Information physics and theoretical limits of extremely old DNA?

[Bryan Bishop]

I've been wondering about ancient DNA.

There is at least one claim from the panspermia folks that says, among other things, that DNA and microbes can travel on asteroids for millions of years. But at the same time, nobody has figured out a reliable PCR protocol for extracting DNA from million-year-old bugs trapped in ambers. We've successfully extracted DNA from "recently" deceased hominids and other creatures- say, those that have been living within 50 kya.

"Assuming physiological salt concentrations, neutral pH and a temperature of 15 C, it would take about 100k years for hydrolytic damage to destroy all DNA that could be reasonably retrieved (Hoxreiter et al., 2001)."

via: http://email.eva.mpg.de/~paabo/pdf1/HofreiterAncDNA_NatRev2001.pdf

which primary cites "Instability and decay of the primary structure of DNA" (too old to find a copy?).

Meanwhile.. the panspermia claim is over here from Wikipedia: "Studies of bacteria frozen in Antarctic glaciers have shown that DNA has a half-life of 1.1 million years under such conditions, suggesting that while life may have potentially moved around within the Solar System it is unlikely that it could have arrived from an interstellar source. [68]"

http://ur.rutgers.edu/medrel/viewArticle.html?ArticleID=5898

... ha, a "half-life". Anyway, their reference doesn't exist anymore, so if anyone knows the actual study in question, I'd like to know about it too.

I haven't seen any particular study about million year old DNA molecules. Gamma photons will probably screw it up over time, and the salt concentration has to play a role somewhat. But I would expect something like a theoretical study about the possible ways that DNA could be stored reliably, and then seek out fossilized or ancient DNA by looking for similar conditions. I am not convinced that "drill into amber, insert some buffer mix into a fly carcass, PCR the mix" is a reliable strategy for extracting old DNA. The DNA could be found first through some physical technique, like scanning probes or something.

Does anyone have some better documents I could look over?

- Bryan
http://heybryan.org/
1 512 203 0507

[Avery louie]

Svante Pääbo had something to say about it at the GET conference.

you could check and see if that video is up.  It was a good talk!

--A

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[Nathan McCorkle]

On Mon, May 14, 2012 at 9:59 AM, Bryan Bishop <kan...@gmail.com> wrote:

> I've been wondering about ancient DNA.
>
> There is at least one claim from the panspermia folks that says, among other
> things, that DNA and microbes can travel on asteroids for millions of years.
> But at the same time, nobody has figured out a reliable PCR protocol for
> extracting DNA from million-year-old bugs trapped in ambers. We've
> successfully extracted DNA from "recently" deceased hominids and other
> creatures- say, those that have been living within 50 kya.
>
> "Assuming physiological salt concentrations, neutral pH and a temperature of
> 15 C, it would take about 100k years for hydrolytic damage to destroy all
> DNA that could be reasonably retrieved (Hoxreiter et al., 2001)."
> via: http://email.eva.mpg.de/~paabo/pdf1/HofreiterAncDNA_NatRev2001.pdf
> which primary cites "Instability and decay of the primary structure of DNA"
> (too old to find a copy?).

Original paper is here:
http://www.nature.com/nature/journal/v362/n6422/pdf/362709a0.pdf

and here's a copy
http://diyhpl.us/~nmz787/instability%20and%20decay%20of%20the%20primary%20structure%20of%20DNA.pdf


--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

[rwst]

I remember reading many years ago about the physical effects that
even at absolute zero persist, where you would think nothing more will
happen. This would have made long-term cryopreservation impossible
due to virtual particle production by quantum tunneling, slowly eroding
every structure. However, I cannot find this atm.

Regarding panspermia, wouldn't it suffice to have *some DNA instead
of an exact copy? Maybe also big numbers would make a difference?

[Patrik D'haeseleer]

I think this is the Rutgers paper on DNA from Antarctic microbes:

http://dblab.rutgers.edu/genome_cooperative/publications/Bidle2007_PNAS_AntarcticIce.pdf

"Analyses of five ice samples, spanning the last 8 million years in this region, demonstrated an exponential decline in the average community DNA size with a half-life of !1.1 million years, thereby constraining the geological preservation ofmicrobes in icy environments and the possible exchange of genetic material to the oceans."

[Jordan Miller]

solvents, especially water, are the biggest enemy for long term storage. we think of water as inert but it has many chemical properties and effects that are still only beginning to be understood.

amber is technically quite wet (it's a resin, not a rock). egyptian mummies, on the other hand, have been demonstrated to be extremely well preserved because the storage conditions were soooo dry.

I suspect dessicated organic material protected from radiation would last the longest possible.

many microbes take this very approach, encasing themselves in solid spores that can survive extreme dry and vacuum.

if I were sending organic material through space, that'd be the way i'd do it (probably inside a rocky asteroid to protect from radiation).

but DNA likely wouldn't be enough to send. you need organic reagents and assorted organic "machinery" to process and understand it on arrival...

jordan

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[Zebedee Boy]

Thanks to another Svante (Arrhenius in this instance) the relative reaction rate for the hydrolysis reactions away from the effects of direct sunlight in space (T approx -270oC) is going to be many orders of magnitude lower. At 100k years you would only need it to drop by 16 fold to get the to same age as the universe (don't ask me to calculate it though :-).
 
Does leave the little problem of where life came from in the first place...
 
Either way the first DNA sequencer on Mars might hopefully give an answer as to whether the theory is possible.
 
Re ancient DNA I wonder whether anyone has looked in crude oil for non-bacterial DNA/protein sequences. I know you can find things like porphryin in there but I guess it might be too non-polar for DNA, you might find some lipophilic pepdites though.
 
Zeb
 

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Date: Mon, 14 May 2012 10:36:31 -0400
Subject: Re: [DIYbio] Information physics and theoretical limits of extremely old DNA?
From: inact...@gmail.com
To: diy...@googlegroups.com

[Cathal Garvey]

> Does leave the little problem of where life
> came from in the first place...

No it doesn't. We have great experiments going back decades showing how
easy it is for complex chemistry to emerge from early earth conditions,
and from there chaos theory takes over; self-replicating patterns will
emerge and, by their very nature, self-perpetuate until they dominate
chemistry in the environment.

Next thing you know, the pool of available randomness to convert runs
out; suddenly your self-perpetuating patterns are eating one another,
and evolution begins. Somewhere from here, you get what we might define
as life, but it's a very fuzzy boundary.

Early (and present) Earth has all you need; steep energy gradients, lots
of tasty elemental and molecular precursors, and enough solvent to make
it all happen in the same container.

While exobiologists love the idea of life being seeded from a
space-missile, there's really no need for an asteroid/comet/other to
explain life on earth. We already know how it can happen without space
missiles, and it's more than plausible.

> Re ancient DNA I wonder whether anyone has looked in crude
> oil for non-bacterial DNA/protein sequences. I know you can find
> things like porphryin in there but I guess it might be too non-polar
> for DNA, you might find some lipophilic pepdites though.

Oil and other fossil fuels aren't old enough for "early life" fossils,
AFAIK. But you'll find plenty of non-bacterial DNA there; archaea, at
the very least!

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[Zebedee Boy]

I was sort of replying to the premise of the first poster that "DNA and microbes can travel on asteroids for millions of years." In this situation if the DNA/microbe is to be stable enough to survive in an information viable form for long enough to drift between stars then it would probably be too cold to go through the vast numbers of reactions required for exogenesis. I would concede that a comet cycling round its star every 100 years for a billion years might possibly provide a suitable reaction vessel, but then this isn't really panspermia as it would be localised to a rather small corner of the Universe.
 
I'm quite happy with the contents of the Sigma catalogue raining down from space as a kick start for the generation of life on earth though. But from there to self-perpetuating life forms seems to be really mostly theory at the moment.
 
Zeb
 

> Date: Tue, 22 May 2012 16:25:07 +0100
> From: cathal...@gmail.com
> To: diy...@googlegroups.com

> Subject: Re: [DIYbio] Information physics and theoretical limits of extremely old DNA?
>
>