(08-01-2022, 11:22 PM)Bernd Wrote: You are not allowed to view links. Register or Login to view.My question - assuming DNA fragments from multiple humans are isolated, what are the current limits of sorting and using them for SNP analysis? Has this been tested? Next Gen Sequencing already is extremely challenging for microorganisms in environmental samples but at least these are highly dissimilar compared to humans.
Hi, Bernd:
I think this question has more in common with forensic analysis than biocodicology at this point. Thus, l would start with this very recent review about DNA mixture analysis:
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I did find software-based detection that differentiated contaminating modern DNA from “ancient DNA” based on amount of degradation- but in that publication they were talking about human ancestor species vs modern - so 10,000s of years. I didn’t get the impression that it was sensitive enough to see a 600 year gap - or would ever be able to tell as enough differences may not exist as to that particular change (the same deanimation process discussed in the York Gospels article).
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But something may be developed in the future on some kind of differentiation basis other than primary sequence (e.g. SNPs).
Excellent, the NIST paper is exactly what I was looking for.
The field of forensics is a powerful ally because it is well staffed and funded for obvious reasons.
We clearly see the limitations and pitfalls of analyzing complex DNA mixtures here and considering the DNA on the VM is additionally highly degraded, from an unknown number of unknown people without reference sequences and contaminated by microorganisms, deconvoluting this haystack is not going to be an easy task, even with advanced models like probabilistic genotyping. Yet I'm more optimistic now than before, with enough sampling material (and funding) it should very much be possible to get useful data from both humans and especially the animals used for vellum.
It would be interesting to conduct a test experiment tailored to our needs - eg create a complex mixture of DNA from 10 known people in concentrations expected to find on a manuscript, artificially degrade it to the expected level and then see if these 10 profiles can be resolved by NextGen sequencing and if we get accurate, less or even more reads by artifacts. As the NIST paper states most mixture interpretation was only done with a large amount of fresh DNA from 2 to max 5 persons and does not necessarily reflect the conditions of (semi)ancient DNA, thus greatly reducing the realiability of these forensic models.
I think the idea of sequence the DNA from the vellum as Michelle has already so expertly described is an excellent idea and if possible should certainly be done. However the one advantage that I can see from sequencing human DNA from the manuscript is that large databases of human DNA already exist and do not need to be created unlike the situation with the vellum. So whilst it seems likely that there will be significant difficulties with sequencing human DNA from the manuscript compares to sequencing the DNA from the vellum it has at least this one advantage.
I personally think all tests that do not significantly harm the manuscript should be done once the technology makes it possible. So this includes DNA from the vellum, human DNA and DNA from the ink
as You are not allowed to view links. Register or Login to view. has suggested.
(08-01-2022, 08:45 PM)Koen G Wrote: You are not allowed to view links. Register or Login to view.None of this will work if the DNA cannot be dated accurately down to one or two decades, which most likely is not possible. Without such accuracy, I think it would be better to not have the information at all. It would just turn into yet another Rorschach test for everyone to interpret as they like.
I think that this last point would mainly be a problem inside the various Voynich fora. The occasional misplaced media hype would be stopped quickly enough.
(08-01-2022, 08:45 PM)Koen G Wrote: You are not allowed to view links. Register or Login to view.I think it would be better to not have the information at all.
The more information we have about the Voynich manuscript the better, I think. The fact that some people might misinterpret that information and draw erroneous conclusions is not a problem with having the information, but is a problem with the person who misinterpreted that information.
(10-01-2022, 12:49 PM)Mark Knowles Wrote: You are not allowed to view links. Register or Login to view.The more information we have about the Voynich manuscript the better, I think. The fact that some people might misinterpret that information and draw erroneous conclusions is not a problem with having the information, but is a problem with the person who misinterpreted that information.
My point is that if the recovered DNA cannot be dated, the information it provides is irrelevant. On the other hand, the new strains of theorists' speculations we would have to deal with might be significant.
I would have thought it might be possible to roughly date human DNA on the basis of comparison with the DNA of living people. For example if DNA is 300 years old you won't find anyone alive who is a very close relative of that person unless that person comes from a very isolated inbred community. A parent or a sibling will have a lot of DNA in common with an individual. So the more closely related the person is to some small number of people alive today the newer the DNA. So I wonder if on that basis there is some kind of mechanism for estimating roughly how many generations back the DNA goes and thereby roughly dating it. I also believe that some times marker genes can be used to date human DNA. I am not expert in this area, as I have said before, but those are my thoughts.
If the DNA is located somewhere where the scribe is much more likely to have left DNA than someone else then that greatly increases the likelihood that it is scribal DNA.
In theory you are correct but keep in mind that at least in Europe we are fortunate to have something called data protection laws. Luckily we are not yet at the point where we have publicly available DNA profiles of the majority of the population.
But of course this may be used to exclude some sequences, especially if they are modern contamination form US citizens. You'd still have a very high chance of false negatives that are relatively modern even without any close database matches.
As with the vellum it might be useful to create a reference database from late medieval graveyards in different places of middle Europe.
Another approach would be excluding sequences by outstanding quality without expected degradation as Michelle has shown, or looking at DNA quantity across the entire VM assuming a scribe would leave a different amount of DNA in certain places than a reader.
In any case the results are likely to remain highly speculative compared to animal DNA from vellum.
(10-01-2022, 03:17 PM)Mark Knowles Wrote: You are not allowed to view links. Register or Login to view.I would have thought it might be possible to roughly date human DNA on the basis of comparison with the DNA of living people.
Hi, Mark:
I did find a paper where they were able to date the entry of particular SNPs into the human genome (also discussed as "allele age"). This is super high level (population) work and the dating is related to hundreds or even thousands (rather than 10s) of generations. I believe the shortest time frame discussed is 858 generations -- so about 22,000 years.
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Interestingly, it did allow for identification of the date of a likely common ancestor for a pair of different individuals (see results in You are not allowed to view links.
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Login to view.) which could maybe be adapted into buckets that could distinguishing between various individuals in a mix -- but I am not certain the values would be great enough difference to be able to categorize "old" from "new" when we've only got a 600 years of difference to work with (especially if those individuals aren't all that different genetically from a long term point of view). Adding this kind of analysis on top of the basic issue of distinguishing reads from one individual from reads coming from another individual makes this really, really challenging.
But as you know this is really speculative and may be possible in the future -- I hope you get at a general level why this isn't practical at this point. But this kind of work could form the basis for such a distinguishing if it were possible in the future.
On the subject of dating DNA I found the following:
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