Dna Has A Half-Life Of 521 Years

[Kosmoceras]

DNA has a half-life of 521 years, this means the idea of a Jurassic Park could never happen. http://www.nature.co...lf-life-1.11555

Edited October 10, 2012 by Kosmoceras

[Scylla]

I think that Auspex will have apoplexy when he sees the illustration of what they did to Moa bones!

[AgrilusHunter]

A good threshold for useable DNA is usually cited at 10,000 years. This paper extends that threshold to 1.5 million years, and with the newest de novo genome assembly software this may be possible, even with highly fragmented DNA. However, once the average sequence length drops below 40-50 nucleotides it becomes very difficult to reassemble any meaningful data. For me this study validates paleontology's place within the modern sciences, no other branch of science had yet succeeded in empirically estimating this half-life, and its a tribute to the power of collaboration between those sciences.

Look at me still talking when there's science to do.

[THobern]

The article should have been clearer when it used the term "half life". It doesn't make any sense in the context unless you clarify the fundamental unit of DNA that they're measuring, and what degree of break down constitutes decay. Is it a cell's entire genome; or is it chromosome, which would suggest that even after 150my, an intact chromosome could still be recovered from a initial volume of 2^300,000 strands. Does decay mean a single break in the chain, which might allow for a genome to still be pieced together, or complete molecular break-down?

Going to the actual paper is less exciting, as they are dealing with 242bp sequences. Which is a shame as, for all they offer, birds are sub-par dinosaurs.

[AgrilusHunter]

The article should have been clearer when it used the term "half life". It doesn't make any sense in the context unless you clarify the fundamental unit of DNA that they're measuring, and what degree of break down constitutes decay. Is it a cell's entire genome; or is it chromosome, which would suggest that even after 150my, an intact chromosome could still be recovered from a initial volume of 2^300,000 strands. Does decay mean a single break in the chain, which might allow for a genome to still be pieced together, or complete molecular break-down?

"The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 × 10^–6 per year"

Taken directly from the abstract of the paper. This is not a new hypothesis, they have simply confirmed previous hypotheses empirically, they state as much in the paper. Basically they confirm an exponential decay relationship between fragmentation events and time, nothing to fancy beyond that. The finding is for a given length of DNA over time. It doesn't matter if it is a chromosome, or the whole genome, or just one gene. All that matter is the length of that sequence and time. That is the idea anyway. Now, it is true that they only test one part of the mitochondrial genome, other sections of the circular chromosome may decay at different rates, though that is highly unlikely.

Perhaps the more important finding than the rate of decay for the mtDNA sequence was they found the rate of decay in the nuclear genome to be at least twice as fast. This too fits with previous hypotheses since the mitochondrial genome, for the organisms we are discussing, is a circular covalently closed strand and is thought to be more stable than larger nuclear chromosomes.

Thobern, I like a good debate and appreciate when I can have a detailed conversation about an issue like this with someone, thank you. Hmmm ... I'm wondering how much interest there would be in a Fossil Forum journal club? There are many good palaeontology journals out there to sustain a group here on The Forum. Heck some of members here even publish in them! Any takers?

Edited October 11, 2012 by AgrilusHunter

[ashcraft]

Hmmm ... I'm wondering how much interest there would be in a Fossil Forum journal club? There are many good palaeontology journals out there to sustain a group here on The Forum. Heck some of members here even publish in them! Any takers?

I am always up for a good discussion, and I have the added plus that I really don't need to know what I am talking about.

Seriously though, the biggest problem I had with the paper is that one particular type of DNA from one particular preservation scenario. It may prove that all DNA behaves in a similar fashion in all situations, but they seem to jumping the gun a bit. Further testing will tell.

Brent Ashcraft

[THobern]

"The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 × 10^–6 per year"

Taken directly from the abstract of the paper. This is not a new hypothesis, they have simply confirmed previous hypotheses empirically, they state as much in the paper. Basically they confirm an exponential decay relationship between fragmentation events and time, nothing to fancy beyond that. The finding is for a given length of DNA over time. It doesn't matter if it is a chromosome, or the whole genome, or just one gene. All that matter is the length of that sequence and time. That is the idea anyway. Now, it is true that they only test one part of the mitochondrial genome, other sections of the circular chromosome may decay at different rates, though that is highly unlikely.

Perhaps the more important finding than the rate of decay for the mtDNA sequence was they found the rate of decay in the nuclear genome to be at least twice as fast. This too fits with previous hypotheses since the mitochondrial genome, for the organisms we are discussing, is a circular covalently closed strand and is thought to be more stable than larger nuclear chromosomes.

Thobern, I like a good debate and appreciate when I can have a detailed conversation about an issue like this with someone, thank you. Hmmm ... I'm wondering how much interest there would be in a Fossil Forum journal club? There are many good palaeontology journals out there to sustain a group here on The Forum. Heck some of members here even publish in them! Any takers?

I read the article. It was the reporting that annoyed me, as the half-life analogy is meaningless without better parameters. Science reporting in general, though, is pretty abysmal.

Has there been any question that mitochondrial DNA is circular?

[AgrilusHunter]

Science reporting in general, though, is pretty abysmal.

So true.

Has there been any question that mitochondrial DNA is circular?

No, it is well known that not all eukaryotic mitochondrial genomes are circular, though I'm a little confused by this question. Are you asking if I thought someone had questioned this idea in this thread? I did not question that at all, I was merely following a tangent when I commented on the mitochondrial DNA, as it was something I found interesting.

Edited October 11, 2012 by AgrilusHunter

[Scylla]

DNA "half life" would imply the bond between two nucleotides breaking. The problem with this concept is that unlike radioactive decay the DNA "half life" would be altered by temperature, pH, humidity, etc. I'm willing to bet that DNA preserved in a dry valley in Antartica will last a little longer than in New Zealand. Unless the increase in space radiation at the poles is significant. Journal club? Hmmm. But then I'll actually have to read something

[Auspex]

Yes, the processes of organic chemistry are subject to all manner of variables.

[ashcraft]

Organic chemistry (He shivers and develops a cold sweat in rememberance of reaction mechanisms)

Brent Ashcraft

[THobern]

So true.

No, it is well known that not all eukaryotic mitochondrial genomes are circular, though I'm a little confused by this question. Are you asking if I thought someone had questioned this idea in this thread? I did not question that at all, I was merely following a tangent when I commented on the mitochondrial DNA, as it was something I found interesting.

I didn't think that's what you were suggesting, I just read the second sentence too quickly. I thought that you were suggesting that the evidence supports hypotheses about mitochondrial DNA structure, but rereading it I realised that you meant it supported hypotheses about decay rates.

Perhaps the more important finding than the rate of decay for the mtDNA sequence was they found the rate of decay in the nuclear genome to be at least twice as fast. This too fits with previous hypotheses since the mitochondrial genome, for the organisms we are discussing, is a circular covalently closed strand and is thought to be more stable than larger nuclear chromosomes.