Biocodicology - A Deeper Dive

[MichelleL11]

The reading for today discusses the use of the "next" next generation sequencing (NGS) -- sometimes this is called "third" generation and sometimes its called "fourth" generation sequencing -- depending on how many "technology generations" the authors recognize.

The technique is nanopore sequencing, and a very high level summary of how it compares to "Illumina" sequencing (generally categorized as a type of NGS) is available You are not allowed to view links. Register or Login to view..

I haven't posted a whole series of articles in this sub-area, because in my view I think this has less of a chance of being applicable to the Voynich Manuscript (VM) -- but I could be wrong (see speculation below).  Plus, knowing about all the technologies available and their pros and cons is helpful.

A good overview to this technique as it applies to historical document analysis is You are not allowed to view links. Register or Login to view. by Sterflinger and Piñar (2021).

They have used nanopore technology in a series of publications that are summarized in this book chapter.

Importantly, the focus is on building data for all DNA present in the manuscripts/artifacts.  

This means not only source species for parchment and human DNA from handling but DNA from all the organisms/microorganisms present -- which are a lot.  This has immediate implications for conservation and the Piñar lab made its name in 2015 You are not allowed to view links. Register or Login to view. of a common conservation issue -- microorganism communities that result in purple spots on the pages -- and this lab is currently using nanopore technology on these kinds of analyses.

At a high level, nanopore sequencing technology involves running the unwound DNA sequence fragments through a very, very small hole and identifying the bases by the change in charge.

   

Because this technique does not involve amplification but just sequences what is available, it does remove "bias" that is induced by the polymerase chain reaction (PCR) aspects of particularly Sanger (first gen) sequencing, but also NGS -- which involves some PCR amplification during the library formation.

The lack of PCR does mean that sequence integrity is more important, so for old DNA, that can be an issue.  However, software can help to "bridge the gap" between both (1) degraded DNA and (2) the inherently greater amount of errors in the nanopore system.  Of course, all software needs reference sequences to be useful, so it is an ongoing process in areas where less reference sequence is available.

As of today, it remains that these sources of error makes this approach less ideal for single nucleotide variation analysis (e.g. comparing single nucleotide polymorphisms (SNPs)) which is likely to be important for the VM (but that error rate is likely to change over time).

As summarized in the book chapter, Piñar's lab has utilized this "whole microorganism community" approach to try to solve mysteries about artifacts -- such as the identification of a micro-organism that is from Taiwan (plus a bunch of soil organisms) growing on a statue head that had been stolen and its whereabouts while it was missing is unknown.  Does this mean the statue was buried in Taiwan during its missing time?  Maybe.

But this kind of stuff is pretty speculative, in my view.  Trying to apply this to the VM, would a whole micro-organism community analysis reveal anything other than a "Yale Library Rare Book Room" signature community?  Or even, "the shelf that holds Beinecke MS 408" signature community?  Or probably more likely, "the shelf in the Jesuit library that held the Voynich Manuscript before it was bought by Voynich" signature community?    
Who knows?  

But depending on how the investigation was structured and what other manuscripts were tested as comparators/controls, maybe more of the story could be figured out with this information.