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	<title>Comments on: Want to Get 70 Billion Copies of Your Book In Print? Print It In DNA</title>
	<atom:link href="http://blogs.discovermagazine.com/loom/2012/08/16/want-to-get-70-billion-copies-of-your-book-in-print-print-it-in-dna/feed/" rel="self" type="application/rss+xml" />
	<link>http://blogs.discovermagazine.com/loom/2012/08/16/want-to-get-70-billion-copies-of-your-book-in-print-print-it-in-dna/</link>
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		<title>By: jambatrumpet</title>
		<link>http://blogs.discovermagazine.com/loom/2012/08/16/want-to-get-70-billion-copies-of-your-book-in-print-print-it-in-dna/#comment-18826</link>
		<dc:creator>jambatrumpet</dc:creator>
		<pubDate>Mon, 08 Oct 2012 03:58:37 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/?p=6247#comment-18826</guid>
		<description>just wondering...Has Andrew Dalby read the book yet?</description>
		<content:encoded><![CDATA[<p>just wondering&#8230;Has Andrew Dalby read the book yet?</p>
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		<title>By: Feed #9 &#124; Svoogle News</title>
		<link>http://blogs.discovermagazine.com/loom/2012/08/16/want-to-get-70-billion-copies-of-your-book-in-print-print-it-in-dna/#comment-18825</link>
		<dc:creator>Feed #9 &#124; Svoogle News</dc:creator>
		<pubDate>Sat, 25 Aug 2012 02:32:39 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/?p=6247#comment-18825</guid>
		<description>[...] Nature and Ourselves gli autori hanno ben pensato di usare il codice genetico per tradurlo in una stringa di DNA. Sempre utilizzando le normali tecniche da laboratorio, il DNA è stato poi sequenziato e il testo [...] </description>
		<content:encoded><![CDATA[<p>[...] Nature and Ourselves gli autori hanno ben pensato di usare il codice genetico per tradurlo in una stringa di DNA. Sempre utilizzando le normali tecniche da laboratorio, il DNA è stato poi sequenziato e il testo [...] </p>
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		<title>By: Feed #9 &#171; Oggi Scienza</title>
		<link>http://blogs.discovermagazine.com/loom/2012/08/16/want-to-get-70-billion-copies-of-your-book-in-print-print-it-in-dna/#comment-18824</link>
		<dc:creator>Feed #9 &#171; Oggi Scienza</dc:creator>
		<pubDate>Fri, 24 Aug 2012 13:31:27 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/?p=6247#comment-18824</guid>
		<description>[...] Nature and Ourselves gli autori hanno ben pensato di usare il codice genetico per tradurlo in una stringa di DNA. Sempre utilizzando le normali tecniche da laboratorio, il DNA è stato poi sequenziato e il testo [...] </description>
		<content:encoded><![CDATA[<p>[...] Nature and Ourselves gli autori hanno ben pensato di usare il codice genetico per tradurlo in una stringa di DNA. Sempre utilizzando le normali tecniche da laboratorio, il DNA è stato poi sequenziato e il testo [...] </p>
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		<title>By: Andrew Dalby</title>
		<link>http://blogs.discovermagazine.com/loom/2012/08/16/want-to-get-70-billion-copies-of-your-book-in-print-print-it-in-dna/#comment-18823</link>
		<dc:creator>Andrew Dalby</dc:creator>
		<pubDate>Thu, 23 Aug 2012 17:43:08 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/?p=6247#comment-18823</guid>
		<description>If we could use DNA proof reading from organisms easily we would be in a much better state for sequencing and amplification in general. Including it in an organism would be tricky as it is not coding DNA - so it needs to be in regulatory space or in introns and this makes it more likely to undergo mutations and rules out putting it in bacteria. It is an interesting proof of concept but a concept I do not expect to see used very often.

I am sure that Arcticio will never see a mammoth. They might see an elephant with mammoth DNA but a mammoth will never come back. That is the big problem about the DNA codes for an organism viewpoint - it is the same as a blueprint codes for my house. It doesn&#039;t unless I have a builder. So unless someone finds a mammoth egg that is not going to happen.

As for stability - it depends on storage. A living organism is very environment dependent. A nutrient free organism is a dead one but my ssd does not need a sandwich or a drink. The shuttles used regular hard drives for storage and they took more than a few shocks and could be restored, organic storage is much less effective and also much more error prone at making subjective interpretation of observations and data.

I am wondering how you can fiind out the DNA replication error rates at a level which is below the accuracy of the measurement device (the sequencing device itself). Surely that is impossible. I cannot measure to the nearest nanometre on a metre rule. Somatic mutation rates are difficult to estimate and we always sequence populations. There is a move in recent papers to sequence single cells to compare them for circulating cancers for example and there can be large differences.</description>
		<content:encoded><![CDATA[<p>If we could use DNA proof reading from organisms easily we would be in a much better state for sequencing and amplification in general. Including it in an organism would be tricky as it is not coding DNA &#8211; so it needs to be in regulatory space or in introns and this makes it more likely to undergo mutations and rules out putting it in bacteria. It is an interesting proof of concept but a concept I do not expect to see used very often.</p>
<p>I am sure that Arcticio will never see a mammoth. They might see an elephant with mammoth DNA but a mammoth will never come back. That is the big problem about the DNA codes for an organism viewpoint &#8211; it is the same as a blueprint codes for my house. It doesn&#8217;t unless I have a builder. So unless someone finds a mammoth egg that is not going to happen.</p>
<p>As for stability &#8211; it depends on storage. A living organism is very environment dependent. A nutrient free organism is a dead one but my ssd does not need a sandwich or a drink. The shuttles used regular hard drives for storage and they took more than a few shocks and could be restored, organic storage is much less effective and also much more error prone at making subjective interpretation of observations and data.</p>
<p>I am wondering how you can fiind out the DNA replication error rates at a level which is below the accuracy of the measurement device (the sequencing device itself). Surely that is impossible. I cannot measure to the nearest nanometre on a metre rule. Somatic mutation rates are difficult to estimate and we always sequence populations. There is a move in recent papers to sequence single cells to compare them for circulating cancers for example and there can be large differences.</p>
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		<title>By: Links 20/8/2012: Wine 1.5.11, Frugalware 1.7 &#124; Techrights</title>
		<link>http://blogs.discovermagazine.com/loom/2012/08/16/want-to-get-70-billion-copies-of-your-book-in-print-print-it-in-dna/#comment-18822</link>
		<dc:creator>Links 20/8/2012: Wine 1.5.11, Frugalware 1.7 &#124; Techrights</dc:creator>
		<pubDate>Mon, 20 Aug 2012 12:18:15 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/?p=6247#comment-18822</guid>
		<description>[...] Want to Get 70 Billion Copies of Your Book In Print? Print It In DNA I have been meaning to read a book coming out soon called Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves. It’s written by Harvard biologist George Church and science writer Ed Regis. Church is doing stunning work on a number of fronts, from creating synthetic microbes to sequencing human genomes, so I definitely am interested in what he has to say. I don’t know how many other people will be, so I have no idea how well the book will do. But in a tour de force of biochemical publishing, he has created 70 billion copies. Instead of paper and ink, or pdf’s and pixels, he’s used DNA. [...] </description>
		<content:encoded><![CDATA[<p>[...] Want to Get 70 Billion Copies of Your Book In Print? Print It In DNA I have been meaning to read a book coming out soon called Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves. It’s written by Harvard biologist George Church and science writer Ed Regis. Church is doing stunning work on a number of fronts, from creating synthetic microbes to sequencing human genomes, so I definitely am interested in what he has to say. I don’t know how many other people will be, so I have no idea how well the book will do. But in a tour de force of biochemical publishing, he has created 70 billion copies. Instead of paper and ink, or pdf’s and pixels, he’s used DNA. [...] </p>
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		<title>By: Doug</title>
		<link>http://blogs.discovermagazine.com/loom/2012/08/16/want-to-get-70-billion-copies-of-your-book-in-print-print-it-in-dna/#comment-18821</link>
		<dc:creator>Doug</dc:creator>
		<pubDate>Mon, 20 Aug 2012 06:07:24 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/?p=6247#comment-18821</guid>
		<description>What will this do to the value of first editions?</description>
		<content:encoded><![CDATA[<p>What will this do to the value of first editions?</p>
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		<title>By: MPS</title>
		<link>http://blogs.discovermagazine.com/loom/2012/08/16/want-to-get-70-billion-copies-of-your-book-in-print-print-it-in-dna/#comment-18820</link>
		<dc:creator>MPS</dc:creator>
		<pubDate>Mon, 20 Aug 2012 05:44:23 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/?p=6247#comment-18820</guid>
		<description>Now if we can get the DNA book to bring itself up to date and keep bibliography and references up to date by keeping it in a &quot;library soup&quot; with all the other DNA books in the library, he may be onto something.</description>
		<content:encoded><![CDATA[<p>Now if we can get the DNA book to bring itself up to date and keep bibliography and references up to date by keeping it in a &#8220;library soup&#8221; with all the other DNA books in the library, he may be onto something.</p>
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		<title>By: Wang-Lo</title>
		<link>http://blogs.discovermagazine.com/loom/2012/08/16/want-to-get-70-billion-copies-of-your-book-in-print-print-it-in-dna/#comment-18819</link>
		<dc:creator>Wang-Lo</dc:creator>
		<pubDate>Mon, 20 Aug 2012 01:56:47 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/?p=6247#comment-18819</guid>
		<description>&quot;john naddaf Says:
how can zero have an absolute value when zero has no bottom,,,,id need to go into much more detail…&lt;snip&gt;…zero has two main values of +,and -,,,can be either or but always a set and value never =0﻿&quot;
I wish I&#039;d said that.

-Wang-Lo.</description>
		<content:encoded><![CDATA[<p>&#8220;john naddaf Says:<br />
how can zero have an absolute value when zero has no bottom,,,,id need to go into much more detail…&lt;snip&gt;…zero has two main values of +,and -,,,can be either or but always a set and value never =0﻿&#8221;<br />
I wish I&#8217;d said that.</p>
<p>-Wang-Lo.</p>
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		<title>By: Sidney Markowitz</title>
		<link>http://blogs.discovermagazine.com/loom/2012/08/16/want-to-get-70-billion-copies-of-your-book-in-print-print-it-in-dna/#comment-18818</link>
		<dc:creator>Sidney Markowitz</dc:creator>
		<pubDate>Mon, 20 Aug 2012 01:46:12 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/?p=6247#comment-18818</guid>
		<description>A back of the envelope estimate for how stable the information would be after 10,000 years in generations of bacteria: Church&#039;s experiment split the data into 96 bit chunks, each with a 19 bit address that was used to put the pieces back together, which would require 115/96 times 5.27 megabits (not MB as it says in the article) or about 6.3 million base pairs for storage for one copy of the book.

If the data is stored in e. coli in some place in the genome that would not affect their viability, the entire 6.3 megabit  would not fit in the 4.2Mbp e. coli genome.  But the book could be spread over as many individual bacteria as necessary. According to the blog post at http://sandwalk.blogspot.co.nz/2007/07/mutation-rates.html the rate of neutral mutation (mutations that have no positive or negative effect on viability) in e. coli after accounting for the DNA repair mechanism is approximately 1 out of every 1e10 nucleotide base pair replications. Assuming 24 hours per generation (a more realistic real world number than the faster replication under laboratory conditions) and approximating 365.25 days in a year, that is about 3.6 million generations, or a total of 6.3 million times 3.6 million nucleotide replications, for an estimated number of errors at the end of 3.6e6 times 6.3e6 times 1e-10  which is 2268 errors in each 6.3 million bit copy of the book. or less than a 0.04% error rate. That is a tiny amount that can be compensated for with a simple error correction code that would not add many bits to the total. By comparison, the Reed-Solomon code used for the first stage error correction of an audio CD requires 32 bits in all to encode 28 bits of data, and it can correct up to 2 bytes of error out of every 32 byte block.

So if you could somehow arrange to maintain the proper environment to support the colony of e. coli for 10,000 years and have someone around to decode them at the end, the book should be readable.&lt;strong&gt;

[CZ: Just to clarify--Church and his colleagues did not insert the DNA into a living organism. The molecule sits in a chip.]&lt;/strong&gt;</description>
		<content:encoded><![CDATA[<p>A back of the envelope estimate for how stable the information would be after 10,000 years in generations of bacteria: Church&#8217;s experiment split the data into 96 bit chunks, each with a 19 bit address that was used to put the pieces back together, which would require 115/96 times 5.27 megabits (not MB as it says in the article) or about 6.3 million base pairs for storage for one copy of the book.</p>
<p>If the data is stored in e. coli in some place in the genome that would not affect their viability, the entire 6.3 megabit  would not fit in the 4.2Mbp e. coli genome.  But the book could be spread over as many individual bacteria as necessary. According to the blog post at <a href="http://sandwalk.blogspot.co.nz/2007/07/mutation-rates.html" rel="nofollow">http://sandwalk.blogspot.co.nz/2007/07/mutation-rates.html</a> the rate of neutral mutation (mutations that have no positive or negative effect on viability) in e. coli after accounting for the DNA repair mechanism is approximately 1 out of every 1e10 nucleotide base pair replications. Assuming 24 hours per generation (a more realistic real world number than the faster replication under laboratory conditions) and approximating 365.25 days in a year, that is about 3.6 million generations, or a total of 6.3 million times 3.6 million nucleotide replications, for an estimated number of errors at the end of 3.6e6 times 6.3e6 times 1e-10  which is 2268 errors in each 6.3 million bit copy of the book. or less than a 0.04% error rate. That is a tiny amount that can be compensated for with a simple error correction code that would not add many bits to the total. By comparison, the Reed-Solomon code used for the first stage error correction of an audio CD requires 32 bits in all to encode 28 bits of data, and it can correct up to 2 bytes of error out of every 32 byte block.</p>
<p>So if you could somehow arrange to maintain the proper environment to support the colony of e. coli for 10,000 years and have someone around to decode them at the end, the book should be readable.<strong></p>
<p>[CZ: Just to clarify--Church and his colleagues did not insert the DNA into a living organism. The molecule sits in a chip.]</strong></p>
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		<title>By: אמצעי אחסון ביולוגי: חוקרים הצליחו לקודד ספר שלם ב-DNA &#124; Newsgeek</title>
		<link>http://blogs.discovermagazine.com/loom/2012/08/16/want-to-get-70-billion-copies-of-your-book-in-print-print-it-in-dna/#comment-18817</link>
		<dc:creator>אמצעי אחסון ביולוגי: חוקרים הצליחו לקודד ספר שלם ב-DNA &#124; Newsgeek</dc:creator>
		<pubDate>Sun, 19 Aug 2012 07:24:21 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/?p=6247#comment-18817</guid>
		<description>[...] של הספר המדובר, כך שאין ספק כי מדובר בהצלחה.אחסון עתידיהניסוי שהציגו החוקרים למעשה מוכיח כי החומרים המצויים בתוך הגנים של האדם, [...] </description>
		<content:encoded><![CDATA[<p>[...] של הספר המדובר, כך שאין ספק כי מדובר בהצלחה.אחסון עתידיהניסוי שהציגו החוקרים למעשה מוכיח כי החומרים המצויים בתוך הגנים של האדם, [...] </p>
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