- Options
- Login
- Desktop Style
Options
Biocodicology - A Deeper Dive
- Biocodicology - A Deeper Dive
-
RE: Biocodicology - A Deeper Dive
tavie > 07-01-2022, 03:03 PM
(07-01-2022, 01:24 PM)Mark Knowles Wrote: You are not allowed to view links. Register or Login to view.For me personally it would be useful as I have a hypothesis as to who the scribe(s) could be and I know where a DNA of one of them could probably be obtained from his skeleton
What is your hypothesis? -
RE: Biocodicology - A Deeper Dive
Mark Knowles > 07-01-2022, 03:12 PM
(07-01-2022, 01:58 PM)Koen G Wrote: You are not allowed to view links. Register or Login to view.It seems that everything builds upon a basis of our ability to date a DNA sample, right?
I addressed this in my previous two posts.
For me that is not really the key difficulty. For me the key difficulty is how much DNA did the scribe leave behind and how degraded that DNA is 600 years later. If the scribe left lots of DNA on the manuscript and it hasn't degraded a lot then obtaining a sample of scriba DNA should not be so difficult I would guess.
I don't know how one would estimate how much DNA the scribe left on the manuscript and I don't how degraded 600 year old "Touch DNA" would be today. I am not yet completely sure also where the best places to look to take a sample of the scribe's DNA from. (Is there anywhere where the scribe might have left his saliva, hair or even blood in the manuscript? As this would be a gold mine for DNA I would have thought.) -
RE: Biocodicology - A Deeper Dive
Mark Knowles > 07-01-2022, 03:16 PM
(07-01-2022, 03:03 PM)tavie Wrote: You are not allowed to view links. Register or Login to view.What is your hypothesis?
That I am not yet making public, though I hope in the next couple of months to do so. At the moment I am waiting for photoreproductions of enciphered letters in the Florence State Archives. -
RE: Biocodicology - A Deeper Dive
Bernd > 07-01-2022, 11:17 PM
You cannot reliably 'date' DNA by degradation, at least not without knowing what amount of DNA was present in the beginning and what conditions it was subjected to. The main killer of ancient DNA is a warm, moist acidic environment which leads to depurination. On a surface you are also dealing with a horde of microorganisms secreting nucleases which shred DNA.
You are not allowed to view links. Register or Login to view.
The conditions the VM has encountered in the past 600 years are unknown (temperature, humidity, exposure to sunlight) and may even vary between different bifolios. Local chemistry (mainly pH) of the vellum likely also plays an important role in binding/preserving DNA from spot to spot. This needs to be tested out, no idea what's the state of science here and if human DNA can be successfully sequenced from vellum of that age at all. That's a completely different beast than bones from a cave or saliva protected under a less than 100 year old stamp.
Also merely extracting DNA from the vellum surface will yield myriads of tiny fragments of a multitude of people that have handled the VM, most of them likely fairly recently. It is a tremendous to impossible task to sort and reconstruct larger DNA sequences from this mess and the dangers of creating an artificial chimera are high. While it is possible to exclude DNA sequences generated from large intact fragments and thus likely of modern origin, degradation does not necessarily correlate with age but rather with amount of DNA and local conditions. Even DNA contamination during sampling may produce some small fragments indistinguishable from ancient DNA. This has happened before in anthropology and led to great embarrassment.
As I already said, if we have single author who spent his life on the VM there would likely be a lot of DNA from that person. By sheer amount the chance of getting something readable increases. At least a little bit.
By the way, did scribes touch the parchment with their palm during writing or was this avoided? This would leave a lot more DNA that the average reader. I'd stay away from corners for this very reason if you are interested in the author(s). The ideal sampling spot on a bifolio would be where the scribe touches the surface for a prolonged time while a reader is unlikely to do so. -
RE: Biocodicology - A Deeper Dive
Mark Knowles > 08-01-2022, 03:05 PM
(07-01-2022, 11:17 PM)Bernd Wrote: You are not allowed to view links. Register or Login to view.As I already said, if we have single author who spent his life on the VM there would likely be a lot of DNA from that person. By sheer amount the chance of getting something readable increases. At least a little bit.
By the way, did scribes touch the parchment with their palm during writing or was this avoided? This would leave a lot more DNA that the average reader. I'd stay away from corners for this very reason if you are interested in the author(s). The ideal sampling spot on a bifolio would be where the scribe touches the surface for a prolonged time while a reader is unlikely to do so.
I absolutely agree with you that the key is selecting where in the manuscript to take the samples from. This should be places where the scribe left as much DNA as possible and where other later readers would have left little or no DNA and where the DNA would have been best preserved. Hopefully this should result in samples with a significant amount of intact scribal DNA for sequencing and little or no other DNA. Selecting these "sites" where very small samples such that they don't damage the manuscript would be taken from would require real thought and careful inspection of the digitised scans of the Voynich manuscript to identify the best spots.
What do you think about DNA in the ink? Is it more likely to be preserved or destroyed there relative to on the parchment? It would seem to me that such DNA would be deposited before the ink is dry and so will exclude DNA from a later period. -
RE: Biocodicology - A Deeper Dive
pfeaster > 08-01-2022, 05:04 PM
(07-01-2022, 02:41 PM)Mark Knowles Wrote: You are not allowed to view links. Register or Login to view.1) I would suggest taking/looking for a location in the manuscript to take a sample(s) from where only the scribe left his/her DNA.
I remember once spotting a strand of hair stuck to the page of an early modern printed book -- maybe seventeenth century -- by the ink in such a way that it had clearly acted as a mask during printing between the type and the paper. My thought at the time was that the hair probably belonged to the printer or someone close to him and had probably been newly shed in the year the book was printed. Even if not, though, it must have been present specifically at the moment of printing to have interacted with the ink as it did.
I don't suppose that specific scenario would have arisen with the VM. But is this a reasonable example of the *category* of evidence you're hoping to find here? -
RE: Biocodicology - A Deeper Dive
Koen G > 08-01-2022, 08:45 PM
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. -
RE: Biocodicology - A Deeper Dive
Bernd > 08-01-2022, 08:51 PM
Finding a hair or eyelash stuck in ink or paint would be ideal but I'd guess a diligent scribe would have removed such immediately. The scans of the VM are quite good and something like this should be visible.
(08-01-2022, 03:05 PM)Mark Knowles Wrote: You are not allowed to view links. Register or Login to view.What do you think about DNA in the ink? Is it more likely to be preserved or destroyed there relative to on the parchment? It would seem to me that such DNA would be deposited before the ink is dry and so will exclude DNA from a later period
The idea of looking under paint is good but I don't think it's feasible due to its destructive approach.
I'm not familiar with the exact composition of the ink used in the VM but iron gall ink is among the worst storage agents for DNA I can think of. It's acidic which alone promotes hydrolyzation and depurination and tannic acid acts as a powerful DNA killer in combination with Cu(II) by creating reactive oxygen species. It can also crosslink and intercalate DNA making it unreadable and ultimately tannins are also known to inhibit PCR. I'd say the ink is even worse for DNA sequencing than boggy soil.
You are not allowed to view links. Register or Login to view.
Apart from that, even if we stick to less harsh paint instead of ink, we would likely need to scrape off a considerable amount to get even a trace of human DNA, thus causing considerable damage to the VM.
But all of this is for the real biocodicologists to test out on expendable manuscripts, surely would make several good PhD theses. -
RE: Biocodicology - A Deeper Dive
MichelleL11 > 08-01-2022, 09:29 PM
The next paper we're going to review is going back to, in my view, a relatively practical use of biocodicology for the Voynich -- the possibility of determining where the cows that were used to make the parchment came from. That's not to say these less practical goals are not useful to talk about -- but I'm going to examine more in depth approaches that have in my opinion the best likelihood to provide immediately useful data: namely matching the DNA characteristics of the source animals for the parchment to a geographic database.
Here is the full cite of the paper:
The York Gospels: a 1000-year biological palimpsest
Matthew D. Teasdale , Sarah Fiddyment , Jiří Vnouček , Valeria Mattiangeli , Camilla Speller , Annelise Binois , Martin Carver , Catherine Dand , Timothy P. Newfield , Christopher C. Webb , Daniel G. Bradley and Matthew J. Collins
R. Soc. open sci.4170988170988; You are not allowed to view links. Register or Login to view. (October, 2017).
The full paper is available You are not allowed to view links. Register or Login to view..
Some important aspects of this paper from the point of view of the Voynich are:
i) What is being analyzed? The York Gospels, a 1000 year old manuscript (You are not allowed to view links. Register or Login to view.) - so significantly older than the VM, based on the carbon dating
ii) How are the samples being collected? Non-invasive PVC eraser crumbs. Enough for ZooMS for all folios, enough for DNA sequencing for eight.
iii) What techniques were performed? ZooMS on almost all folios, next generation DNA sequencing from the eraser crumbs on eight folios, DNA damage analysis on those same eight folios, and SNP analysis of three folios
I'm not going to go over all the experiments at a close level, as they are generally applications of techniques we've seen before. But here are some unique conclusions that should be kept in mind related to DNA quality that could be attributed to the eraser crumb sampling technique:
1. On average, about 19% of the DNA results aligned with a genome from a "source species" of the parchment - however the range for the eight folios were from .7% to 51.4%. They examined the 51.4% results more carefully and when quality standards (e.g. reads that can be mapped with high confidence) were applied to the reads, this fell to 5.6%, much more loss than expected. Such an amount of reduction in "quality reads" could be due to a) selective preservation of DNA type during parchment production (thus, this issue is still possible) or b) selective sampling due to the eraser crumbs approach.
Background info needed
Note that DNA is present in the cell wrapped around packaging proteins called histones. You are not allowed to view links. Register or Login to view. is more information about how histones work and a cartoon.
When the DNA is being used to produce protein, the association with histones necessarily is reduced (in fact, this process is thought to be part of the regulation of protein production). The authors of this paper hypothesize that when producing the parchment, those DNA sequences that are not associated with histones (called euchromatin) may be selectively destructed compared to that which is associated with histones (called heterochromatin). Unfortunately, it is euchromatin sequences (e.g. those being used to produce protein) that provide the most likely ability to distinguish between one species and another. Using proxy sequences, the difference in coverage for folio 125 was figured and the greater coverage for heterochromatin supports this hypothesis, see Supp. Figure 2, below.
However, as a practical note, there was enough data to make a positive identification of the species for all the folios (except for those that had undergone a destructive conservation process, covering the folios with silk gauze) between the ZooMS results with confirmation by the DNA results for the eight folios tested (see, Figure 1).
Note that because destructive sampling could not be done, the possibility that the selective bias toward repetitive (histone associated) DNA sequences was due to the sampling technique could not be eliminated.
2. But on the positive side, from a DNA end deanimation point of view (a chemical sign of ancient DNA degradation), parchment appears to be a better conservation environment than inside bones as less of this type of damage was seen as compared to what would be expected for DNA of the same age isolated from bone. Interestingly, the human DNA isolated (see discussion below) had less DNA damage than the "source species" DNA isolated, lending further support to the "parchment production is damaging" hypothesis (but it also could be just newer date).
3. Of the eight folios where DNA sequencing was done, three of these had sufficient results to undergo SNP analysis, through to a modern database of cow sequences. Figures from the You are not allowed to view links. Register or Login to view. of the paper are reproduced below.
Here's the world wide association (DNA from the three folios are the triangle, circle, and square) showing general association with European cow genus (Taurus).
Here's a close in view of the European mappings -- colors are geography and the three letter data points are keyed to breed names -- (ANG=Angus, BLO=Blonde d'Aquitaine, BSW=Brown Swiss, CHL=Charolais, GNS=Guernsey, HOL=Holstein, JER=Jersey, LMS=Limousin, MON=Montbeliarde, NOR=Normande, NRC=Norwegian Red Cattle, PMT=Piedmontese, RGU=Red Angus, RMG=Romagnola, SIM=Simmental).
So -- none of the three hit exactly on any modern cow species -- but that wouldn't really be expected, given the 1000 year time span for evolution and the intense amount of cow breeding that has occurred in that time. But it definitely shades toward the known geographic location of Northwest Europe.
Just a quick side note that this kind of data that doesn't overlap with anything exactly is a bit reminiscent of the various Voynich text comparisons to all the world wide languages -- but that could just be the frustrating experiences talking.
4. A couple of quick conclusions for those whose biggest interest is in human sequences: an average of 11% (range of 4.2%-20.8%) of the aligned sequences were human and this was about twice the amount of human DNA as archived legal documents sampled in the same way. Note that applying quality standards to one set of the best of the human reads dropped the percent from 19% to 16% (much less of a drop than above for the source species reads) which is more support for the "parchment process degrades DNA" issue. Also, more human DNA was found on pages where "oaths" that were periodically administered were found -- supporting that the more often a page was referenced, the more human DNA was found (even when that use has been long in the past).
TLDR: The potential destructive processes of parchment production looms yet one more time as it is clear that next gen DNA sequencing alone likely isn't going to fix that issue completely. However, a non-destructive sampling technique was able to sometimes get enough DNA to do a SNP analysis -- but much more comparative data is likely needed for true geographic pinpointing. Other dated, known geographical historic parchment is probably the most relevant source for such comparative DNA sequences.
I believe it is now clearer what kind of additional data would be needed in order to get a much higher chance of meaningful results for the VM. We need DNA results from as many as possible manuscripts from around the carbon dating where it is known what geography the manuscripts were produced. I know that this is a tall ask -- as my impression of manuscripts from the early 1400s is that precise information is often lacking. But it might take less information than presently thought, if there are clear differences in the cow species of that time period -- which is definitely possible.
A piece of hope is the observed phenomenon of "population isolates" in DNA sequences. This is where isolated populations have evolved very specific patterns that are not found elsewhere. You are not allowed to view links. Register or Login to view. is a paper discussing this phenomenon in relation to human populations and the Basque, which unfortunately contradicts that such population isolates even exist -- but things may be different for cows. Thus, it is possible that if a precise match could be found that is a best possible outcome (low probability, but still) -- but such a result will definitely not be known until it is tried. Along with more data, we need a bit of luck . . . -
RE: Biocodicology - A Deeper Dive
Bernd > 08-01-2022, 11:22 PM
Thanks, this is indeed fascinating!
(08-01-2022, 09:29 PM)MichelleL11 Wrote: You are not allowed to view links. Register or Login to view.from a DNA end deanimation point of view (a chemical sign of ancient DNA degradation), parchment appears to be a better conservation environment than inside bones as less of this type of damage was seen as compared to what would be expected for DNA of the same age isolated from bone.
I would not have expected this if we consider DNA is usually sampled from deep within bones which had been in the ground at a low temperature. Still depends a lot on soil chemistry. Anything from an acidic bog usually has very poor DNA preservation - if bones are preserved at all - compared to a dry cold limestone cave.
But it may well be that the tanning process of parchment is a double edged sword. Surely a lot of DNA is destroyed in the process, but a portion is likely stabilized by tannic acid which is known to tightly bind to DNA. Still unexpectedly good results considering only the very surface of the parchment was sampled where we would expect maximal damage due to exposure to the environment and DNAses from microorganisms.
Regarding population isolates, I think this is a matter of trade routes. In regions without frequent long distance livestock trade such as an alpine valley, one would expect more isolated populations than in a busy trade hub like a big town along an important road which frequently imports animals.
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.