In 2013 a remarkable DNA sequence was reported by geneticists studying ancient DNA. It was a nearly complete genome extracted and decoded from the remains of a tooth of a horse preserved in permafrost sediments in Alaska. This partially-fossilized horse was dated to more than 500,000 years old and is the most complete sequence of an ancient sample attained to date. In addition to this ancient genome, partial genomes of additional horses from 43,000 to 5000 years old have also been sequenced allowing us to compare genetic variation of horses from the past with those from the present.
I have written a series of posts about the origins of horses. The context of these post has been an evaluation of how young earth creationists (YECs) have sought to understand the origins of equine biological diversity. We have observed that many YECs have moved rather dramatically from denying the “horse sequence” of evolution to accepting that all living and extinct species of equines are all descendants of a shared common ancestor—the horse “kind.” However, this common ancestor lived just 4300 years ago rather than 40 to 50 million years ago as the evolutionary narrative holds.
Given this YEC perspective of biological ancestry including what we have rapid or hyper-evolutionary model we might ask: does DNA sequence extracted from this ancient horse prove helpful to the YEC viewpoint or does it provide another problem, among countless others, that the YEC faces as they promote their alternative explanation for the origins of biological diversity on earth?
Not long after the genome of this ancient horse was published, Elizabeth Mitchell, writing for the chief YEC apologetics ministry, Answers in Genesis, commented on this story (see: A horse is a horse, unless of course it isn’t a horse). I wish she had read my article of a similar title (A horse is a horse, unless of course it isn’t a horse) which was first published not long before hers. She seems to have missed the most important implications of the horse genome with respect to the young earth origns model that I detail in my series of articles about origins of horses (see links in the “Additional Reading” sidebar).
Let’s take a look at just a few of the conclusions we can draw from this ancient horse DNA:
This ancient horse is a horse and was a horse long ago: Here we have hundreds of millions of bases of DNA code from a horse that died long before the most recent Ice Age (we know this from the geological context in which the fossil was found). By aligning that sequence with genomes sequenes of other equine species it is clear that this ancient genome belonged to a horse. By this I mean that it DNA is so similar to the modern horse species, Equus ferus, that it could be assigned to that species of horse, or very close sibling species. This suggests that the species of horse from which domesticated horses were derived from was already genetically distinct from other horse species (i.e. donkeys, zebras etc..) as long ago as 500,000 years.
While the YEC would not agree with the ancient date of this fossil would they expect that a distinct linage of horse would already have formed before th Ice Age which the believe occurred right after the common ancestor horse “kind” left Noah’s Ark?
Let’s start with a quote about horse evolution from Georgia Purdom, AIG’s resident geneticist, which is included in Mitchel’s article:
While we would disagree that the horse ancestor lived millions of years ago (based on radiometric dating which uses unverifiable assumptions about the past), we would agree that all horses came from a common ancestor which, according to the Bible, was on the ark only around 4,300 years ago. The similarity of this fossil horse DNA to modern horse DNA further confirms that God created animals according to their kind (Genesis 1). There is variation within the kind, but even after the proposed hundreds of thousands of years the fossil and modern horse DNA are still very similar. We don’t observe the types of changes necessary for a horse to evolve into a different kind of animal.
A pair of the equine kind got off Noah’s ark about 4,300 years ago, and genetic information in that pair provided the raw material for all the equine varieties we see today. Speciation mediated through natural selection and other means enabled their descendants to adapt to many environments in the post-Flood world.
First, lets observe the obvious and important point that what we have here is confirmation of what I stated in previous articles: that AIG’s current position on the origin of horses is that all horses (donkeys, asses, zebras, domestic horses and wild horses) are the descendants of a single pair of equine ancestors on Noah’s ark just 4300 year ago. Therefore, at that time there were no zebras, donkeys or horses but some sort of combination of all of them into just two individual animals that were the common ancestors of all of them.
Second, I believe Dr. Purdom is very confused about the significance of the lack of sequence divergence in this fossils horse. Elsewhere, Purdom calls this diversification from a common ancestor “genetic sorting of raw material.” We might ask, how much raw variation was there in this original pair and where is the evidence that only a short time ago donkey’s, domestic horses, zebras, etc.. didn’t exist but only a single ancestral equine-like pair? This ancient horse sequence provides us with some clues about how long the living horse species (Equus ferus) have been distinguishable as equine lineages/species.
Examining the figures I have included you can see that the Thistle Creek (the permafrost fossil sample we are focused on here) horse exhibits the greatest genetic differentiation (ie. more DNA differences as visualized as longer lines connecting them to other horses) than all the other horses though it is still most closely associated with domesticated horses and the wild horse (Przewalski’s horse) rather than the more genetically distinct donkey and not shown zebras.
At first it may see that a YEC such as Dr. Purdom may think that evidence that a horse sequence hasn’t changed much over thousands of years might lend support to their view that there are limits to evolutionary change. But taking a minute to reflect further it quickly becomes clear that this ancient horse is of no help to the YEC. Positing that this horse demonstrate little evolvability undermines the YEC belief that horses were quick to change from a common acestor into a hundred or more genetically distinct lingeages of equines. If a horse has been a horse for thousands of years how can the YEC claim that horses have a common ancestor with donkey’s, zebras etc… just 4500 years ago?
The second figure shows the genetic variation in mitochondrial DNA for many living horses and quite a few “ancient” horses samples which come from bones at archaeological sites. Only the Thistle Creek, labeled TC, and 34,000 year-old bone exhibit DNA sequences that are significantly divergent from all other horses. Even so, these fossil sequences along with many other horse bones conventionally dated to more than 5000 years old still have DNA sequences that are very similar to living horses.
Within the context of YEC chronology, the 5000 year, 43000 year and 500,000 year old samples must all be less than 4500 years old. However, we have a reference point that YECs should all agree limits the age of the fossils within there chonology. That reference point is the fact that the later two samples are found underneath Ice Age deposits. Therefore in the YEC chronology these bones must be older than 4000 years but less than 4300 years old because their ancestor was on Noah’s Ark at that time. When the ancestor of all equine species departed from Noah’s Ark 4300 years go its offspring must have diverged into horses, horses, donkeys, zebras and all extinct species of equines in the space of just a few hundred years.
How did the genomes of the two common ancestors on the ark get “sorted out” so quickly into the distinct genomes we find in horses, zebras and donkeys today? Why are there no ancient horses with genomes that are intermediate between donkeys and horses? And why, even if they diverged very quickly, have horse genomes then barely changed in the past 4000 years after undergoing such radical change in just a few hundred years?
The characteristics of the DNA sequence of this ancient horse are perfectly consistent with the expectations of modern genetics and evoltuionary biology. In particular, the genetic divergence of this DNA sequence is consistent with the rate of genetic change we observe in the present and thus fit the conventional dating of the fossil being hundreds of thousands of years old.
Creationists believe is ultra-high speed evolution of species from a common ancestor but they have yet to provide any compelling evidence (genetic models or ancient DNA samples) that provide any hint that this rapid divergence has actually occurred in the last 4300 years.
Does DNA preserved for 500,000 years support a young-earth or ancient earth?
A second question is raised from this ancient DNA genome sequence. Mitchell is quick to cast doubt on the conventional ancient age of the horse fossils. Why? No doubt she doesn’t believe the dating methods employed but in this case she references what she thinks is a problem with DNA preservation and her expectation that DNA molecules should not be able to survive 500,000 years. Therefore she believes this is compelling evidence that these fossils are young. But as I have written many times before, (see: Where’s the DNA? Young Earth Creationism and the Search for Ancient DNA) even if ancient DNA were a problem for an ancient earth, and it doesn’t appear to be, the existence of ancient DNA raises a significant problem for Mitchell’s young-earth viewpoint.
If the world were only a few thousand years old we might ask: why is DNA not found in abundance in all fossil teeth not just ones from the very top of the fossil record? Rather than abundant in fossils, we observe that DNA is very difficult to find intact. No dinosaur teeth have DNA and yet we could expect to pull the entire genome of mammoth from nearly every mammoth tooth we have every found. What Mitchell doesn’t tell her readers is that the DNA from the 500,000 year old horse was not the same as DNA extracted from a living horse. It was found fractured into mostly small 10-50 base pair fragments for which fancy repair enzymes had to be fashioned to “fix” DNA damage before even those short fragments could be sequenced. This is exactly what we would expect to find if this DNA was very old. Even in permafrost which is the ideal environment to preserve DNA this horse DNA was degraded quite extensively.
Let’s contrast this to the 43,000 year old fossil horse which Mitchell does not mention in her article. This horse was also sequenced as part of the same study as the 500,000 year old horse. The bones from this “younger” horse were not preserved under ideal conditions and yet the DNA extracted from them was in far better shape! So the fossil estimated to be much older had DNA that was much more degraded just as expected/predicted by those who assume an ancient earth. However, in the YEC model these two sub-fossils (not completely fossilized technically) were found in sediments that young earth creationists likely would predicte were laid down immediately after the flood and probably within just a few years of one another. Effectively they believe they are roughtly the same age rather than separated by a half-a-millioin years. If this is the case why does the one that is preserved in the best conditions have the worst DNA and why is the DNA really all that decayed at all?
There are thousands of fossils that are from bones preserved during the most recent Ice Age that YECs believe are from a time just after the Flood. These fossils have DNA that is in very good condition and easily sequenced. Why do these bones not have highly degraded DNA? According to AIG dinosaurs died during Noah’s Flood just 4300 years ago why is DNA not found in abundance in them when they were quickly preserved just a few hundred years before these horse fossils. YECs have provided no explanation/mechanism to explain why DNA is NOT found in all or most fossils.
There are large inconsistencies in the stories that AIG is telling its audience about DNA and its implications. Charitably, I don’t think they even think about the ramifications of their own claims when they are trying to discredit mainstream science but they should consider how their claims would affect their own hypotheses. If they did they might see that what they are saying is inconsistent at best.
Ludovic Orlando, et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature499,74–78(04 July 2013) doi:10.1038/nature1232