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400,000-year-old human DNA adds new tangle to our origin story

Alan Boyle, Science Editor         NBC News

18 hours ago

Image: Sima de los Huesos people

Javier Trueba / Madrid Scientific Films
The Sima de los Huesos people lived about 400,000 years ago in  Spain.

The oldest human DNA ever recovered is throwing scientists for a loop: The 400,000-year-old genetic material comes from bones that have been linked to Neanderthals in Spain — but its signature is most similar to that of a different ancient human population from Siberia, known as the Denisovans.

The researchers who did the analysis said their findings show an “unexpected link” between two of our extinct cousin species. Follow-up studies could crack the mystery — not only for the early humans who lived in the cave complex known as Sima de los Huesos (Spanish for “Pit of Bones”), but for other mysterious populations in the Pleistocene epoch.

“Ancient DNA sequencing techniques have become sensitive enough to warrant further investigation of DNA survival at sites where Middle Pleistocene hominins are found,” the research team, led by Matthias Meyer and Svante Pääbo of Germany’s Max Planck Institute for Evolutionary Anthropology, wrote in Thursday’s issue of the journal Nature. (“Hominin” is the currently accepted term for humans and our close evolutionary cousins.)

As anthropologists are getting better at extracting DNA from ancient bones, genetic mysteries are cropping up more frequently: Last month, researchers at scientific meetings talked about not-yet-published findings that hinted at interbreeding among Neanderthals, Denisovans and previously unknown populations of early humans.

A new standard The age of the mitochondrial DNA analyzed for the Nature study sets a new standard: Researchers used statistical analysis of the DNA and other samples to estimate that the material was roughly 400,000 years old. That meshed with the estimated age for similar DNA extracted from bear bones found in the same cave.

More than 6,000 human fossils, representing about 28 individuals, have been recovered from the Sima de los Huesos site, a hard-to-get-to cave chamber that lies about 100 feet (30 meters) below the surface in northern Spain. The fossils are unusually well-preserved, thanks in part to the undisturbed cave’s constant cool temperature and high humidity.

Image: Femur bone

Javier Trueba / Madrid Scientific Films
The thigh bone of a 400,000-year-old hominin yielded mitochondrial DNA for analysis.

Researchers drilled a series of tiny holes into the cracks in a human femur recovered from the cave to obtain nearly 2 grams (0.07 ounce) of powdered bone. At first, they looked for the signature of ancient nuclear DNA, which could have provided information about the genome of the individual behind the femur — but that information was overwhelmed by the signature of modern-day human contamination.

Then they turned their attention to the mitochondrial DNA, which lies outside the cell’s nucleus and is passed down from a mother to her children. That strategy was more successful.

Unusual finding Previous analysis of bones from the cave had led researchers to assume that the Sima de los Huesos people were closely related to  Neanderthals on the basis of their skeletal features. But the mitochondrial DNA was far more similar to that of the Denisovans, an early human population that was thought to have split off from Neanderthals around 640,000 years ago. The first Denisovan specimens were identified in 2010, based on an analysis of 30,000-year-old bones excavated in Siberia.

Image: Sima skeleton

Javier Trueba / Madrid Scientific Films
This skeleton from the Sima de los Huesos cave has been assigned to an early human species known as Homo heidelbergensis. However, researchers say the skeletal structure is similar to that of Neanderthals – so much so that some say the Sima de los Huesos people were actually Neanderthals rather than representatives of Homo heidelbergensis.

The latest DNA analysis sent scientists scrambling for an explanation.

“This unusual finding could be due to at least two different scenarios, both relating to the material inheritance of mtDNA [mitochondrial DNA] and the ease with which it can be lost in a lineage,” Chris Stringer, a paleoanthropologist at London’s Natural History Museum who was not involved in the Nature study, wrote in an email.

One scenario could be that the DNA was passed down the maternal line from a population that was ancestral to the Sima de los Huesos humans as well as the Denisovans, but that the lineage died out among Neanderthals and modern humans.

The other scenario is that an as-yet-undetermined population interbred with ancestors of the Spanish cave-dwellers as well as the Denisovans. Meyer, Pääbo and their colleagues tentatively favor that scenario. “Based on the fossil record, more than one evolutionary lineage may have existed in Europe during the Middle Pleistocene,” they write.

“Either way, this new finding can help us start to disentangle the relationships of the various human groups known from the last 600,000 years,” Stringer said. “If more mtDNA can be recovered from the Sima ‘population’ of fossils, it may demonstrate how these individuals were related to each other, and how varied their population was.”

Update for 10:30 p.m. ET Dec. 4: Erik Trinkaus, a paleoanthropologist at Washington University in St. Louis, told NBC News that the DNA findings were interesting from a technical standpoint — but he pointed out that the mitochondrial DNA alone doesn’t reveal how the Sima de los Huesos people and their ancestors lived. He suspects that further DNA studies will show that the relationships between populations of early humans were messier and more tangled than the typical diagrams of human origins would suggest. That’s appropriate, he said, “because I think the real world is messy.”

More about our tangled origin story:

In addition to Meyer and Pääbo, authors of “A Mitochondrial Genome Sequence of a Hominin From Sima de los Huesos” include Qiaomei Fu, Ayinuer Aximu-Petri, Isabelle Glocke, Birgit Nickel, Juan-Luis Arsuaga, Ignacio Martínez, Ana Gracia, José María Bermúdez de Castro and Eudald Carbonell.

Alan Boyle is’s science editor. Connect with the Cosmic Log community by “liking” the NBC News Science Facebook page, following @b0yle on Twitter and adding +Alan Boyle to your Google+ circles. To keep up with’s stories about science and space, sign up for the Tech & Science newsletter, delivered to your email in-box every weekday. You can also check out “The Case for Pluto,” my book about the controversial dwarf planet and the search for new worlds.



Derecho a La Intimidad

Constitucion Argentina 1853 (Art 19)

University of Louisville / Children’s Hospital and G.H 


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I was an just graduated Argentine MD in pediatric training at Children’s Hospital and General Hospital of University of Louisville, (UOL) Kentucky in the late sixties. As come to The US  planning to go back to Argentina‘s Patagonia to practice there when my training was complete; I chose that University because it was one of the oldest and smallest Municipal Universities in The Union. –  UOL was academically excellent, but even more important to me: “It was small enough to avoid human, personal disconnection with patients“. – To take care of both –(across the street)- hospitals, our Pediatric Department needed 25 to 30 MD residents, but that year we were only 8; so I was lucky!… I have plenty of work and no time to fool around! – Because my ESL (English as Second Language) was limited, my first post was at the newborn and premature nursery. My Pediatric Professor a mentor (Dr. Water Hughs) call me to his office one day; to discuss a baby case I was discharged the previous day.  The new born baby was born to a syphilitic mother. We treat the mother and the baby. As the baby blood diagnostic test for syphilis was positive my discharge diagnosis was “Lues Congenital”. My discharge diagnosis was read by a clerk at the file room while processing that chart. The clerk called his supervisor. The supervisor called my Chief, and he called me to tell me: “Gaston your diagnosis and treatment of this baby has been excellent. The baby’s blood test for lues are positive, so in a way that diagnosis may be right… BUT if you stamp that diagnosis to his records; this baby is going to be a civil dead for the rest of his life. He won’t be able to get any job, insurances … On the other hand… the treatment has been so good that he is not really sick…” – We change that diagnosis and routinely followed the baby as a normal out patient; and I learn precisely what I expect to learn in my medical training “Medicine is about human been, individual persons, NO just “cases, tests, X-rays, either stats”. I was right to Choose UOL!  –  It was not just my Chief who save that baby! It was a plain alert clerk, part of a teamwork  of an excellent small University! –As an actual contrast: What is going on today with those same principles? “The Right to OUR PRIVACY!” – To day: a simple buccal mucosal swab can make public, thousand times more PRIVATE information than 1 cc of blood drained from a baby, 40 years ago!. It can predict (for example) serious incapacitating genetic diseases 30 or more years before the disease became symptomatic! Are we going to “LEGALLY KILL all that people? And do that just to let corporation make more money?  – Is this a modern more efficient technique for INFANTICIDIOS? – Please read the CATO note about “BALANCING” and DNA SWABSINFANTICIDIO del REY HERODES

“Balancing” and DNA Swabs

Posted: 05 Jun 2013 05:22 AM PDT

Julian Sanchez

My colleagues IlyaJimRoger, and Walter have said most of what needs to be said about the Supreme Court’s recent decision in the DNA sampling case Maryland v. King. So let me just hover for a moment on a point Roger makes.  Everyone seems to agree that Justice Kennedy’s majority opinion strains the bounds of language by arguing that the state purpose of “identification” served by DNA sampling arrestees includes establishing a “context” for understanding “who the person really is,” including their “past conduct.” By the same logic, we might justify searching the homes of every drunk driver for evidence of unrelated crimes, since this too would give us a sense of “who they really are,” and whether they have reason to jump bail lest other crimes be discovered. The real argument, disingenuously shoehorned into this rubric of “identification,” is that this is indeed a warrantless search for ordinary investigative purposes, but that once a person has already been legitimately detained, the marginal intrusion involved in a cheek swab is trivial—and the benefit to society of enabling serious crimes to be solved so great—that an exception to the normal Fourth Amendment rules is justifiable.  This is, as Roger suggests, a closer call.

Let’s go further and make the argument that Justice Kennedy, determined to cast this as a matter of “identification,” didn’t bother with.  He could, after all, have cited to the Supreme Court’s major dog-sniff cases, Place and Caballes, in support of the following argument:

Animation of the structure of a section of DNA...

Animation of the structure of a section of DNA. The bases lie horizontally between the two spiraling strands. (Photo credit: Wikipedia)

The limited DNA profile actually entered into the CODIS database is only useful for matching, not for revealing other sensitive facts about medical conditions or genetic predispositions.  In essence, then, this is a search that only reveals whether one is the unidentified perpetrator of a crime—which, like possession of contraband, is a fact in which a person has no “reasonable expectation of privacy.”  So one might argue.

The first point to make is that the narrow “if you have nothing to hide, you have nothing to fear” argument doesn’t really work.  A murder investigation will naturally involve collection of foreign DNA samples on the victim, which may well belong to persons that had nothing to do with the crime. Thus a search of an innocent arrested persons DNA could easily reveal the existence of, say, an unrelated but secret sexual relationship with the victim, or merely the presence of the searched person at the scene of a crime they had no involvement in. So this is not really a search with no realistic risk of exposing innocent but legitimately private information.

The larger point, though, is that the provisions of the Bill of Rights were meant to avoid precisely this kind of granular case-by-case “balancing” process, to the extent possible. An analogy to the First Amendment may be helpful here. Let’s concede: It is totally plausible that prohibiting Nazis from marching through a community of Holocaust survivors, or the grotesque Westboro Baptist Church from picketing military funerals with signs that read “Thank God for Dead Soldiers” and “God Hates Fags,” would suppress particular instances of speech with no real social value and spare decent people anguish they do not deserve. In a vacuum, probably neither instance of speech would survive a “balancing test.”  But the courts correctly protected both nevertheless, because the First Amendment articulates a meta-balancing judgment that we do not want the government engaged in this kind of specific case-by-case balancing analysis of which speech is valuable enough to be protected. The Framers of the Constitution had already done a balancing test about when it is better not to engage in balancing tests.

So it is, I would argue, with the Fourth Amendment. In the short term, it is easy enough to say that a few cheek swabs are a trivial marginal intrusion, even if they sometimes expose innocent private information, compared with the social benefit of catching murderers and rapists. But especially as DNA testing technology evolves, what are the consequences of establishing a massive repository of genetic information about the one-third of Americans who will be arrested by the age of 23—especially if that database disproportionately encompasses poor minorities, many of whom are never convicted of any crime? (Those who ARE convicted, as Justice Scalia’s dissent in King observed, get sampled anyway—so the policy in  question here only really makes a difference to the innocent.)  How do you “balance” the crimes solved at the margin when samples are taken from people arrested though ultimately acquitted against the creation of an architecture of genetic information-gathering, which may in itself encourage pretextual arrests for trivial offenses to circumvent the need for search warrants for genetic material, whose long-term uses are impossible to foresee? The general attitude of the courts, after all, is that once information or evidence has been legitimately acquired by police, there is no Fourth Amendment barrier to further analysis of that evidence, even if unrelated to the purpose for whcih it was acquired. (There are, I think, good theoretical reasons to regard this as a mistake, but that’s how things presently stand.)

In this case, then, the Court has invoked the idea of “identification” to obscure what is fundamentally an application of a “balancing test” to a warrantless investigative technique. But the Court is balancing benefits it can see reasonably clearly with costs it cannot.  Perhaps, even in the long run, the benefits will outweigh the costs. But the point of the Fourth Amendment is to provide a basis for limiting governmental information gathering that, to the extent possible, avoids saddling the Court with the responsibility for engaging in this sort of utilitarian calculus. It cannot be avoided entirely, of course—that much is implicit in the inclusion of the normative term “unreasonable” in the text of the Fourth Amendment—but it should not be the ordinary grounds for deciding which particular searches are permissible. Sometimes, as Hayek understood, we stick to simple rules, not because they are truly optimal, but because we are not clever or prescient enough to develop more nuanced rules that do better.