveloped midface and jaw, and 10 ribs instead of the usual dozen. Nolan figured Ata had suffered from some form of dwarfism, but the evidence was lacking.
The mystery deepened soon after the 2013 analysis, when Paolo Viscardi, a natural history curator at the Horiman Museum in London, complained that the skeleton couldn’t possibly have come from a child, and that it was more likely the remains of an aborted foetus that died between the ages of 14 to 16 weeks, and was subsequently and unceremoniously dumped near a church in the Atacama desert.
Five years later, Nolan, along with colleague Atul Butte, director of the Institute for Computational Health Sciences at the University of California-San Francisco and a Priscilla Chan and Mark Zuckerberg Distinguished Professor, have performed a highly detailed genetic and physical analysis of Ata, offering new insights into the enigmatic mummy. The new study, published today in Genome Research, highlights a series of mutations responsible for the malformed specimen, revealing genetic anomalies in not one but several genes responsible for healthy bone development – including some mutations and resulting physical manifestations that have never been recorded before in a human.
For the study, DNA was extracted from the specimen’s bone marrow, and owing to its pristine condition, the researchers were able to sequence Ata’s entire genome.
“What we are reporting now are the specific mutations that we think are associated with the unusual condition seen in this child,” Butte told Gizmodo. “We went searching for rare mutations — mutations that we really haven’t seen in other humans that have been sequenced so far, with the thinking that it must have been something very rare to cause this condition, which really hasn’t been seen elsewhere before.”
According to the new analysis, Ata was a human girl of Chilean descent. And indeed, she was very likely still a developing foetus when she died, even though she exhibited the bone composition of a six-year old child. The reason for this, claim the researchers, is that Ata suffered from a rare bone-ageing disorder. In total, the researchers identified mutations in at least seven genes that, either separately or in tandem, contributed to Ata’s odd physical characteristics, including facial malformations, bone deformities, and apparent dwarfism (known as skeletal dysplasia). Some of the genes analysed in the study were already known to cause disease, but this is the first time that some of the mutations were linked to abnormal bone growth or other developmental problems.
“It is quite surprising how many mutations this child has,” said Butte. “And that’s pretty relevant today. Children with rare and undiagnosed diseases are now more frequently getting genetic sequencing, and typically we in the medical field search for the ‘one gene’ with the problem. It’s like a genetic Occam’s Razor, with the thinking that the simplest explanation is often the right one.”
But in this particular case, the researchers found many genes with mutations.
“That teaches me now that when we try to explain [health issues in] current-day patients, we shouldn’t just stop at one gene explaining the one condition — that many genes might actually have a problem,” he said. “And that might help us with choosing the right therapies some day.”
In terms of limits to the research, Butte said his team can only guess that these DNA variants, or mutations, are what caused the unusual symptoms seen in the specimen. “We don’t really know for sure about the ‘causality’ here,” he told Gizmodo.
That said, one of the coolest aspects of this study is how scientific advancements sometimes come from the strangest places. Years ago, few would have thought that this strange little skeleton could one day teach us something new about diagnosing and treating rare genetic diseases.
Correction: A previous version of this article incorrectly stated that Dr. Nolan’s 2013 study concluded that the Ata specimen was between 6 to 8 years old when it died. Rather, the study claimed that the bones gave that impression. In an email sent to Gizmodo, Nolan clarified the situation:
I was widely mistaken or misquoted on that point. I only ever said the bone density and mature formation made it APPEAR that the specimen (if human) would have been 6-8 years old. That obviously was at variance with the size of the specimen.
The genetic studies since then were about finding probable cause. Remarkably, multiple mutations show up in the now human child (female) — with a plethora of mutations in bone development. They all point towards bone genetic disorders (several verified by other studies we reference) as the cause. To figure out EXACTLY which mutations are relevant would be another 5-10 year study to introduce these mutations into mice and see if we can replicate anything comparable. I will leave that now to the bone development scientists to determine if it’s appropriate to do.