The Pit of Bones: A Death Chamber Time Capsule

A small chamber in a deep, dark cave. Tens of thousands of bones. Animal bones and human bones. Buried under dust and dirt and bat dung.

Welcome to an ancient chamber of horrors. This is the Pit of Bones (aka Sima de los Huesos).

In 1997, scientists discovered this small chamber within a much larger complex cave system. They’ve found other human occupation sites within it, but The Pit of Bones was no place for the living. To date, more than 50,000 partially fossilized bones have been collected. These bones include more than 6500 belonging to an ancient hominid species, in addition to bones of over 160 individuals of an extinct species of cave bear, a panther, lynxes, canines, and small mammals.

The Pit of Bones shows evidence for the deep-time perspective that I’ve argued for elsewhere on this site. What is found in this pit should cause everyone to reflect on their origins but young-earth creationists should find its contents most troublesome. Let’s find out why.

Fig. 1. Drawing of the Sima del los Huesos (the pit of bones) cave.  The vertical shaft.  The figure is from Arsuaga et al. "Sima de los Huesos (Sierra de Atapuerca, Spain), The Site"  JHE 33 (1997): 109-127.

Fig. 1. Drawing of the Sima del los Huesos (the pit of bones) cave. The vertical shaft. The figure is from Arsuaga et al. “Sima de los Huesos (Sierra de Atapuerca, Spain), The Site” JHE 33 (1997): 109-127.

Where is the Pit of Bones, and What’s in It?

The Pit of Bones was found in a large cave system in northern Spain discovered during the cutting of a railway line through a hill. The actual chamber is at the end of a 40-foot ramp, leading up to the base of a 43-foot vertical shaft (Fig. 2), 1500 feet from any cave entrance. It is, literally, a dead end. After careful inspection, it became clear that this chamber has had only one entry—the 43-foot vertical shaft. It is highly unlikely that anything that dropped or fell down that shaft could ever come back up.

To date, scientists have examined less than half of the fossil-bearing layers of cave sediments, but a gruesome picture has emerged.  There are tens of thousands of bones in the chamber, most belonging to cave bears. But buried beneath the animal bones is a more significant discovery: more than 6500 hominid bones representing at least 28 individuals.  With ongoing excavations, researchers expect that the number of the hominid Homo heidelbergensis remains found will likely double.

The nature of these deposits points to an environment with very little disturbance over time and gradual accumulation. The hominid bones have been found in the deepest sediments that fill the pit. Most of the hominid bones are beneath the other carnivore bones, with a few hominid bones mixed with carnivore bones. The bones are embedded in layers of clay, along with many thin sheets of fragile “calcite rafts” and other cave deposits. These sheets and deposits indicate the presence of a shallow and very quiet pool of water and very slow precipitation of minerals, which have coated and buried the bones. On top of several feet of human and carnivore bones are layers of rock debris from roof falls. On top of that is another layer—several inches to several feet of bat guano. The lack of any bones in the upper sediment and rock layers, and the layer of bat guano, suggests that during this time of the chamber’s existence, the cave entrance was probably very small. Its size prohibited any larger animals from entering.

So How Did the Bones Get into the Pit of Bones?

Fig. 2. Excavation in a portion of The Pit of Bones in Spain.  Image from:

Fig. 2. Excavation in a portion of The Pit of Bones in Spain. Image from:–20131204-0118.html

Researchers have been asking themselves how the hominid bones got into the Pit of Bones. Interestingly, there have been no hominid artifacts found yet, other than a single stone axe. This tell us that the bones did not come from people living in this part of the cave.

Here’s another puzzle: all of the animals in the pit are carnivores or omnivores. The absence of any prey species—such as any number of common deer—means this was probably not a place that carnivores brought their food to eat.

So could the hominid bones have been dragged there by large cats and bears?  That’s not likely. There are few signs of gnawed hominid bones, and the vast majority of hominid bones are found lying below the bones of the other carnivores. This suggests that the hominid bones were deposited there before—perhaps long before—the other carnivores died and deposited their bones onsite.

Fig. 3. The Pit of Bones excavation in progress since 1997

Fig. 3. The Pit of Bones excavation in progress since 1997

It appears that cave bears and other animals got into The Pit of Bones by accidental falls. One possibility is that they heard or smelled animals that had fallen in the pit, and they tried to climb down for an easy meal. Clearly, the vertical shaft was in a portion of the cave where no light would have been present—since it’s a third of a mile from any cave exit. However the animals fell in, once they were in the pit there was no way out.  There are many gnaw marks on the cave-bear bones, which suggests that some animals survived their fall and chewed on the bones of past victims, until they too finally died.

Some of the hominid bones recovered from The Pit of Bones

Some of the hominid bones recovered from The Pit of Bones

But what about the 28 hominids that have been found so far?  Many of those that have studied the bones in this pit think that the best explanation is that hominid remains were deposited there intentionally. There are adult male and female bones, as well as at least one juvenile.  Was this a body disposal site? Or was this a site of ritualistic burial?

The answer isn’t known for sure, but the large concentration of bones in just one layer in this pit strongly suggests that a series of accidental hominid falls is unlikely. Cave bear and other animal bones are far more numerous, but they are distributed in more sediments and over a larger area of the cave, suggesting an accumulation of accidental falls over much longer periods of time in contrast to the origin of hominid bones.

A cross section of the pit of bones showing where excavations have taken place and the contents of the layers of sediments.   Figure is from Arsuaga et al "Sima de los Huesos (Sierra de Atapuerca, Spain), The site" J. Human Evolution 1997, 33:109-127.

Fig. 4.  A cross section of the pit of bones showing where excavations have taken place and the contents of the layers of sediments. Figure is from Arsuaga et al “Sima de los Huesos (Sierra de Atapuerca, Spain), The site” J. Human Evolution 1997, 33:109-127.

Just How Much Time Would It Take for the Pit of Bones to Accumulate Bones?

Look at Figure 4 above. If you examine this image of a cross-section of the cave, you’ll see multiple distinct layers of rock and fossils. These attest to a long history of events in this cave.

Through observation, we can reconstruct a chronology of events, showing how the Pit of Bones formed. Below, I summarize those events, which is based on what I have gleaned from published literature:

1)      First, a large cave system formed over time in a large limestone formation. In that large cave system, a large pit formed and some sediment was deposited on its floor.
2)      Next, the cave became available for hominid and animal occupation—it was dry enough and there was a large-enough entrance at this point.
3)      At least 28 hominids, and probably many more, fell or were thrown down the 43-foot shaft to the pit below.
4)     Over several hundred thousand years, additional animals experienced accidental falls into the pit. Some survived and their movement in the cave disturbed and mixed some of the bones.
5)     Eventually, the cave system became closed to the outside, or the climate changed (e.g., an ice age), preventing animals from using the cave. During this time, deposition of cave debris such as dripstone occurred.
6)    The cave opened enough to allow a habitat for bat colonies, which resulted in several feet of bat guano at the base of the vertical shaft.
7)    Finally, the cave once again was accessible for human occupation. Modern humans occupied portions of the cave system for thousands of years, with layers of bones and other cultural debris attesting to changing technologies. Parts of the cave system were discovered in the 16th century, with no occupation likely during the previous 2000 years.

The order of these events seems clear and uncontroversial. But what exactly is the length of time covered by this timeline? Multiple dating techniques put this series of events as occurring over 500,000 years—beginning with the initial formation of the cave (3).

The Pit of Bones from a Deep-Time Perspective

Again, how did these human bones appear in the pit, underneath the animal bones, bat guano, and cave deposits? As mysterious as the exact circumstances are, the context of the cave system and the deposits in particular are not difficult to understand within a deep-time perspective. The cave likely required hundreds of thousands of years to form, and the presence of many layers of rock and sediment with different properties are consistent with changing climatic conditions over time, resulting in differential deposition. There are layers of sediments in the pit with no bones at all in them, suggesting prolonged periods in which the cave entrances were cut off to animals and humans. Much later in the pit’s existence, there was a period in which bats inhabited the cave.

Number 7 in the chronology above adds an additional twist to the story of this cave system. There is good evidence of periodic modern human occupation from around 2000 to 16,000 years ago —which equals about six feet of sediments on the cave floor (3). In these sediments, unlike The Pit of Bones, there are thousands of bones that include prey animals that the inhabitants ate along with thousands of tools and pieces of pottery.  In the deepest sediments, there are anatomically modern humans with relatively simple hunting technology. As you move up sedimentary layers, towards the surface sediments, you find ever more sophisticated tools and pottery pieces, which evidence Bronze-Age technology and eventually even Roman period artifacts at the top.

How Would Does The Pit of Bones Align with a Young-Earth Timeline?

The archaeological context of the bones at the Pit of Bones site presents considerable difficulties to any young earth creationists’ timeline of history.  (As part of my continuing series on the geological context of fossils and its implications for the origins debate see: The frequently overlooked geological context of human fossils; Neaderthals and the Italian Supervolcano, Fossil Human Footprints Found Below Ice Age Deposits), I would just point out that this The Pit of Bones is not as complex as some of the prior sites we have explored. And yet it is still a great challenge to the YEC hypothesis.)

Young-earth geology—which hypothesizes an Earth that’s only a bit more than 6,000 years old—makes a clear prediction regarding the bones in these two locations at the site under discussion. (Those locations are the cave entrance and The Pit of Bones.) The prediction is that both locations should contain material of nearly the same age, even if different populations of humans were found there.

But this prediction fails badly. The site shows strong evidence against it.

The bones in the upper portion of the cave have been dated by multiple techniques to be 2000 to 16,000 years old. While using some of the same techniques, only a few of which involve radiometric isotopes, the hominid bones from The Pit of Bones are dated to around 430,000 years of age (2). The dates for the cave-bear bones span over a hundred thousand years, which again is consistent with the other hypothesis—that the animals fell over time accidentally into the pit. Why would human bones found so close together in the same cave system date 400,000 years apart, if they were all from peoples inhabiting the caves during a singular ice age about 4,200 years ago as proposed by young earth creationists?

This 430,000-year span make sense in light of the geological evidence in the cave. For example, as I’ve said, the cave-bear fossils in the inhabited upper portion of the cave are all found below the bones from human occupation sites, while in The Pit of Bones they are found above the human bones. This fits with other data from other sites in Europe that tell us that cave bears went extinct around 25,000 years ago and so should not be found with remains of humans that date to only 4 to 10 thousand years old.

Artistic depiction of Homo heidelbergensis hominids whose bones are found in The Pit of Bones. Photo: Javier Trueba, Madrid Scientific Films

Fig. 5. Artistic depiction of Homo heidelbergensis hominids whose bones are found in The Pit of Bones. Photo: Javier Trueba, Madrid Scientific Films

The human bones from the pit are also clearly not from the same people as those found in the younger portions of the cave. The hominids from the Pit of Bones has been described as Homo heidelbergensis, which is thought to be the ancestor of the Neanderthals.   These earlier people do not appear to have inhabited the cave, having left no sign of their presence other than a large set of bones in a pit far from the cave opening. Furthermore, the chronological sequence of modern human remains and cultural artifacts is very similar to patterns observed in multiple other locations across Europe attesting to the reliability of the conventional timeline of modern human development.

Ancient DNA Further Confirms Dates for the Pit of Bones

I was originally interested in the geological context of these bones because of a bone pulled from the rocky matrix at the bottom of this pit, which yielded a tiny amount of highly degraded DNA (5).  The sequence of that mitochondrial DNA from that bone was widely reported. Analysis of that sequence revealed it to be most similar to DNA extracted from a tooth and tiny bone from the Denisova cave in Siberia.  At around 430,000 years old, this is the oldest human DNA yet recovered from a fossil.

I mentioned this DNA and its sequence in my recent article, Young Earth Creationism and Ancient DNA.  In 2013, one of the cave bear bones from the Pit of Bones was used to generate the whole genome sequence of a cave bear, which showed, in part, that they were genetically distinct from all bear species alive today. Not surprising since that bone was dated to approximately 300,000 years old.

When the hominid DNA sequence was published (6), creationists heralded the DNA findings from the homo heidelbergensis bone as evidence that these bones simply represent a population of humans.  For example, a few days after the sequence was published, Elizabeth Mitchell wrote (4) on the Answers in Genesis website that:

After the global Flood of Noah’s time, about 4,350 years ago, the human gene pool, which had begun around 1,700 years earlier with Adam and Eve, was whittled down to 8 people. Their descendants eventually dispersed from the Tower of Babel. Though they were all related, once they became isolated and in some cases reduced to small groups, distinctive traits would have emerged—characteristics that we now associate with the fossils of various “archaic” (i.e. ancient and extinct) people, who were nevertheless fully human.

Fig. 7. Nature (2013) doi:10.1038/nature12788 A mitochondrial genome sequence of a hominin from Sima de los Huesos.  Matthias Meyer et al.

Fig. 6.   This is Fig. 4 from Matthias Meye et al. in Nature (2013) doi:10.1038/nature12788
A comparison of mitochondrial genome sequences of a hominid from Sima de los Huesos with other hominids and all living humans.
Most notable here is the differences between the sample from the Pit of Bones and all living humans (Blue and Yellow bars).  The fossils in the upper part of the cave that date younger would fall in the Asian and European group while the bones in the pit would likely all be like the Sima de los Huesos DNA sample.

She downplays the actually differences in the DNA that were found in these bones to make the case that their bones were just from people who lived during a recent Ice Age but the DNA sequences lie outside the bounds of variation found in all living people today. (Fig. 6) The DNA was highly degraded as expected for such ancient sample. Irrespective of the lack of appreciation for the genetic differences in these hominids, what is more disconcerting is her suggestion that humans found their way to this cave in Spain less than 4,000 years ago, and that some of them found themselves buried under debris in the bottom of a pit in the back of this cave system.

These claims seem to contradict all the archaeological, geological, chemical, and biological evidence from this site.

The young-earth theory, in other words, doesn’t fit the evidence here.

Conclusion: The Pit of Bones is a Serious Problem for the YEC Hypothesis

Organizations such as Answers in Genesis claim to provide an alternative reading of the natural world, one that brings the evidence of creation in line with their specific literalist reading of Genesis. They write articles that claim that it is easy to fit bones and DNA evidence from sites like The Pit of Bones into the young-earth timeline. For example, Mitchell’s article ends with the following claim:

Denisovans and Neanderthals and the people of Sima de los Huesos (whether they are called Homo heidelbergensis  or something else) were simply humans who lived in the post-Flood world and left their fossilized remains in Ice Age sediment.

Given The Pit of Bones site, this is what the YECs are effectively saying about its formation. At the dispersal from the Tower of Babel, 4350 years ago, a group of humans—who had distinctively different bone morphology than modern humans—traveled very quickly to Spain. There, they found a cave during the Ice Age. Somehow, 28 of them fell into a pit in the back of the cave. After that, at least 160 cave bears fell into the pit, along with many other mammals. All of these falls happened within 100 to 200 years of each other, since cave bears and all the other animals in that pit have been extinct in recorded history for the last 4,000 years.

So how did 160 bears and many other animals manage to wander a third of a mile back into a cave and fall down a shaft in such a short period of time? How did they do this right after 28 hominids had fallen into the pit? How and why did these animals stop falling into the pit?

On top of these tough questions, all of the remains in the pit—animal and hominid—were then covered by cave deposits themselves, the result of the slow dripping of liquids into pit. At a later time, but apparently still during the young-earth Ice Age, other anatomically modern humans then took up occupancy in the cave, after all the cave bears had fallen into the pit. They lived there long enough to produce thousands of shards of pottery and various tools. In the YEC timeline all of this activity had to occur within a 2000 year window as the last of the signs of habitation are from the Roman era.

The evidence at the Pit of Bones is very difficult to fit into a young-earth timeline.

Mitchell doesn’t address the facts of the cave, other than mentioning that there are human fossils found in it. I have looked and so far found no detailed descriptions of the cave and the context of these fossils in the young-earth creationist literature. To ignore the context in which they are found is scientifically troubling. But to assert that the people who left bones were “simply humans who lived in the post-Flood world and left their fossilized remains in Ice Age sediment” does little else but provide false hope to those looking for comforting answers to perceived challenges from secular science. What Ken Ham and other YEC organizations provide are not real answers to hard questions, but shallow answers to complex problems.

It is likely that most lay Christians will never realize that the fossils at the Pit of Bones provide no support either genetically or geologically for a young-earth hypothesis. However, given that this highly selective reporting of the facts is the normative approach in the creation literature, many Christians will eventually find themselves staring at some piece of data that Answers in Genesis has ill-equipped them to address.

There is no doubt that hominid fossils such as those found at the Pit of Bones pose difficult questions for Christians who wish take the Scriptures seriously. That they pose challenges, though, doesn’t require that Christians simply accept ad-hoc answers.


1. National Geographic summary of 17 skulls from Sima de los Huesos:  Bonanza of Skulls in ‘Pit of Bones’ Changes View of Neanderthals

2. J. L. Arsuaga et al. 2014.  Neandertal roots: Cranial and chronological evidence from Sima de los HuesosScience 20 June 2014: 344 (6190), 1358-1363. [DOI:10.1126/science.1253958] Abstract  Full Text Full Text (PDF)  Supplementary Materials

3. Carretero, José Miguel, Ana Isabel Ortega, Laura Juez, Alfredo Pérez-González, Juan Luis Arsuaga, Raquel Pérez-Martínez, and Maria Cruz Ortega. “A Late Pleistocene-Early Holocene archaeological sequence of Portalón de Cueva Mayor (Sierra de Atapuerca, Burgos, Spain).” Munibe (Antropologia-Arkeologia) 59 (2008): 67-80.

4. Sima de los Huesos Reveals Surprising Genetic Connections. In: News to Know by Dr. Elizabeth Mitchellon December 16, 2013 Answers in

5. Dabney, et al. 2013. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments PNAS 2013 ; published ahead of print September 9, 2013, doi:10.1073/pnas.1314445110

6.  Meyer, Matthias, Qiaomei Fu, Ayinuer Aximu-Petri, Isabelle Glocke, Birgit Nickel, Juan-Luis Arsuaga, Ignacio Martínez et al. “A mitochondrial genome sequence of a hominin from Sima de los Huesos.Nature (2013).


  1. Cave Man says:

    Sometimes I think it’s OK for the YECs and the normal people to go their separate ways. Time will tell which world-view makes for a fitter population. In a similar way, the differences in economic policy between red and blue states will lead to radically different outcomes, and people should be able to make informed decisions about which regime they would rather live under.


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