Analysis of Ancient Humans

KEVIN HARRIS: “New analysis of ancient human protein could unlock secrets of evolution.” This article, by Robin McKie, science editor for The Guardian^[1], begins by saying,

Tiny traces of protein lingering in the bones and teeth of ancient humans could soon transform scientists’ efforts to unravel the secrets of the evolution of our species.

I guess one thing it reveals is that ancient people didn’t floss! Actually, you discuss proteomics in In Quest of the Historical Adam so you are familiar with this research.

DR. CRAIG: Yes. In In Quest of The Historical Adam, I looked at the new science of protein proteomics and its application to fossilized human beings and what these protein analyses, particularly of the teeth enamel on these skeletal remains, can tell us about the relationships of these prehistoric humans.

KEVIN HARRIS: The article says,

Researchers believe a technique known as proteomics – newly applied in the field of human fossils – could allow them to identify the proteins from which our predecessors’ bodies were constructed and bring new insights into the past 2 million years of humanity’s history.

Analysis of these microscopic remnants could then help to solve major evolutionary mysteries such as the identity of the common ancestors of Homo sapiens and the Neanderthals.

What are your thoughts on common ancestry these days?

DR. CRAIG: The phrase “common ancestry” is ambiguous. It depends on what biological category you are applying it to. For example, if we want to talk about the common ancestry of human beings, we would be looking at the common ancestry of Neanderthals, Denisovans, and Homo sapiens. This is not committed to there being a common ancestor of chimpanzees and human beings, for example; or of chimpanzees, gorillas, and human beings. What we're interested in here is simply the relationships among these fossil remains of people who have been classified as belonging to the species Homo.

KEVIN HARRIS: Yeah, it's kind of used as a catch-all phrase when there's more to it. Common ancestry is usually thrown out there on the Internet as meaning one thing – that we all came from an amoeba or whatever. You are saying that there are nuances to that phrase?

DR. CRAIG: Yes, that's right. I think when we want to talk about the descent of all life from a common ancestor we should use the phrase “universal common ancestry.” But when we're talking about limited common ancestry – for example, the common ancestry of all dogs. All dogs belong to the same species. They all have the same ancestor. Then common ancestry is unobjectionable and uncontroversial, I think, in many cases. The way I applied it in my study in In Quest of the Historical Adam was to try to find the common ancestor that gave rise to Neanderthals and Denisovans in Europe and Asia and to Homo sapiens in Africa.

KEVIN HARRIS: Next the article says,

The ramifications of the technology would mirror the impact of the recently developed technology of ancient DNA analysis which, over the past 20 years, has helped uncover dramatic secrets about humanity’s past. These include the discovery that many modern humans possess Neanderthal genes and that the two species must have interbred at some point over the last 100,000 years.

This topic is discussed in your book.

DR. CRAIG: Yeah, that's right. A remarkable fact is that all of us – you and I – carry Neanderthal genes in our genetic library (in our genome). In fact, since writing the book, I have read that a tribe was identified in the Philippines by anthropologists who have as much as five percent of their genome is Denisovan – Denisovan DNA. It's remarkable the interbreeding that went on among these human beings and has filtered down to us as their descendants today. The fact that they could all interbreed has suggested to many biologists that in fact these are not distinct species. Very often a species is described as an interbreeding population. If two populations cannot interbreed, then they belong to distinct species. If you follow that biological species concept, it would follow that really Neanderthals, Denisovans, and Homo sapiens are not distinct species but they're all just members of the same human species.

KEVIN HARRIS: Here’s what the article says about Denisovans,

Part of the research will involve using a handheld scanner that can be passed over a fossil in order to reveal how much protein it contains. . . .

The development of proteomics follows scientists’ success in analysing DNA extracted from ancient human fossils. By studying scraps of genetic material from fossils, scientists have discovered that men and women of non-African origin carry some Neanderthal genes. They have also revealed the existence of a completely new species of early humans – known as the Denisovans – from genetic material found in tooth and bone fragments in a Siberian cave.

All of this we’ve become familiar with in your book.

DR. CRAIG: That's right. Another thing that I document in the book that is remarkable is that it's not simply non-Africans who carry these Neanderthal genes, but rather it has been documented that Neanderthal genes are found in people living today of African descent. So this interbreeding that went on even carried right down into Africa, and today African tribes will carry these genetic descendants from the Neanderthal genome just like you and I do.

KEVIN HARRIS: The article says,

But the analysis of ancient DNA has limitations. “DNA is fragile and decays fairly quickly, especially in warm conditions,” said Pontus Skoglund of the Francis Crick Institute. “So it is mainly useful for studying fossils that are less than 100,000 years old and found in moderately cool or cold places.”

. . .

Our bodies are made of proteins whose manufacture is controlled by our DNA and so, by unravelling their structure, insights can be gained into the make-up of ancient individuals. Crucially, proteins survive longer in warm conditions.

This latter advantage offers hopes of gaining new insights into several baffling newly discovered species. These include Homo naledi, a 300,000-year-old hominin that was found in South Africa in 2013. Specimens appear to be primitive although other evidence suggests they also have buried their dead. In addition, the origins of Homo floresiensis, [from the island of Flores in Indonesia] a small archaic species of humans – nicknamed the hobbit folk . . .

Do you know anything about these little guys?

DR. CRAIG: I think in the case of both Homo naledi and Homo floresiensis that we are dealing with non-human hominins. Although they are classed as Homo, they have brains that are scarcely any larger than the Australopithecines which were just bipedal apes. They have smaller brains than virtually any other Homo species that's been identified. As I explained in the book, one mustn’t think that just because a primitive hominin is identified as being part of the genus Homo that that is a genuine human being. I think that in these two cases that we're dealing simply with advanced primates that were, I think, clearly sub-human. The claim that Homo naledi buried its dead I think is fanciful. What they discovered is that in a cave they dumped the carcasses of the dead down a crevasse so that deep, deep down in the interior of the cave all of these carcasses had collected. Well, that's not proper burial of the dead such as Neanderthals engaged in where the dead would be interred with certain artifacts perhaps that belonged to them or that it somehow were associated with them. I think these hominin species were just engaged in house cleaning, so to speak. You don't want a stinking carcass lying around the cave so they dump it down the crevasse.

KEVIN HARRIS: I went online to learn how to pronounce all these species, but it's done me no good! When I start the podcast my adrenal gland kicks in, and I forget how to pronounce it. But, at any rate, I did try.

The article concludes,

Nevertheless, proteomics has already produced early promising results. Studies by Frido Welker of the University of Copenhagen have shown that collagen proteins found in a piece of hominin jawbone at Baishiya Karst cave high on the Tibetan plateau in China matches those of Denisovans.

“This is the first hint at what a Denisovan might have looked like and suggests that proteomics has a lot to offer our understanding of human evolution,” Welker told the Observer last week. “It is certainly encouraging.”

Tie all this in to your In Quest of the Historical Adam. What do you hope that proteomics will continue to show?

DR. CRAIG: I am waiting for proteomic analysis to be carried out on the remains of Homo heidelbergensis that were left at places like Box Grove, England. The proteomic analysis of remains from certain hominin species in Spain showed that Homo antacessor was not in fact an ancestor of Neanderthals, Denisovans, and Homo sapiens. Instead, Welker says it was a sister species – a kind of branch off of the line of development. My curiosity is what these analyses would reveal with regard to Homo heidelbergensis which I have tentatively identified as being the species to which Adam and Eve belonged. I wrote to Welker about this, and in our correspondence he said this just hasn't been done yet. No one has yet tested any of the remains from Homo heidelbergensis to reveal its relationship to Neanderthals, Denisovans, and Homo sapiens. But that will be something that will be extremely interesting when it is eventually carried out.^[2]