Introducing The Ancient BioChain — and why its second phase will turn towards ancient pathogens.
At the end of a story about an epidemic, there is often a question that refuses to go away: what was actually making people ill?
We may have followed a ruler’s desperate prayers, examined a physician’s strange clothing, or read an account of families frightened to enter one another’s homes, and begun to understand what disease meant to the people living through it. Identifying the disease itself is another matter — and even when a scientific paper appears to offer an answer, a second question follows: how do we know?
For me, that question connects the historical curiosity behind Ancient Epidemics with a different part of my work: The Ancient BioChain, a research initiative and public demonstration environment for The BioChain. It begins with publicly available ancient DNA and archaeogenomic information, using the past to explore how the history of scientific evidence can be preserved, and its next planned phase will focus on ancient pathogens.
The connection is more natural than it might first appear. Both projects involve following a story backwards, asking where it began and looking carefully at what happened along the way — one follows the experience of disease through history, the other is concerned with the evidence through which we investigate that history.
A discovery has a history of its own
Imagine an ancient tooth — not a particular specimen, but a hypothetical example. It has been recovered from a burial, recorded, studied and eventually sampled for genetic research. Material from it passes through laboratory work, producing data that researchers can analyse, and later some of that data appears in a public repository, where another research group uses it to ask a question quite different from the one that prompted the original study.
The tooth has not moved through all those subsequent investigations. Its digital descendants have. Along the way, it may have acquired several identifiers, its estimated date may have been refined, and its data may have been processed again using different methods. What looks like a single entry in a research dataset can therefore represent a complicated sequence of decisions, transformations and interpretations — this is the kind of journey explored in The Ancient BioChain’s journal, Origins.
Now imagine encountering a conclusion based partly on that specimen. You might want to know which version of the data was used, whether a later correction reached the analysis, or simply want to follow the references back far enough to establish how the finding came about.
The scientific result has a history, just as the tooth does. Keeping that history accessible is the problem of provenance.
What provenance means here
The word can sound rather formal. In practice, it begins with ordinary questions: where did this come from? What happened to it? Who made this change? Which later result depends upon it?
The BioChain is being developed as an evidence and provenance layer across existing systems. Its purpose is not to replace the repositories that store sequences, the platforms that perform analyses or the publications that explain findings — it is concerned with preserving the relationships between them, so that a result does not become detached from the records that give it meaning.
Think of the difference between receiving a photograph and being told the story of the photograph. You can see what is in the image, but knowing when it was taken, what happened outside the frame and whether it has been altered changes what you can reasonably say about it. Scientific records are more complicated, but the underlying question is familiar: what do we need to know about something before we can use it responsibly?
For ancient evidence, that question becomes especially important because the original material may be finite, sampling may be destructive, and the people studying the resulting data may be far removed from the specimen itself. The Ancient BioChain’s first phase uses ancient DNA to investigate how that surrounding history can remain connected to the research.
Why build a demonstration around the past?
A carefully invented demonstration can be wonderfully tidy. Every record can have the right name, every relationship can be documented, every expected result can appear exactly where it should. Real research is a more demanding test.
The Ancient BioChain was conceived as a public demonstration of The BioChain using existing scientific information, rather than a polished collection of fictional records. Its stated approach is to work with the inconsistencies and missing links found in real datasets, and it makes an important distinction: a documented connection, an inferred connection and a gap in the record should not be treated as though they were the same thing. That is part of what interests me about it.
Finding a missing link is not necessarily a disappointing result — it may tell us precisely where a reader needs to be more cautious, or where a researcher must return to the original source. Beginning with public records also places a boundary around what can be claimed: a later system cannot retroactively witness an excavation or a laboratory procedure, only work with the surviving documentation of those events. Where that documentation stops, a convincing-looking connection would be less useful than an honest gap.
The point of the demonstration is to learn from the evidence as it exists, rather than make the evidence look tidier than it is.
When the microbes enter the story
The planned second phase brings this work much closer to the subjects we explore at Ancient Epidemics. Ancient pathogen research asks questions about the organisms associated with disease in the past, and for The Ancient BioChain the proposed challenge is to connect the archaeological setting, the sample, the laboratory evidence, the checks used to establish authenticity, the computational analysis and the interpretation that follows. Phase 2 is a planned extension of the demonstrator, not a claim that a complete ancient-pathogen research platform has already been delivered.
The wider scientific field gives a sense of why that is worth exploring. In 2011, Kirsten Bos and colleagues published a reconstructed genome of Yersinia pestis from people who died during the Black Death in London, with the remains dated to 1348–1350, allowing researchers to compare genetic evidence from the medieval organism with that of later strains. This was not simply another account of what witnesses had seen — it was molecular evidence recovered from the people caught in the catastrophe. That research long predates The Ancient BioChain; it belongs here as an example of what the field can achieve, not as a discovery made by our project.
Consider what changes when evidence of that kind becomes available. A disease can move from being something described by frightened observers to something investigated through its genetic material, and the questions can become more specific. But the strength of the answer still depends upon how the material was identified, analysed and placed in context. The excitement of the discovery does not remove the need to follow its history. It makes that history more valuable.
The finding that needs another look
There is a less celebrated kind of scientific story that matters just as much: the promising identification that does not survive closer examination. In a study published in 2014, Michael G. Campana and colleagues investigated sixteenth-century remains from Teposcolula-Yucundaa, Mexico. Comparing the samples against surrounding soil and against pre-contact individuals from the same site showed how environmental organisms could confuse the analysis — without those controls, the researchers explained, their results could have been misread as evidence for plague bacteria or rickettsial disease.
It is a useful example precisely because it interrupts the satisfying story: a sample, an intriguing result, a familiar pathogen appearing to offer an explanation — then another comparison changes what the result means. The careful part is not the least interesting part. It is the part that keeps an apparent discovery from becoming a misleading one.
This is why Phase 2 is intended to look beyond a simple label saying that a pathogen was detected. The proposed evidence history includes authentication, contamination assessment, the reference material used for comparison and the processing that led to the eventual interpretation — records that would help someone understand why a finding was accepted, questioned or revised.
For a reader interested in the past, the practical question is straightforward: what would we need to see before accepting the story we are being told? A name in a results table may be the beginning of that enquiry, rather than its conclusion.
A record is not a verdict
There is an important limit to the whole undertaking: a faithfully preserved mistake is still a mistake. Knowing where a claim came from does not, by itself, establish that the claim is correct. An interpretation can be well documented and still turn out to be incomplete; a method can be recorded precisely and still be unsuitable for the question being asked.
The Ancient BioChain’s published description makes this distinction explicit. The objective of its future pathogen demonstrator is not to decide whether a scientific conclusion is true — it is to make the history behind that conclusion easier to inspect, reproduce and reassess. That is a more useful ambition than a promise of certainty.
For the historical questions that bring people to Ancient Epidemics, it means there should be room for answers of different strengths. There is a difference between observing a molecular signal, interpreting it as evidence of infection, and using it to explain the course of an epidemic — and the further the story travels, the more carefully we need to examine the steps that carried it there.
No digital infrastructure should turn a possibility into a settled diagnosis simply because a confident answer would make a better ending.
The people behind the data
There is another reason I find this work worth pursuing. It is remarkably easy to move from a person to a specimen, from a specimen to a record, and from a record to a point on a chart. Those changes make some kinds of research possible, but they can also change the way we think about the subject — a person whose life contained relationships, work, illness and uncertainty becomes an identifier that fits neatly into a table. For me, keeping track of context should help resist that flattening.
A record cannot restore a person’s name when it has been lost, nor can a genetic finding tell us everything about how they experienced an illness. But we can be careful about the distinction between what remains, what has been observed and what we have inferred — that care belongs in the storytelling as much as in the science.
Ancient Epidemics is not meant to become a catalogue of diagnoses. The human experience remains central: how people understood illness, whom they trusted, what they feared and how they cared for one another. The connection with The Ancient BioChain is a shared interest in making the route to a conclusion visible, rather than allowing the conclusion to stand alone.
A beginning, rather than a boundary
Ancient DNA is the starting point of The Ancient BioChain, not its entire scope. The published roadmap places ancient pathogens in Phase 2; beyond that, it describes an ambition to connect a wider range of ancient evidence, including human and animal DNA, environmental DNA, proteins, microbiomes and isotopic information, with a later phase concerned with reusable research infrastructure and institutional connections. These are future directions, not a catalogue of completed features.
What draws me to that direction is the possibility of asking a question without losing sight of the different kinds of evidence needed to approach it. A genetic result might illuminate one part of a historical problem, archaeology might supply another, and written testimony may preserve something neither can recover. Bringing them into conversation should not mean pretending that they all speak with the same voice. It should mean understanding what each contributes, and where its authority ends.
Following the next chapter
The Ancient BioChain has its own journal, Origins, which follows the project’s questions about ancient DNA, pathogens, scientific data and the history of evidence — a place to explore the work as it develops, alongside the broader demonstration. Here at Ancient Epidemics, we will approach the connection through the stories it opens up: what can a scientific finding add to an account written centuries ago? When does a new result change the way we understand an old epidemic? What should we do when the evidence supports something less certain — and perhaps more interesting — than the familiar explanation? Those are questions I want to keep following.
The appeal of ancient pathogens is not simply that traces of disease may remain long after an outbreak has passed. It is that investigating those traces can make us look again at lives and events we thought we understood.
But a new story deserves the same care as an old one. We should be able to ask where it came from.
Further Reading
The question underneath all of this — where does biological data actually come from, and what gets lost translating it into something usable — is also the subject of Noviota’s Biological Representation Is Not a Data-Formatting Problem.
References
- Bos, K.I. et al. (2011). “A draft genome of Yersinia pestis from victims of the Black Death.” Nature, 478, 506–510. Read the paper
- Campana, M.G. et al. (2014). “False positives complicate ancient pathogen identifications using high-throughput shotgun sequencing.” BMC Research Notes, 7, 111. Read the paper
Key Takeaways
- Ancient Epidemics is introducing a connection to The Ancient BioChain, a research initiative and public demonstration environment for The BioChain, focused on the provenance of scientific evidence rather than the underlying biology itself.
- Its first phase works with publicly available ancient DNA and archaeogenomic data; a planned second phase will extend the same evidence-history approach specifically to ancient pathogens.
- Two real studies show why that history matters: Bos et al. (2011) recovered a Yersinia pestis genome from Black Death victims in London, while Campana et al. (2014) showed that without environmental and archaeological controls, 16th-century Mexican remains could have been misread as evidence of plague or rickettsial disease.
- The project's stated aim is not to verify whether a scientific conclusion is true, but to make the evidence behind it — authentication, contamination checks, reference data, methodology — easier to inspect, reproduce and reassess.
- Ancient Epidemics itself is not becoming a diagnosis catalogue: the human experience of illness stays central, with the BioChain connection adding a complementary question alongside "what happened" — namely, "how do we know?"
Questions & Answers
What is The Ancient BioChain?
A research initiative and public demonstration environment for The BioChain, using publicly available ancient DNA and archaeogenomic data to show how the provenance of scientific evidence can be preserved and inspected.
How is The Ancient BioChain different from research that identifies ancient pathogens?
It doesn't aim to identify pathogens itself. Its planned Phase 2 aims to track the evidence trail behind such identifications — sample, lab methods, authentication checks, reference data — so a finding can be inspected and reassessed, not just cited.
What's an example of ancient pathogen research going right, and going wrong?
Bos et al. (2011) successfully reconstructed a Yersinia pestis genome from Black Death victims in London. By contrast, Campana et al. (2014) found that without comparing against soil and pre-contact remains, 16th-century Mexican samples could have been misread as evidence of plague or rickettsial disease — a caution about false positives, not a discovery.
Does documenting where evidence came from prove a scientific claim is correct?
No. A well-documented claim can still turn out to be wrong. Provenance makes a claim easier to inspect and reassess — it doesn't make it automatically true.
