DNA Unlocks the Secrets of the Dead Sea Scrolls

Is every word in the Bible holy? When did prayers replace sacrificial offerings? The Dead Sea Scrolls consist of 25,000 fragments, but no one knows how to put them together. A new study suggests a way to solve that puzzle, which sheds new light on life in this land 2,000 years ago

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Jeremiah 10:1. Illustration: Aron Ehrlich
Asaf Ronel
Asaf Ronel

Over 70 years ago, a Bedouin shepherd named Muhammed ed-Dib entered a cave in the Qumran area west of the Dead Sea. In it he found large clay jars containing parchment scrolls wrapped in linen. Ed-Dib didn’t know it, but he had stumbled upon the first pieces of one of the most important archaeological discoveries of the 20th century, which would come to be known as the “Dead Sea Scrolls.” The scrolls opened a window to the spiritual world and quotidian life of the Second Temple period – one of the most tempestuous eras in Jewish history – and shed light on the process by which various Jewish sects sprang up during that time, one of which would morph into Christianity. But even today these archaeological finds continue to raise more questions than answers.

A major reason for the contentious disputes is that the collection of scrolls in Israel today consists of nearly 25,000 fragments of parchment and papyrus (the lion’s share of all the known scroll artifacts in the world) which, it is estimated, come from more than 930 different ancient manuscripts. This vast jigsaw puzzle, with an unknown number of pieces that have been lost over time, includes the earliest versions found to date of all the books of the Hebrew Bible (with the exception of the Book of Esther), as well as the biblical apocrypha and many other works previously unknown.

The conventional theory is that some of those works were written or copied by a zealous Jewish sect, identified by most scholars as the Essenes, who led an ascetic life in the desert. However, there is now general agreement that the collection also includes scrolls that originated from outside the sect, written by other learned individuals of that period. Accordingly, the question of which texts are unique to the sect and which were brought in from outside is crucial for understanding the significance of the texts, and to what extent they represent the ideas in currency in Judea of the latter Second Temple period (334 B.C.E.-70 C.E.). A study published this week as the cover story of the scientific journal Cell has harnessed the most advanced tools of biological research in order to help solve the mystery.

The study was conducted by researchers from Tel Aviv University, led by Prof. Oded Rechavi, from the George S. Wise Faculty of Life Sciences and the Sagol School of Neuroscience, and Prof. Noam Mizrahi from the department of biblical studies, in collaboration with Prof. Mattias Jakobsson of Uppsala University in Sweden, the Israel Antiquities Authority, Prof. Dorothee Huchon-Pupko from TAU’s zoology department, and Prof. Christopher E. Mason of Weill Cornell Medicine.

Two pieces of the Dead Sea Scrolls at the Israel Museum.
Two pieces of the Dead Sea Scrolls at the Israel Museum.Credit: Ohad Zwigenberg

Using techniques of DNA sequencing and sophisticated methods of computation, the scientists were able to identify and catalog 26 parchment fragments (plus another 13 leather artifacts) according to the DNA of the animals on whose skins the scrolls were written, and thus to determine which fragments are related to one another, and which ones not.

“There are many scrolls fragments that we don’t know how to connect, and if we connect wrong pieces together it can change dramatically the interpretation of any scroll,” says Prof. Rechavi. “Assuming that fragments that come from the same sheep belong to the same scroll, it is like piecing together parts of a puzzle.”

The methods the researchers employed have already helped to shed light on a host of important historical and religious issues: how the concept of sacredness in regard to the texts of biblical books changed over time; when basic notions arose in the realm of Jewish mysticism from which the kabbala sprang; and what the origin was of the idea that prayer could replace sacrificial offerings – an idea that was formerly thought to have emerged only following the destruction of the Second Temple, in 70 C.E.

But before applying themselves to matters of remote Jewish history, the researchers had first to overcome a series of challenges, starting with how to collect the sensitive samples. In most cases, to avoid damage to the priceless antiquities, the researchers extracted DNA from tiny scroll crumbs (“dust”) that fell off, or were scraped off the backs of the fragments. The researchers even demonstrated that they could retrieve authentic ancient DNA from adhesive tape – used in the 1950s to piece fragments together – that was removed from scrolls.

How scroll fragments are turned into a window on Jewish history.
How scroll fragments are turned into a window on Jewish history. Illustration by Nadav Gazit

“We were not even allowed to touch the scrolls,” says Dr. Sarit Anava, from Rechavi’s laboratory at TAU. The solution, she explains, was for the Israel Antiquities Authority, which stores all of the scroll pieces in its laboratories at the Israel Museum, to place the samples in test tubes, which she took to Sweden to the laboratory of geneticist Mattias Jakobsson at Uppsala University, which was specially adapted to enable the isolation of ancient genetic materials. In this way, a scroll-crumb is transformed into a window onto Jewish history.

“We’ve thought for years that the scrolls’ DNA should be examined,” says Prof. Jonathan Ben-Dov, an expert on the Dead Sea Scrolls from the University of Haifa’s department of Jewish history and biblical studies. “Everyone waited for it to happen, and it finally succeeded,” adds Ben-Dov, who was not involved in the new study.

If so, what has been discovered?

Comparing texts

The first insight divined by the researchers related to the way inhabitants of Judea in the Second Temple period viewed the texts of the Bible. Apparently, the Judaism of that era didn’t have one standard version of each of the sacred texts; in other words, not every jot and tittle in the Bible was regarded with the same holiness it would later possess. The scholars reached this conclusion by examining four fragments of parchment containing sections from the Book of Jeremiah.

Today all editions of the Hebrew Bible are absolutely identical, down to the letter. This was the case even before the invention of printing, in fact since the emergence of the authoritative Masoretic Text of the Bible in Tiberias in the early Middle Ages – a version that has been preserved almost without alteration to this day. However, other, even-older versions of the Scriptures also exist, notably the Septuagint. This Greek translation of the Hebrew Bible, originating in Alexandria and dating to the third and second centuries B.C.E., was eventually adopted by the Greek Orthodox Church and remains in use today. The differences between the Masoretic Text and the Septuagint are especially striking in Jeremiah.

Cave number 11, where some of the artifacts were discovered. Most of the scrolls weren't found by archaeologists but by Bedouin who didn't want to reveal where the valuable antiquities came from.
Cave number 11, where some of the artifacts were discovered. Most of the scrolls weren't found by archaeologists but by Bedouin who didn't want to reveal where the valuable antiquities came from. Credit: Shai Halevi / Israel Antiquities Authority

“It’s not a matter of the interchange of a letter here and there, or differences between a few isolated words,” says Noam Mizrahi, the biblical scholar. “The Septuagint text of Jeremiah is 15 percent shorter than the long version reflected in the Masoretic Text. Furthermore, the two texts differ in the way their sections are arranged; in some of the prophecies there are differences in the order and in the content of the verses. The result is, in effect, completely different ‘editions’ of the prophetic text, and at times entirely different texts.”

Differences of this sort in the books of the Hebrew Bible disappeared in the wake of the destruction of the Temple.

“What remained are smaller differences at the orthographical level, which persisted into the Middle Ages because the books were copied by hand,” Mizrahi continues. “In late antiquity and the Middle Ages, rigorous mechanisms of ‘quality control’ were applied, which ensured that the differences would hardly ever affect an understanding of the content.”

Which versions of Jeremiah appear on the scroll fragments examined by the research team? One fragment contains a long version close the Masoretic text, two contain a short version that resembles the Septuagint, and a fourth has a different, independent text.

Mizrahi: “There was a scholarly debate over three of these segments, about whether they originally belonged to the same scroll or came from different scrolls, because they look very similar to each other but differ in the handwriting of the copyist.”

What Ancient DNA Can Tell Us About the Scrolls
Three methods of analysis
1. Differences between species
Mitochondria are cell organelles from which DNA can be extracted
Comparing sequences in the mitochondrial DNA of different fragments showed that the scrolls were written on sheepskin and cow skin
2. Identifying a common group
Circular DNA in mitochondria makes it possible to identify a common primeval mother 
Thus it was discovered that the Qumran scrolls were made from sheep of one primeval group, while a scroll at Masada was made from a sheep of a different group
3. Degree of proximity
Computational methods make it possible to analyze in depth the fragmented nuclear DNA
This analysis made it possible to identify a cluster of scrolls made from animals with a high genetic proximity
Illustration by Nadav GazitCredit: Illustration by Nadav Gazit

Enter genetic classification: The scientists discovered that the vast majority of scroll pieces they examined were written on the skin of sheep – an animal that could also be bred in the climatic conditions of the Judean Desert 2,000 years ago. The fragments of the Book of Jeremiah that stirred debate, however, were written on the skins of two different animals: two on sheep and two on the skin of a cow, an animal that was not ordinarily raised in the Judean Desert.

For the scientists, discovery of which animal skin was used for copying the texts represents a significant, genetic confirmation of the hypothesis that the writing was not solely the work of the desert sect but of someone from the outside.

“Cow-skin scrolls were manifestly not produced there, but originated externally,” Mizrahi says. “And while theoretically they might have been brought to Qumran as blank parchments, such a scenario makes very little sense from a practical and economic point of view, so it seems they were brought already as written manuscripts. The conclusion that these are two separate versions of Jeremiah neither of which, apparently, was copied by the local sect, but rather originated in a different context and place, points to the possibility that an openness to divergent texts of the Holy Scriptures reflects a more general approach in Judea at that time.”

He adds, “As long as there was only the Greek translation, it could be argued that [the existence of different versions could be attributed to] the Diaspora [the Jews of Alexandria]. But the scrolls indicate that the multiplicity of versions was a basic feature of Judaism as a whole, during that period, and particularly in Judea.”

According to Prof. Michael Segal – an expert in the Dead Sea Scrolls and the dean of humanities at the Hebrew University of Jerusalem – the new findings are consistent with a current theory that holds that some of the scrolls came from outside Qumran. “One reason is that some of them antedate the founding of the community itself,” notes Segal, who was not involved in the current study. To which Jonathan Ben-Dov adds, “We have been playing with theories about the biblical text for hundreds of years. Now, thanks to biology, we have an ‘Archimedes fulcrum,’ with whose aid we can examine those theories.”

Heavenly temple

One of the greatest challenges of DNA research is to locate genetic material of sufficiently high quality to enable laboratory analysis. According to Prof. Yitzhak Pilpel, head of the molecular genetics department of the Weizmann Institute of Science in Rehovot, who was not involved in the study, this is particularly true in cases of genetic samples that need to be extracted from the most minuscule fragments of ancient relics. To overcome this obstacle, scientists involved in the new research used a variety of methods that enabled them to examine the surviving ancient genetic material at different resolutions. For example, the species of animal from which the scrolls were fashioned – sheep or cow – was identified by comparing sections of the mitochondrial DNA found in the cells of the parchment skin to that of more than 10 species of animals until a match was found. Other methods allowed the scientists to determine the genetic relationship between the different sheep whose skins were used in creating the scrolls.

A copy of the “Songs of the Sabbath Sacrifice” that was found outside of Qumran.
A copy of the “Songs of the Sabbath Sacrifice” that was found outside of Qumran.Credit: Ohad Zwigenberg

The second method – analyzing the basic genetic groups (haplogroups) of the sheep – made it possible for the researchers to derive insight concerning “Songs of the Sabbath Sacrifice,” one of the most intriguing and important texts found in the Qumran scrolls.

“This is a composition that was unknown before the discovery of the scrolls, but 10 copies of it were found among the scrolls themselves – clear evidence of its importance,” Prof. Mizrahi explains. “What was not clear was whether the importance of ‘Songs of the Sabbath Sacrifice’ was unique to the sectarian group that left the scrolls behind, or whether it represents the work’s popularity among a broader community.”

One reason for the considerable interest in this composition is that one copy of the “Songs” was found 55 kilometers south of the Qumran caves, in the excavations on Mt. Masada. Many scholars had discerned a connection between the discoveries at both sites. In their view, during the Great Revolt of 66-70 C.E, when the Romans who ruled the country were preparing to lay siege to Jerusalem, and the Qumran community was annihilated – the sect’s survivors fled and joined the Jewish rebels who had barricaded themselves at Masada.

The new study calls this hypothesis into question, at least as far as the textual evidence is concerned. A comparison of the DNA of the sheep showed that the scrolls found at Qumran were all made from animals belonging to one genetic population group, whereas the scroll found at Masada was made from the skin of a sheep from a different group.

“We did not expect that result,” Mizrahi admits. “It shows that it is unlikely that this copy of the ‘Songs’ was brought to Masada by a refugee from Qumran, because this scroll differs biologically, materially, from the scrolls found at Qumran.”

According to Ben-Dov, the new biological information that’s come to light does not rule out a connection between the sites. “After all, the study itself showed that at Qumran there were scrolls made from the skin of different animals, such as cows,” he says. Still, he adds, the findings reinforce the possibility that the Masada scroll is not directly connected to Qumran. This possibility – that this religious work was widely circulated in the Judea at that time, outside the sect – has significant implications for understanding the spiritual life of Second Temple Judea.

Qumran timeline

Mizrahi adds that discovering the source of the copies of “Songs of the Sabbath Sacrifice” is particularly important, because of the uniqueness of the text. It is a liturgical composition – a collection of Sabbath prayers – but also contains an internal narrative. It describes the heavenly temple and the angels’ rite of worship. It can be inferred, then, that the authors and readers of the text assumed that there is in heaven a temple parallel to the earthly one and that angel-priests in it are engaged in worship. However, activity in the heavenly temple did not center around offering sacrifices as was true in the Jerusalem Temple, but focused on nonstop uttering of praises of God.

Why is this important? “This was a period when the Temple was still operating,” Mizrahi explains. “The conventional view of researchers until a generation ago was that the idea of fixed and statutory prayer replacing sacrificial offerings in the Temple emerged in Judaism only after the destruction of the Second Temple.” Accordingly, at the dawn of Qumran studies, the approach that derived from analysis of the Dead Sea Scrolls and the discovery of the prayer collections they contain, was that the Judean Desert sect predated Judaism’s transition from sacrificial rituals to the practice of prayer. Scholars in the past explained that the disputes between different sects of the Second Temple period sects, and the insistence of one of them on particularly strict rules of ritual purification led to the latter keeping their distance from the Jerusalem Temple and remaining secluded in the desert – hence their development of the idea of prayers as a substitute.

However, Mizrahi says now, this hypothesis needs to be reconsidered in light of the discovery that the Masada copy of “Songs of the Sabbath Sacrifice” is not genetically linked to the Qumran copies.

“It turns out that the idea of prayer as the center of worship was popular beyond Qumran. Were these other communities of the [same] sect that lived in other places? Possibly,” he says, referring to a theory that offshoots of the main sect were active elsewhere. “But now we know that the centrality of prayer in the worship of God was not unique to Qumran.”

Beyond this, there are additional distinctive features of the “Songs of the Sabbath Sacrifice,” among them elements that would surface centuries later in early Jewish mystical writings known as “Hekhalot and Merkhavah” (literally, the “Heavenly Palaces and the Divine Chariot-Throne”) literature. This is a collection of mystical compositions of which the earliest manuscripts were found in the Cairo Genizah. Scholars are divided about the dating of the original works, but it’s conventionally thought that they were written in the second half of the first millennium C.E.

Research team members, including, at center, from left, Mizrahi (with beard), Shor and Rechavi. Using biological research’s most advanced tools.
Research team members, including, at center, from left, Mizrahi (with beard), Shor and Rechavi. Using biological research’s most advanced tools.Credit: Ohad Zwigenberg

Says Mizrahi: “This is the oldest layer of Jewish mystical literature, and the foundation on which other mystical doctrines were built, including what would subsequently feed the kabbala literature.”

For example, the concept of the chariot of God, which first appears in Ezekiel, develops in the “Songs of the Sabbath Sacrifice” – and hundreds of years later in the Hekhalot literature – into the idea that the believer can, through a spiritual journey, be “elevated” to the heavenly temple, enter the Holy of Holies and see God’s chariot. For 30 years, scholars have been arguing about the nature of the connection between the “Songs of the Sabbath Sacrifice” and the mystical literature that appeared later.

Over the years, the discovery of this text and the fact that it was attributed to the Qumran community contributed to cultivating the notion that the sect served as a source of inspiration for ideas that later informed Jewish and Christian mysticism. The problem was that until now, no one knew exactly how the transition came about.

“As long as ‘Songs of the Sabbath Sacrifice’ was perceived as a work unique to Qumran, there was a missing link between Qumran and the whole mystical tradition that develops in late antiquity, the early Middle Ages and afterward,” Mizrahi says. “But if we know now that ‘Songs of the Sabbath Sacrifice’ was a work that was known outside Qumran – and until now there was no clear sign of that – then we can understand that there were other channels of transmission of these texts and ideas that bridge the missing link.”

The Judean Desert.
The Judean Desert. Credit: Ofer Vaknin

Scroll clusters

Another significant achievement of the new genetic study is to reinforce one of the leading methods today for classifying the Dead Sea Scrolls, which until now was based on an analysis of the way they were written. For this purpose, the scientists analyzed sheep sequence variation in the nuclear genome, by means of “deep” DNA sequencing and algorithms developed by Moran Neuhof, Dr. Hila Gingold and Or Sagy from Prof. Rechavi’s laboratory. These comparisons enabled them to distinguish between a cluster of scrolls made from sheep bearing high genetic similarities, and scrolls made from sheep that do not belong to this cluster and that are also genetically remote from one another.

This time the researchers applied DNA analysis to the nuclear sheep genome (rather than the mitochondrial genome, which doesn’t allow distinguishing between individual sheep), to evaluate the system of classification proposed by Prof. Emanuel Tov, who was editor-in-chief of the international Dead Sea Scrolls Publication Project. The Bible scholar classified the findings into two groups according to 20 scribal signs, such as how the authors of the scrolls inserted corrections, spelled words, marked the explicit name of God (the Tetragrammaton) and so on. According to this classification method, presented in a series of publications, principally during the 1930s, the overwhelming majority of the texts possessing a content unique to the members of the Qumran sect match one scribal style, which was labeled QSP (Qumran Scribal Practice). According to Tov, these scrolls were written by the sect’s scribes. Tov believes that the other scrolls found at Qumran, labeled Non-QSP, were probably brought to the sect from the outside.

“It turns out that all the scrolls we sampled whose nuclear DNA indicates that they belong to one cluster, namely that they are genetically close, were classified as QSP scrolls, whereas the Non-QSP scrolls belong to different clusters,” Rechavi says.

Patrick W. Skehan, one of the first scholars to study the Dead Sea Scrolls, at the Rockefeller Archaeological Museum in Jerusalem, which now serves as the archive of the Israel Antiquities Authority.
Patrick W. Skehan, one of the first scholars to study the Dead Sea Scrolls, at the Rockefeller Archaeological Museum in Jerusalem, which now serves as the archive of the Israel Antiquities Authority. Credit: Najib Albina / Israel Antiquitie

Ben-Dov notes that “in recent years the theory about the Qumran scribal practice came in for criticism,” but now the researchers have shed new light on the subject. “Until now this group of scrolls was characterized according to philological markers, and now we also have biological markers,” he says.

In addition, the fact that no genetic similarity was found between the external scrolls and the first cluster – nor between any of those scrolls in the external cluster – supports the hypothesis that the Non-QSP scrolls originated in various places throughout Judea. One of the copies of “Songs of the Sabbath Sacrifice” found in Qumran now turns out to belong to the second cluster as well.

“This is further reinforcement for the hypothesis that the ‘Songs’ was widespread outside the sect’s circles,” Rechavi avers.

One of the reasons for the confusion about the connection between different scroll fragments stems from the way they were found. Only about a quarter of the scrolls were found in situ by archaeologists, while most were found by Bedouin and sold to researchers in the 1950s, with the sellers not always having an interest in saying exactly where the valuable antiquities had come from. Now, with the aid of the new genetic tools, the scientists are able to unravel part of the tangle, and identify mistakes of earlier researchers. For example, the study found that a fragment from Isaiah, which until now was cataloged as part of the Qumran scrolls, deviates genetically from all the other Qumran scrolls. “This raises intriguing questions: Did the fragment really come from the Qumran caves, or perhaps from a place that hasn’t yet been identified?” Mizrahi notes, adding, “Perhaps segments resembling it are still lurking among the 25,000 scroll fragments found to date.”

What next? Pnina Shor, founder of the Dead Sea Scrolls Project unit in the Israel Antiquities Authority, who took part in the research study, notes that the authority is working to enlist state-of-the-art scientific tools in an effort to improve the deciphering and preservation of the scrolls. With the aid of international collaboration, the IAA is now drawing on tools such as artificial intelligence to make progress in assembling the physical and textual jigsaw puzzle. Another plan is to make use of a particle accelerator to read segments of a scroll that congealed, rendering it impossible to separate its layers. The IAA is also adopting the biological tools. “The present study is proof of its feasibility,” Shor says.

Masada.
Masada.Credit: Moti Milrod

The study examined only a small number of the scrolls, but according to the scientists a promising path to solving the riddles residing in the Qumran scrolls lies in expanding the use of genetic analysis. The development of the methods that made the latest breakthroughs possible took years, but the researchers are convinced that the next stage will be far more rapid. Rechavi: “I hope we will be able to sample a large number of scrolls and discover how to put the puzzle together.”

According to Prof. Oren Harman, a historian of science from Bar-Ilan University, “the use of ancient DNA is like the invention of a new tool, like the microscope or the telescope. It allows us to tell a new story, sometimes a different story from the one the archaeologists, anthropologists and historians told until now.” Like every scientific tool, emphasizes Harman, who was not involved in the study, ancient DNA should also serve to solve good questions, and not stand on its own. “It’s important to remember that analysis of the results of studies that rely on ancient DNA is based on a statistical interpretation of the data, and that different interpretations are possible for the same data.”

Prof. Pilpel, the molecular geneticist, notes that the researchers’ conclusions about the scrolls they examined appear to be solid. One of the reasons for this is the choice of scrolls that are of interest if it is shown that they are not connected to one another. “It is easier to establish that two sections of skin do not belong to the same animal – all you have to do is show that there are a certain number of differences in the DNA, and that can be done even if the genetic material that remains is of low quality.”

The various Bible scholars surveyed by Haaretz all say they are certain that even if the biological information serves only to show that different scroll fragments do not match one another, there are many fascinating questions to ask with the use of this tool. “There is hope of achieving a more accurate classification of the scrolls in the future,” says Michael Segal. According to Ben-Dov, “We [Bible scholars] have been wrestling with different theories for so many years, but biology is providing us with a new way to make our arguments.”

Prof. Mizrahi sums up the field of scrolls research in the following way: “We are adrift on an ocean of uncertainty, and scientific research creates a small island of probability in it. The more we increase knowledge, the more we discover more cogently how much we have left to discover.”

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