DIY Jurrasic Park

[Andreas "Mega" Stuermer]

Good news, everyone, 

Checking back in with a crazy project. 

http://burmiteamberfossil.com/index.php?m=content&c=index&a=show&catid=103&id=109 

This site from time to time sells Burmite amber that contains feathers. They claim that the age of these amber pieces is 90 million years old, so it should be reasonable to assume it's dinosaur feathers. (anyone with access to a carbon dating device??)

I checked years ago, the prize was about 500$ but now it's 1500$ and 2000$ for each of two pieces. 

Now there has been a lot of controversy if any DNA can survive for such a long time. Despite the long half-life of DNA, which is said to be 500 years at room temperature dried, tens  of million years is quite something. There have been studies claiming that they found DNA in amber but then others finding none. I was told RNA is more stable chemically, and if the dehydration process had been fast, it may better survive? In any case, they did find residual peptides in some fossils.

Fact is, resins contain a plethora of chemical substances such as alcohols which in theory should sequester any water around the DNA very fast. (Feathers may be very dry to begin with, compared to tissue samples or insects.) This drop in active water should conserve biomolecules well and prevent hydrolysis or pH damage.

The workflow would be to put the amber in HCl to remove modern DNA contamination, cut away the top piece of resin and dissolve it in an organic solvent. The resin will melt. Add TE buffer, so there will be phase separation and DNA and RNA should dissolve in TE buffer. But how to either read or amplify all the possible DNA or RNA fragments? Even with nanopore we need to ligate adapters to it. Maybe our technology is still too immature? 

I would love to hear your two cents on the feasibility and if it makes sense. 

DISCLAIMER: Destroying a 70-90 million year old dinosaur feather without knowing what you are doing should be considered a historic crime ;) 

Alternative: 

Let's say, all DNA and RNA is gone, but there are chemical remnants embedded within the resin matrix... think of holes in a rock where once base-pairs had been, enriched with nitrogen atoms. Would you be able to detect them with the worlds most precise X-Ray 3D scanner and reconstruct DNA sequences? Obviously we are speaking borderline Sci-fi here and probably room temparature heat makes the molecules move too fast so they fill the gaps over the eons?

[Cathal Garvey]

I've wondered sometimes: just because the DNA is gone, does that necessarily mean that sequence information cannot be recovered from local fossil/resin chemical makeup and structure?

e.g., could you get a kind of ultra-low-fi "read" by identifying individual atoms of the resin and attributing higher-nitrogen regions to decayed purines, maybe then distinguishing these by presence or absence of oxygen?

This assumes a way to do single-atom resolution detection at the angstrom scale which is probably implausible even with destructive methods. AFM can do sub-nanometer but probably without distinguishing atoms by element.

As to the "crime against paleontology" bit, if you retain the detailed scans of the destroyed regions and make those available, I reckon you're adding to our knowledge rather than detracting from it.

--
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[Andreas "Mega" Stuermer]

Ok, amber with dinosaur feathers is pretty expensive. And the shop stopped selling them too. Btw, I learnt that liquid nitrogen may be a great method to free the feathers from the resin without dissolving it. There are lots of people who have done exactly that for museums (insects eg.). And then under modern conditions, the DNA degrades within hours or days, of course. 

They have found protein fragments in dinosaur bones, so we'll be using freshly excavated dinosaur bones. We can't use acid extraction because that degrades DNA. I am thinking of adding way too much EDTA so it will partly demineralize the bones, removing at least calcium. In a shaker and maybe broken into pieces so that there's less time for the DNA to degrade. At 1°C.  The whole thing will happen in 100x TE buffer. 

My impression has always been that fossils are very limited, but apparently there are millions, and they excavate them en masse and then sell them ( = the DNA degrades at room temperature and humidity). Hence I will just try it 

[Abizar Lakdawalla]

Hi Andreas, wondering if you have heard of the Dunning-Kruger effect?

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[Andreas "Mega" Stuermer]

You are saying the experiment is badly designed? 

On Sunday, June 9, 2019 at 10:39:22 PM UTC+2, Abizar Lakdawalla wrote:

Hi Andreas, wondering if you have heard of the Dunning-Kruger effect?

On Sun, Jun 9, 2019 at 1:03 PM Andreas "Mega" Stuermer <andreas....@gmail.com> wrote:

Ok, amber with dinosaur feathers is pretty expensive. And the shop stopped selling them too. Btw, I learnt that liquid nitrogen may be a great method to free the feathers from the resin without dissolving it. There are lots of people who have done exactly that for museums (insects eg.). And then under modern conditions, the DNA degrades within hours or days, of course. 

They have found protein fragments in dinosaur bones, so we'll be using freshly excavated dinosaur bones. We can't use acid extraction because that degrades DNA. I am thinking of adding way too much EDTA so it will partly demineralize the bones, removing at least calcium. In a shaker and maybe broken into pieces so that there's less time for the DNA to degrade. At 1°C.  The whole thing will happen in 100x TE buffer. 

My impression has always been that fossils are very limited, but apparently there are millions, and they excavate them en masse and then sell them ( = the DNA degrades at room temperature and humidity). Hence I will just try it 

On Monday, November 12, 2018 at 6:30:28 PM UTC+1, Andreas "Mega" Stuermer wrote:

Good news, everyone, 

Checking back in with a crazy project. 

http://burmiteamberfossil.com/index.php?m=content&c=index&a=show&catid=103&id=109 

This site from time to time sells Burmite amber that contains feathers. They claim that the age of these amber pieces is 90 million years old, so it should be reasonable to assume it's dinosaur feathers. (anyone with access to a carbon dating device??)

I checked years ago, the prize was about 500$ but now it's 1500$ and 2000$ for each of two pieces. 

Now there has been a lot of controversy if any DNA can survive for such a long time. Despite the long half-life of DNA, which is said to be 500 years at room temperature dried, tens  of million years is quite something. There have been studies claiming that they found DNA in amber but then others finding none. I was told RNA is more stable chemically, and if the dehydration process had been fast, it may better survive? In any case, they did find residual peptides in some fossils.

Fact is, resins contain a plethora of chemical substances such as alcohols which in theory should sequester any water around the DNA very fast. (Feathers may be very dry to begin with, compared to tissue samples or insects.) This drop in active water should conserve biomolecules well and prevent hydrolysis or pH damage.

The workflow would be to put the amber in HCl to remove modern DNA contamination, cut away the top piece of resin and dissolve it in an organic solvent. The resin will melt. Add TE buffer, so there will be phase separation and DNA and RNA should dissolve in TE buffer. But how to either read or amplify all the possible DNA or RNA fragments? Even with nanopore we need to ligate adapters to it. Maybe our technology is still too immature? 

I would love to hear your two cents on the feasibility and if it makes sense. 

DISCLAIMER: Destroying a 70-90 million year old dinosaur feather without knowing what you are doing should be considered a historic crime ;) 

Alternative: 

Let's say, all DNA and RNA is gone, but there are chemical remnants embedded within the resin matrix... think of holes in a rock where once base-pairs had been, enriched with nitrogen atoms. Would you be able to detect them with the worlds most precise X-Ray 3D scanner and reconstruct DNA sequences? Obviously we are speaking borderline Sci-fi here and probably room temparature heat makes the molecules move too fast so they fill the gaps over the eons?

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