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	<title>Comments on: In the Beginning Was Linux?</title>
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	<link>http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/</link>
	<description>A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.</description>
	<lastBuildDate>Sat, 26 May 2012 01:25:59 +0000</lastBuildDate>
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		<title>By: Paul Donnelly</title>
		<link>http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/comment-page-1/#comment-3207</link>
		<dc:creator>Paul Donnelly</dc:creator>
		<pubDate>Tue, 25 Jul 2006 06:15:29 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/#comment-3207</guid>
		<description>This analogy seems thin in some ways, but right on in others.

As a matter of fact, open-source programmers do tend to converge on &quot;common codes&quot; as you might call them. The Linux operating system is one (although there are others), the X Window System is another, and common libraries like Gtk (for user interfaces), Opengl (for 3d graphics), and SDL (for multimedia in games) are others.

However, the same is true of all software, not just open-source software. Even more common than any open-source code are the codes used in Microsoft Windows. Windows as a base, the Windows GDI (for drawing), and DirectX for everthing a game needs are extremely dominant and common.

I do appreciate the parallel between programmers sharing building blocks and organisms sharing DNA, but it&#039;s not an open-source thing. Any non-trivial program will make use of software libraries, which serve as their shared building blocks. DNA blocks as software libraries is a better analogy.

Still, I don&#039;t think there&#039;s a strong parallel between the development of software engineering practices and the evolution of early life. Software never went through a time of freely traded though ill-defined code snippets, and organisms never really worked together like open-source programmers. The comparison especially breaks down when you consider the fact that software is designed, while organisms are feeling through the dark, and reproducing when they don&#039;t fall in an unseen pit first.</description>
		<content:encoded><![CDATA[<p>This analogy seems thin in some ways, but right on in others.</p>
<p>As a matter of fact, open-source programmers do tend to converge on &#8220;common codes&#8221; as you might call them. The Linux operating system is one (although there are others), the X Window System is another, and common libraries like Gtk (for user interfaces), Opengl (for 3d graphics), and SDL (for multimedia in games) are others.</p>
<p>However, the same is true of all software, not just open-source software. Even more common than any open-source code are the codes used in Microsoft Windows. Windows as a base, the Windows GDI (for drawing), and DirectX for everthing a game needs are extremely dominant and common.</p>
<p>I do appreciate the parallel between programmers sharing building blocks and organisms sharing DNA, but it&#8217;s not an open-source thing. Any non-trivial program will make use of software libraries, which serve as their shared building blocks. DNA blocks as software libraries is a better analogy.</p>
<p>Still, I don&#8217;t think there&#8217;s a strong parallel between the development of software engineering practices and the evolution of early life. Software never went through a time of freely traded though ill-defined code snippets, and organisms never really worked together like open-source programmers. The comparison especially breaks down when you consider the fact that software is designed, while organisms are feeling through the dark, and reproducing when they don&#8217;t fall in an unseen pit first.</p>
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		<title>By: Ed Seda</title>
		<link>http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/comment-page-1/#comment-3206</link>
		<dc:creator>Ed Seda</dc:creator>
		<pubDate>Sat, 22 Jul 2006 04:44:38 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/#comment-3206</guid>
		<description>There�s a very cool science fiction book by Rudy Rucker called &quot;The Hacker and the Ants&quot; that explores this idea of genetic algorithms. A couple of hackers create a virtual ant colony that can evolve by itself. They set it loose in the virtual world and, later, it sets itself free in the real world creating all kinds of problems, both funny and terrorising. A very clever and amusing story</description>
		<content:encoded><![CDATA[<p>There�s a very cool science fiction book by Rudy Rucker called &#8220;The Hacker and the Ants&#8221; that explores this idea of genetic algorithms. A couple of hackers create a virtual ant colony that can evolve by itself. They set it loose in the virtual world and, later, it sets itself free in the real world creating all kinds of problems, both funny and terrorising. A very clever and amusing story</p>
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		<title>By: Jeffrey Fredrick</title>
		<link>http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/comment-page-1/#comment-3205</link>
		<dc:creator>Jeffrey Fredrick</dc:creator>
		<pubDate>Sun, 16 Jul 2006 05:15:30 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/#comment-3205</guid>
		<description>I love your biology writing but this analogy is... well near as I can see it is just flawed.

The evolution that matters in software isn&#039;t in the source code, it is in the ideas that the software express or perhaps in the languages and techniques for creating software. I&#039;ve always like the term &#039;meme&#039; and you can see that it is the idea that unifies &quot;spreadsheets&quot; or &quot;webservers&quot; or &quot;photo editing tools&quot;, not the details such as the programing language used for implementation.  across multiple project/products/companies source code is _not_ the equivalent of DNA. (the situation is different if you&#039;re talking about multiple versions of the same program, as the code base &#039;evolves&#039; over time.)

So that&#039;s the software part about it, what about the open sourceness?  Open source is about collaboration and pride and mutual benefit -- which of these concepts apply to transgenic transfer of DNA?

So the analogy is, at best, flawed.

(Fwiw I&#039;m a developer on the open source sofware CruiseControl and a co-founder of the now defunct open source hosting company OpenAvenue.)</description>
		<content:encoded><![CDATA[<p>I love your biology writing but this analogy is&#8230; well near as I can see it is just flawed.</p>
<p>The evolution that matters in software isn&#8217;t in the source code, it is in the ideas that the software express or perhaps in the languages and techniques for creating software. I&#8217;ve always like the term &#8216;meme&#8217; and you can see that it is the idea that unifies &#8220;spreadsheets&#8221; or &#8220;webservers&#8221; or &#8220;photo editing tools&#8221;, not the details such as the programing language used for implementation.  across multiple project/products/companies source code is _not_ the equivalent of DNA. (the situation is different if you&#8217;re talking about multiple versions of the same program, as the code base &#8216;evolves&#8217; over time.)</p>
<p>So that&#8217;s the software part about it, what about the open sourceness?  Open source is about collaboration and pride and mutual benefit &#8212; which of these concepts apply to transgenic transfer of DNA?</p>
<p>So the analogy is, at best, flawed.</p>
<p>(Fwiw I&#8217;m a developer on the open source sofware CruiseControl and a co-founder of the now defunct open source hosting company OpenAvenue.)</p>
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		<title>By: Unmukt</title>
		<link>http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/comment-page-1/#comment-3204</link>
		<dc:creator>Unmukt</dc:creator>
		<pubDate>Fri, 14 Jul 2006 06:19:54 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/#comment-3204</guid>
		<description>I blog in Hindi and often talk about open source. I never realised the connection.</description>
		<content:encoded><![CDATA[<p>I blog in Hindi and often talk about open source. I never realised the connection.</p>
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		<title>By: Jeremy</title>
		<link>http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/comment-page-1/#comment-3203</link>
		<dc:creator>Jeremy</dc:creator>
		<pubDate>Fri, 14 Jul 2006 02:29:20 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/#comment-3203</guid>
		<description>Yeah, I&#039;ve always felt this was the strength in open-source software. Normally, the companies with the most money have their software out there. Open Source provides a set of rules for the &quot;Survival of the Most Useful&quot;.

Let&#039;s say if I write a program that a lot of people find useful, then I&#039;ll probably find a few other programmers working on it. And if they add useful features and fix bugs, then more and more people will use it, attracting more programmers, thus ending up with a great software package such as Apache or The Gimp.

If people don&#039;t find my software useful, then I&#039;ll be the only programmer and it won&#039;t thrive. And the great thing is that the end users, whether just an average Joe like me, or a huge corporation like IBM, determine if a software package continues down the path of software evolution with some features sticking around and some not.</description>
		<content:encoded><![CDATA[<p>Yeah, I&#8217;ve always felt this was the strength in open-source software. Normally, the companies with the most money have their software out there. Open Source provides a set of rules for the &#8220;Survival of the Most Useful&#8221;.</p>
<p>Let&#8217;s say if I write a program that a lot of people find useful, then I&#8217;ll probably find a few other programmers working on it. And if they add useful features and fix bugs, then more and more people will use it, attracting more programmers, thus ending up with a great software package such as Apache or The Gimp.</p>
<p>If people don&#8217;t find my software useful, then I&#8217;ll be the only programmer and it won&#8217;t thrive. And the great thing is that the end users, whether just an average Joe like me, or a huge corporation like IBM, determine if a software package continues down the path of software evolution with some features sticking around and some not.</p>
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		<title>By: Glyn Moody</title>
		<link>http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/comment-page-1/#comment-3202</link>
		<dc:creator>Glyn Moody</dc:creator>
		<pubDate>Thu, 13 Jul 2006 19:22:30 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/#comment-3202</guid>
		<description>Great post.  It provides another perspective on a similar idea I explore in my book &quot;&lt;a href=&quot;http://www.amazon.com/gp/product/0471327883/&quot; rel=&quot;nofollow&quot;&gt;Digital Code of Life: How Bioinformatics is Revolutionizing Science, Medicine, and Business&lt;/a&gt;,&quot; published in 2004.  This, in its turn, is practically the same book as my 2001 history of free software, &quot;&lt;a href=&quot;http://www.amazon.com/gp/product/0738206709/&quot; rel=&quot;nofollow&quot;&gt;Rebel Code: Inside Linux and the Open Source Revolution&lt;/a&gt;&quot;: the stories are almost identical - only the words have been changed.</description>
		<content:encoded><![CDATA[<p>Great post.  It provides another perspective on a similar idea I explore in my book &#8220;<a href="http://www.amazon.com/gp/product/0471327883/" rel="nofollow">Digital Code of Life: How Bioinformatics is Revolutionizing Science, Medicine, and Business</a>,&#8221; published in 2004.  This, in its turn, is practically the same book as my 2001 history of free software, &#8220;<a href="http://www.amazon.com/gp/product/0738206709/" rel="nofollow">Rebel Code: Inside Linux and the Open Source Revolution</a>&#8220;: the stories are almost identical &#8211; only the words have been changed.</p>
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		<title>By: Daniel Doro Ferrante</title>
		<link>http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/comment-page-1/#comment-3201</link>
		<dc:creator>Daniel Doro Ferrante</dc:creator>
		<pubDate>Thu, 13 Jul 2006 15:52:01 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/#comment-3201</guid>
		<description>Hi Carl,

I know some of the commenters above already made this remark, but the GNU/Free Software movement is much older than that and, in fact, is/was the real engine behind all this.

Personally, i&#039;ve been using GNU/Linux since 1994, which gives it at least ~12 years. But, for more on the history of this, i recommend the following links: &lt;a href=&quot;http://en.wikipedia.org/wiki/Free_Software_Foundation&quot; rel=&quot;nofollow&quot;&gt;Free Software Foundation&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/GNU&quot; rel=&quot;nofollow&quot;&gt;GNU&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Free_software_movement&quot; rel=&quot;nofollow&quot;&gt;Free software movement&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Free_Culture_Movement&quot; rel=&quot;nofollow&quot;&gt;Free Culture movement&lt;/a&gt;, &lt;a href=&quot;http://www.gnu.org/philosophy/free-software-for-freedom.html&quot; rel=&quot;nofollow&quot;&gt;Why ``Free Software&#039;&#039; is better than ``Open Source&#039;&#039;&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Open_source&quot; rel=&quot;nofollow&quot;&gt;Open source&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/OSS/FS&quot; rel=&quot;nofollow&quot;&gt;OSS/FS&lt;/a&gt;.

I don&#039;t mean to advocate either way (although i do have a position on the matter), but just to put things under a more historical context and perspective and, thus, show that things are a bit different [and more intricate] than what&#039;s written above.

Having said that, regardless of your (or anyone&#039;s) position on this matter, i recommend watching a talk by &lt;a href=&quot;http://en.wikipedia.org/wiki/Stallman&quot; rel=&quot;nofollow&quot;&gt;Richard Stallman&lt;/a&gt;: it&#039;s highly entertaining!

Anyway, i hope this information helps.

[]&#039;s.</description>
		<content:encoded><![CDATA[<p>Hi Carl,</p>
<p>I know some of the commenters above already made this remark, but the GNU/Free Software movement is much older than that and, in fact, is/was the real engine behind all this.</p>
<p>Personally, i&#8217;ve been using GNU/Linux since 1994, which gives it at least ~12 years. But, for more on the history of this, i recommend the following links: <a href="http://en.wikipedia.org/wiki/Free_Software_Foundation" rel="nofollow">Free Software Foundation</a>, <a href="http://en.wikipedia.org/wiki/GNU" rel="nofollow">GNU</a>, <a href="http://en.wikipedia.org/wiki/Free_software_movement" rel="nofollow">Free software movement</a>, <a href="http://en.wikipedia.org/wiki/Free_Culture_Movement" rel="nofollow">Free Culture movement</a>, <a href="http://www.gnu.org/philosophy/free-software-for-freedom.html" rel="nofollow">Why &#8220;Free Software&#8221; is better than &#8220;Open Source&#8221;</a>, <a href="http://en.wikipedia.org/wiki/Open_source" rel="nofollow">Open source</a> and <a href="http://en.wikipedia.org/wiki/OSS/FS" rel="nofollow">OSS/FS</a>.</p>
<p>I don&#8217;t mean to advocate either way (although i do have a position on the matter), but just to put things under a more historical context and perspective and, thus, show that things are a bit different [and more intricate] than what&#8217;s written above.</p>
<p>Having said that, regardless of your (or anyone&#8217;s) position on this matter, i recommend watching a talk by <a href="http://en.wikipedia.org/wiki/Stallman" rel="nofollow">Richard Stallman</a>: it&#8217;s highly entertaining!</p>
<p>Anyway, i hope this information helps.</p>
<p>[]&#8216;s.</p>
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		<title>By: Peter</title>
		<link>http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/comment-page-1/#comment-3200</link>
		<dc:creator>Peter</dc:creator>
		<pubDate>Thu, 13 Jul 2006 13:08:37 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/#comment-3200</guid>
		<description>I always think of the open source movement as being akin to the protestant reformation. Before Martin Luthor translated the bible into German, the only people who could read it were people who could read latin. So the ordinary people had to rely on the priest to interperet the bible for them, this gave the priest much more power. The depth of these issues can be shown by what happened to William Tyndale when he copied Luthor and created the first proper English bible, Tyndale was burnt at the stake for this. The reason being, by translating the bible into English he  was seen as empowering the common folk. Fast forward five hundred years and we have William Gates sitting on the most obscene mountain of money ever seen, this is because money is the real God of today and Mr Gates is the Pope. He has achieved this by keeping the source code for windows a secret. The sad thing is, if when Micro$oft released Win95 they had have also released its source code, Windows would have become the best operating system in the world, instead of the worst malware and virus laden pile of dung ever seen.</description>
		<content:encoded><![CDATA[<p>I always think of the open source movement as being akin to the protestant reformation. Before Martin Luthor translated the bible into German, the only people who could read it were people who could read latin. So the ordinary people had to rely on the priest to interperet the bible for them, this gave the priest much more power. The depth of these issues can be shown by what happened to William Tyndale when he copied Luthor and created the first proper English bible, Tyndale was burnt at the stake for this. The reason being, by translating the bible into English he  was seen as empowering the common folk. Fast forward five hundred years and we have William Gates sitting on the most obscene mountain of money ever seen, this is because money is the real God of today and Mr Gates is the Pope. He has achieved this by keeping the source code for windows a secret. The sad thing is, if when Micro$oft released Win95 they had have also released its source code, Windows would have become the best operating system in the world, instead of the worst malware and virus laden pile of dung ever seen.</p>
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		<title>By: Dan R.</title>
		<link>http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/comment-page-1/#comment-3199</link>
		<dc:creator>Dan R.</dc:creator>
		<pubDate>Thu, 13 Jul 2006 08:52:07 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/#comment-3199</guid>
		<description>I installed Linux 0.99pF Fall of &#039;93.  Even at that time, I had a full X workstation, which was &quot;very cool&quot; (in a geeky sense) because I could use it to run VMS/VAX software in my dorm room.

Even at that time, the X11 system, EMACS, and a few other pieces of open source software were developed, functioning pieces.  We had GCC (GNU C Compiler) installed on our NeXT machines because it was portable, etc.

Open source is definately older than 8 years old.</description>
		<content:encoded><![CDATA[<p>I installed Linux 0.99pF Fall of &#8217;93.  Even at that time, I had a full X workstation, which was &#8220;very cool&#8221; (in a geeky sense) because I could use it to run VMS/VAX software in my dorm room.</p>
<p>Even at that time, the X11 system, EMACS, and a few other pieces of open source software were developed, functioning pieces.  We had GCC (GNU C Compiler) installed on our NeXT machines because it was portable, etc.</p>
<p>Open source is definately older than 8 years old.</p>
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		<title>By: Avinash</title>
		<link>http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/comment-page-1/#comment-3198</link>
		<dc:creator>Avinash</dc:creator>
		<pubDate>Thu, 13 Jul 2006 05:28:30 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/#comment-3198</guid>
		<description>Cool!

I&#039;m a biologist who has been using OpenSource and Linux for quite some time now, and the parellels didn&#039;t strike me at all.

Just been reading your book &#039;Parasite Rex&#039; and came across this article yesterday. If I had read it a few years back, I might have become a parasitologist - for now, I remain a humble neurobiologist. Maybe I should think about Toxoplasma!!?

&lt;a href=&quot;http://biology.plosjournals.org/perlserv/?request=get-document&amp;doi=10.1371/journal.pbio.0040197&quot; rel=&quot;nofollow&quot;&gt;http://biology.plosjournals.org/perlserv/?request=get-document&amp;doi=10.1371/journal.pbio.0040197&lt;/a&gt;</description>
		<content:encoded><![CDATA[<p>Cool!</p>
<p>I&#8217;m a biologist who has been using OpenSource and Linux for quite some time now, and the parellels didn&#8217;t strike me at all.</p>
<p>Just been reading your book &#8216;Parasite Rex&#8217; and came across this article yesterday. If I had read it a few years back, I might have become a parasitologist &#8211; for now, I remain a humble neurobiologist. Maybe I should think about Toxoplasma!!?</p>
<p><a href="http://biology.plosjournals.org/perlserv/?request=get-document&amp;doi=10.1371/journal.pbio.0040197" rel="nofollow">http://biology.plosjournals.org/perlserv/?request=get-document&#038;doi=10.1371/journal.pbio.0040197</a></p>
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		<title>By: Greg Wilson</title>
		<link>http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/comment-page-1/#comment-3197</link>
		<dc:creator>Greg Wilson</dc:creator>
		<pubDate>Wed, 12 Jul 2006 22:59:59 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/#comment-3197</guid>
		<description>The GNU Manifesto (which started the free/open source software movement) actually dates back to the mid-1980s; Stallman has said many times that science was a direct influence.

&lt;a href=&quot;http://www.gnu.org/gnu/thegnuproject.html&quot; rel=&quot;nofollow&quot;&gt;http://www.gnu.org/gnu/thegnuproject.html&lt;/a&gt;</description>
		<content:encoded><![CDATA[<p>The GNU Manifesto (which started the free/open source software movement) actually dates back to the mid-1980s; Stallman has said many times that science was a direct influence.</p>
<p><a href="http://www.gnu.org/gnu/thegnuproject.html" rel="nofollow">http://www.gnu.org/gnu/thegnuproject.html</a></p>
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		<title>By: Gabe</title>
		<link>http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/comment-page-1/#comment-3196</link>
		<dc:creator>Gabe</dc:creator>
		<pubDate>Wed, 12 Jul 2006 22:20:49 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/loom/2006/07/12/in-the-beginning-was-linux/#comment-3196</guid>
		<description>Ingenious. As a software developer, this article was so easy to understand, it makes me want to take a class in biology. I love this blog.</description>
		<content:encoded><![CDATA[<p>Ingenious. As a software developer, this article was so easy to understand, it makes me want to take a class in biology. I love this blog.</p>
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