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	<title>Comments on: Guest Post: Caleb Scharf on the Shadow Biosphere</title>
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	<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/</link>
	<description>Random samplings from a universe of ideas.</description>
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		<title>By: Caleb</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-121004</link>
		<dc:creator>Caleb</dc:creator>
		<pubDate>Wed, 02 Jun 2010 14:29:55 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-121004</guid>
		<description>As far as I&#039;m aware there is no real evidence for life at the time of the LHB - although stromatolite remains seem to date back to about 3.8 Gyr ago, &#039;just&#039; after the LHB (which ran from about 4.1 to 3.8 Gyr ago). The difficulty of finding such old, preserved, rocks undoubtedly puts huge uncertainty on things.

The LHB itself does seem very likely to have occurred. The lunar cratering record (with radioisotope rock dating of melted forms) strongly supports a peak in large impacts at this time. There is also an excellent explanation for the LHB from the study of how the orbital architecture of the solar system came to be the way it is. Specifically, at an early stage (about 4 Gyr ago), it seems that there was a reconfiguration of the outer planets (Neptune, Uranus) during which time Neptune in particular underwent strong gravitational interaction with all the remnant planetesimals/asteroids/dwarf planets in the outer solar system. As a consequence Neptune&#039;s orbit expanded, and much of this remnant material of smaller bodies (part of which is now the Kuiper belt) was scattered inwards, with some ending up pelting the Earth-Moon system. This also, incidently, seems to explain the different internal structures of the Jovian moons Ganymede and Callisto - because of heating via large impacts.

The Moon formed earlier, about 4.53 Gyr ago, and the model in which it is formed from the debris following the collision of the young Earth with a Mars-sized proto-planet is still very much the best bet - it neatly explains many things, including the relatively high angular momentum of the Earth-Moon system.

The RNA world idea is also quite compelling, and you&#039;re right, it might well have been the stage at which  a core planetary gene set would have begun to &#039;assemble&#039; - although presumably the metabolic processes in such a world might be rather different ?</description>
		<content:encoded><![CDATA[<p>As far as I&#8217;m aware there is no real evidence for life at the time of the LHB &#8211; although stromatolite remains seem to date back to about 3.8 Gyr ago, &#8216;just&#8217; after the LHB (which ran from about 4.1 to 3.8 Gyr ago). The difficulty of finding such old, preserved, rocks undoubtedly puts huge uncertainty on things.</p>
<p>The LHB itself does seem very likely to have occurred. The lunar cratering record (with radioisotope rock dating of melted forms) strongly supports a peak in large impacts at this time. There is also an excellent explanation for the LHB from the study of how the orbital architecture of the solar system came to be the way it is. Specifically, at an early stage (about 4 Gyr ago), it seems that there was a reconfiguration of the outer planets (Neptune, Uranus) during which time Neptune in particular underwent strong gravitational interaction with all the remnant planetesimals/asteroids/dwarf planets in the outer solar system. As a consequence Neptune&#8217;s orbit expanded, and much of this remnant material of smaller bodies (part of which is now the Kuiper belt) was scattered inwards, with some ending up pelting the Earth-Moon system. This also, incidently, seems to explain the different internal structures of the Jovian moons Ganymede and Callisto &#8211; because of heating via large impacts.</p>
<p>The Moon formed earlier, about 4.53 Gyr ago, and the model in which it is formed from the debris following the collision of the young Earth with a Mars-sized proto-planet is still very much the best bet &#8211; it neatly explains many things, including the relatively high angular momentum of the Earth-Moon system.</p>
<p>The RNA world idea is also quite compelling, and you&#8217;re right, it might well have been the stage at which  a core planetary gene set would have begun to &#8216;assemble&#8217; &#8211; although presumably the metabolic processes in such a world might be rather different ?</p>
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		<title>By: Brian Too</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120816</link>
		<dc:creator>Brian Too</dc:creator>
		<pubDate>Thu, 27 May 2010 23:43:11 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120816</guid>
		<description>I believe this approach may have legs.  If genes really are selfish (Dawkins), they may have ancient survival skills that were severely tested in the earliest days of their existence.

Do we have any information, or even informed speculation, on whether life dates back to the Late Heavy Bombardment?  Or does the LHB itself fall into the category of informed speculation rather than established fact?  The reason I ask is that I had understood the Moon&#039;s formation to be known to stem from an impact event.  Yet lately I hear that this is possible but not proven.

Another thought:  What about the notion that early life was RNA based?  Would the existence of a core planetary gene set not be written in RNA, more than in DNA, if the RNA emergence theory was true?

E.O. Wilson wrote about the blossoming of knowledge that occurs when 2 previously separate scientific disciplines meet, in Consilience.  Astrobiology sounds like an example of such a meeting.</description>
		<content:encoded><![CDATA[<p>I believe this approach may have legs.  If genes really are selfish (Dawkins), they may have ancient survival skills that were severely tested in the earliest days of their existence.</p>
<p>Do we have any information, or even informed speculation, on whether life dates back to the Late Heavy Bombardment?  Or does the LHB itself fall into the category of informed speculation rather than established fact?  The reason I ask is that I had understood the Moon&#8217;s formation to be known to stem from an impact event.  Yet lately I hear that this is possible but not proven.</p>
<p>Another thought:  What about the notion that early life was RNA based?  Would the existence of a core planetary gene set not be written in RNA, more than in DNA, if the RNA emergence theory was true?</p>
<p>E.O. Wilson wrote about the blossoming of knowledge that occurs when 2 previously separate scientific disciplines meet, in Consilience.  Astrobiology sounds like an example of such a meeting.</p>
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		<title>By: caleb</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120428</link>
		<dc:creator>caleb</dc:creator>
		<pubDate>Sun, 16 May 2010 14:56:10 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120428</guid>
		<description>Right, the new analysis cannot say whether there were other &#039;grandparents&#039; whose genetic lines are now simply gone (as far as we know), nor can it say when those lines - if any - faded out. It also makes me wonder whether we&#039;re looking at the consequences of an extinction event or other type of evolutionary bottleneck, where only a single species made it through. I put a blog entry on Life, Unbounded about the result. It is also worth emphasizing that the analysis is *statistical*, and based on a number of assumptions.</description>
		<content:encoded><![CDATA[<p>Right, the new analysis cannot say whether there were other &#8216;grandparents&#8217; whose genetic lines are now simply gone (as far as we know), nor can it say when those lines &#8211; if any &#8211; faded out. It also makes me wonder whether we&#8217;re looking at the consequences of an extinction event or other type of evolutionary bottleneck, where only a single species made it through. I put a blog entry on Life, Unbounded about the result. It is also worth emphasizing that the analysis is *statistical*, and based on a number of assumptions.</p>
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		<title>By: RBH</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120412</link>
		<dc:creator>RBH</dc:creator>
		<pubDate>Sun, 16 May 2010 06:40:20 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120412</guid>
		<description>Sure it&#039;s possible that life &lt;i&gt;originated&lt;/i&gt; independently many times, but the Theobald&#039;s data indicate that only one of those occurrences has descendants now.

I&#039;m told Theobald will be blogging on his paper at &lt;a href=&quot;http://pandasthumb.org&quot; rel=&quot;nofollow&quot;&gt;Panda&#039;s Thumb&lt;/a&gt; one of these days real soon now.</description>
		<content:encoded><![CDATA[<p>Sure it&#8217;s possible that life <i>originated</i> independently many times, but the Theobald&#8217;s data indicate that only one of those occurrences has descendants now.</p>
<p>I&#8217;m told Theobald will be blogging on his paper at <a href="http://pandasthumb.org" rel="nofollow">Panda&#8217;s Thumb</a> one of these days real soon now.</p>
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		<title>By: Brian137</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120382</link>
		<dc:creator>Brian137</dc:creator>
		<pubDate>Sat, 15 May 2010 16:58:07 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120382</guid>
		<description>Fascinating.  Caleb&#039;s post #4 above was a much appreciated response to my post #3 above, in which I asked whether life on Earth had begun only once, or whether it might have had several completely independent beginnings.  Too cheap to pay Nature to read the whole article, I found this synopsis and commentary: 

http://www.physorg.com/news192882557.html

But according to Theobold, his findings do not preclude the possibility of multiple independent starts to life on Earth. 

From the link: 
&lt;i&gt;&quot;Let&#039;s say life originated independently multiple times, which UCA allows is possible,&quot; said Theobald.&lt;/i&gt;</description>
		<content:encoded><![CDATA[<p>Fascinating.  Caleb&#8217;s post #4 above was a much appreciated response to my post #3 above, in which I asked whether life on Earth had begun only once, or whether it might have had several completely independent beginnings.  Too cheap to pay Nature to read the whole article, I found this synopsis and commentary: </p>
<p><a href="http://www.physorg.com/news192882557.html" rel="nofollow">http://www.physorg.com/news192882557.html</a></p>
<p>But according to Theobold, his findings do not preclude the possibility of multiple independent starts to life on Earth. </p>
<p>From the link:<br />
<i>&#8220;Let&#8217;s say life originated independently multiple times, which UCA allows is possible,&#8221; said Theobald.</i></p>
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		<title>By: RBH</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120371</link>
		<dc:creator>RBH</dc:creator>
		<pubDate>Sat, 15 May 2010 04:03:25 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120371</guid>
		<description>Caleb wrote&lt;blockquote&gt;... we don’t actually know whether the great domains of bacteria, archaea and eukarya (to which we belong) all have a single common ancestor, right now there isn’t enough information to join those final dots.&lt;/blockquote&gt;Time (and research) marches on: we know more about that this week than we did last week when that sentence was written.  See &lt;a href=&quot;http://www.nature.com/nature/journal/v465/n7295/full/nature09014.html#/&quot; rel=&quot;nofollow&quot;&gt;Doug Theobald&#039;s new paper&lt;/a&gt; in Nature.   Doug will be blogging about it on Panda&#039;s Thumb very soon, and Nick Matzke already has &lt;a href=&quot;http://pandasthumb.org/archives/2010/05/common-ancestry.html&quot; rel=&quot;nofollow&quot;&gt;a summary up there&lt;/a&gt;.</description>
		<content:encoded><![CDATA[<p>Caleb wrote<br />
<blockquote>&#8230; we don’t actually know whether the great domains of bacteria, archaea and eukarya (to which we belong) all have a single common ancestor, right now there isn’t enough information to join those final dots.</p></blockquote>
<p>Time (and research) marches on: we know more about that this week than we did last week when that sentence was written.  See <a href="http://www.nature.com/nature/journal/v465/n7295/full/nature09014.html#/" rel="nofollow">Doug Theobald&#8217;s new paper</a> in Nature.   Doug will be blogging about it on Panda&#8217;s Thumb very soon, and Nick Matzke already has <a href="http://pandasthumb.org/archives/2010/05/common-ancestry.html" rel="nofollow">a summary up there</a>.</p>
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		<title>By: Caleb</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120319</link>
		<dc:creator>Caleb</dc:creator>
		<pubDate>Thu, 13 May 2010 17:53:13 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120319</guid>
		<description>Ah, good call. Well, to be honest I&#039;m quoting the 99.9% from what I&#039;ve heard a couple of microbiologists state, so I don&#039;t have a direct reference. Obviously this number is going to be open to some variation - since we almost certainly don&#039;t yet know exactly how many distinct species there are on the planet, and it if you&#039;re making this determination in the lab it will depend on exactly where the samples are coming from.</description>
		<content:encoded><![CDATA[<p>Ah, good call. Well, to be honest I&#8217;m quoting the 99.9% from what I&#8217;ve heard a couple of microbiologists state, so I don&#8217;t have a direct reference. Obviously this number is going to be open to some variation &#8211; since we almost certainly don&#8217;t yet know exactly how many distinct species there are on the planet, and it if you&#8217;re making this determination in the lab it will depend on exactly where the samples are coming from.</p>
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		<title>By: wds</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120305</link>
		<dc:creator>wds</dc:creator>
		<pubDate>Thu, 13 May 2010 12:45:55 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120305</guid>
		<description>I was wondering where the 99.9% figure comes from. I know it&#039;s said to be high, but I somehow had gotten it into my head it was more like 60-70%. Any references for this number?</description>
		<content:encoded><![CDATA[<p>I was wondering where the 99.9% figure comes from. I know it&#8217;s said to be high, but I somehow had gotten it into my head it was more like 60-70%. Any references for this number?</p>
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		<title>By: Andy Fleming</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120279</link>
		<dc:creator>Andy Fleming</dc:creator>
		<pubDate>Wed, 12 May 2010 23:10:26 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120279</guid>
		<description>A pleasure on my part caleb... it&#039;s a privilege to be a part of the discussion and be party to have access to these blogs. Thank goodness for the &#039;net!</description>
		<content:encoded><![CDATA[<p>A pleasure on my part caleb&#8230; it&#8217;s a privilege to be a part of the discussion and be party to have access to these blogs. Thank goodness for the &#8216;net!</p>
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		<title>By: caleb</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120193</link>
		<dc:creator>caleb</dc:creator>
		<pubDate>Tue, 11 May 2010 00:29:21 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120193</guid>
		<description>Just wanted to register my appreciation of the comments - glad that this stimulates - and happy to have new audiences !</description>
		<content:encoded><![CDATA[<p>Just wanted to register my appreciation of the comments &#8211; glad that this stimulates &#8211; and happy to have new audiences !</p>
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		<title>By: Low Math, Meekly Interacting</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120182</link>
		<dc:creator>Low Math, Meekly Interacting</dc:creator>
		<pubDate>Mon, 10 May 2010 19:17:59 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120182</guid>
		<description>Bit belated, but I loved the post, and am very happy to be made aware of the Life Unbounded blog.

Thanks to Caleb, and Sean for hosting!</description>
		<content:encoded><![CDATA[<p>Bit belated, but I loved the post, and am very happy to be made aware of the Life Unbounded blog.</p>
<p>Thanks to Caleb, and Sean for hosting!</p>
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		<title>By: Andy Fleming</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120145</link>
		<dc:creator>Andy Fleming</dc:creator>
		<pubDate>Sun, 09 May 2010 23:20:11 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120145</guid>
		<description>Thank you Caleb for sharing this with us... a mind-blowing post.

My semi-informed speculation is that microbial life is definitely out there and common in the universe. The building blocks of life are found all over, and the physical laws that governed the evolution of life on this planet appear to be the same throughout the cosmos.

It&#039;s a gargantuan visible universe... which may be just an infinitesimally small part of something much larger, or even infinite. In a Cosmos so large and so old, perhaps infinitely old - everything that can happen has and will happen... probably a gazillion  times. In an infinitely large universe, even an infinite number of times!

The speculation that there are other intelligent species on other planets is the ultimate application of the Copernican Principle/Principle of Mediocrity. As a layperson, my knowledge is far from complete, but that we are no alone makes sense.  It also makes sense however, bearing in mind interstellar distances, that it may be many centuries, if at all before we obtain conclusive proof of ETI. The mean distances between civilisations may be huge!</description>
		<content:encoded><![CDATA[<p>Thank you Caleb for sharing this with us&#8230; a mind-blowing post.</p>
<p>My semi-informed speculation is that microbial life is definitely out there and common in the universe. The building blocks of life are found all over, and the physical laws that governed the evolution of life on this planet appear to be the same throughout the cosmos.</p>
<p>It&#8217;s a gargantuan visible universe&#8230; which may be just an infinitesimally small part of something much larger, or even infinite. In a Cosmos so large and so old, perhaps infinitely old &#8211; everything that can happen has and will happen&#8230; probably a gazillion  times. In an infinitely large universe, even an infinite number of times!</p>
<p>The speculation that there are other intelligent species on other planets is the ultimate application of the Copernican Principle/Principle of Mediocrity. As a layperson, my knowledge is far from complete, but that we are no alone makes sense.  It also makes sense however, bearing in mind interstellar distances, that it may be many centuries, if at all before we obtain conclusive proof of ETI. The mean distances between civilisations may be huge!</p>
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		<title>By: spyder</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120095</link>
		<dc:creator>spyder</dc:creator>
		<pubDate>Sat, 08 May 2010 00:56:21 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120095</guid>
		<description>Thank you hugely for sharing a few basic insights into your work and that of others like you.  Now i must add yet another daily blog to my bookmarks and look forward to more detailed accounts.</description>
		<content:encoded><![CDATA[<p>Thank you hugely for sharing a few basic insights into your work and that of others like you.  Now i must add yet another daily blog to my bookmarks and look forward to more detailed accounts.</p>
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		<title>By: Mantis</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120067</link>
		<dc:creator>Mantis</dc:creator>
		<pubDate>Fri, 07 May 2010 07:46:54 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120067</guid>
		<description>Thank you for clarifications. 

Astrobiology as you describe it - as a label for (mostly) &quot;traditionally&quot; trained scientists whose work has bearing on the question of life beyond Earth - makes much more sense to me then a completely separate discipline.</description>
		<content:encoded><![CDATA[<p>Thank you for clarifications. </p>
<p>Astrobiology as you describe it &#8211; as a label for (mostly) &#8220;traditionally&#8221; trained scientists whose work has bearing on the question of life beyond Earth &#8211; makes much more sense to me then a completely separate discipline.</p>
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		<title>By: caleb</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120055</link>
		<dc:creator>caleb</dc:creator>
		<pubDate>Thu, 06 May 2010 23:55:30 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120055</guid>
		<description>In response to Brian137. This is an excellent question and gets to the heart of a longstanding issue. It&#039;s common when people assemble &#039;tree of life&#039; type diagrams (typically these days based on phylogenetics - the similarity of one or more key bits of genetic material shared by all organisms) to show the base roots or trunk of the tree all converging to one point in the genetic past. This is total conjecture, we don&#039;t actually know whether the great domains of bacteria, archaea and eukarya (to which we belong) all have a single common ancestor, right now there isn&#039;t enough information to join those final dots. By the same token, we don&#039;t know whether &#039;life&#039; arose more than once - perhaps on different parts of a young Earth, or in multiple wide spread molecular &#039;events&#039; - indeed we don&#039;t actually know how, when, where &#039;life&#039; got going at all. It does seem likely that before the kinds of organisms we recognize today (and clearly we&#039;re just beginning to scrape the surface of what&#039;s out there) there may have been a so-called RNA-world, without the critical, but more inflexible storage mechanism of DNA. RNA molecules are versatile, and as well as carrying information they can perform the duties of enzymes and so on. It&#039;s been argued that a whole proto-life system could run on RNA. Such a system would, I imagine, offer many possibilities for separate &#039;upgrade&#039; events (wow, I seem to really like computer metaphors...).

So, where am I going with this ? I think it&#039;s all going to hinge on exactly how rich a chemical mix ends up on the surface (or in the subsurface) of a potential harbor like a terrestrial planet (other environments could work too). Rich and complex enough and then at the very earliest stages of self-organizing behavior I could imagine multiple styles of life arising, ultimately ending up in layers of symbiotic and endosymbiotic (fully merged) relationships - to the point where it&#039;s impossible to disentangle the ancestral patterns. I&#039;m hedging my bets - I&#039;d say that very early on then independent beginnings might indeed have occurred, but that these are likely to merge and erase evidence for that history. 

Could a separate start to life have occurred later on - after recognizable things like bacteria were already around ? Maybe, but I&#039;d think it&#039;d still have the same RNA mix, or something similar, at its root, I also think it would have a hard time finding a free niche - unless it got very specialized - *or* quickly figured out how to join in the biochemical party with everyone else.

I agree that the details have big implications for whether life is a common or rare phenomenon in the universe.</description>
		<content:encoded><![CDATA[<p>In response to Brian137. This is an excellent question and gets to the heart of a longstanding issue. It&#8217;s common when people assemble &#8216;tree of life&#8217; type diagrams (typically these days based on phylogenetics &#8211; the similarity of one or more key bits of genetic material shared by all organisms) to show the base roots or trunk of the tree all converging to one point in the genetic past. This is total conjecture, we don&#8217;t actually know whether the great domains of bacteria, archaea and eukarya (to which we belong) all have a single common ancestor, right now there isn&#8217;t enough information to join those final dots. By the same token, we don&#8217;t know whether &#8216;life&#8217; arose more than once &#8211; perhaps on different parts of a young Earth, or in multiple wide spread molecular &#8216;events&#8217; &#8211; indeed we don&#8217;t actually know how, when, where &#8216;life&#8217; got going at all. It does seem likely that before the kinds of organisms we recognize today (and clearly we&#8217;re just beginning to scrape the surface of what&#8217;s out there) there may have been a so-called RNA-world, without the critical, but more inflexible storage mechanism of DNA. RNA molecules are versatile, and as well as carrying information they can perform the duties of enzymes and so on. It&#8217;s been argued that a whole proto-life system could run on RNA. Such a system would, I imagine, offer many possibilities for separate &#8216;upgrade&#8217; events (wow, I seem to really like computer metaphors&#8230;).</p>
<p>So, where am I going with this ? I think it&#8217;s all going to hinge on exactly how rich a chemical mix ends up on the surface (or in the subsurface) of a potential harbor like a terrestrial planet (other environments could work too). Rich and complex enough and then at the very earliest stages of self-organizing behavior I could imagine multiple styles of life arising, ultimately ending up in layers of symbiotic and endosymbiotic (fully merged) relationships &#8211; to the point where it&#8217;s impossible to disentangle the ancestral patterns. I&#8217;m hedging my bets &#8211; I&#8217;d say that very early on then independent beginnings might indeed have occurred, but that these are likely to merge and erase evidence for that history. </p>
<p>Could a separate start to life have occurred later on &#8211; after recognizable things like bacteria were already around ? Maybe, but I&#8217;d think it&#8217;d still have the same RNA mix, or something similar, at its root, I also think it would have a hard time finding a free niche &#8211; unless it got very specialized &#8211; *or* quickly figured out how to join in the biochemical party with everyone else.</p>
<p>I agree that the details have big implications for whether life is a common or rare phenomenon in the universe.</p>
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		<title>By: Brian137</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120054</link>
		<dc:creator>Brian137</dc:creator>
		<pubDate>Thu, 06 May 2010 22:45:27 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120054</guid>
		<description>Hi Caleb,
     Thank you for the post.
      We see that life on Earth exists under extremely diverse conditions, extracting energy through a number of different mechanisms.  That fact encourages us to speculate that carbon-based life might be rather widespread throughout the universe.  But another factor might be the ease or difficulty of life beginning &lt;i&gt;ex nihilo&lt;/i&gt; where no life existed previously.    
     
So the question which interests me most right now is whether life on Earth began only once or whether it had at least two completely independent beginnings.  If all our diverse biospheres evolved from the same beginning, then life may be a very rare occurrence despite its ability to evolve and adapt once initiated.  I hope I have made myself clear, and I would welcome input from Caleb or anyone else.  </description>
		<content:encoded><![CDATA[<p>Hi Caleb,<br />
     Thank you for the post.<br />
      We see that life on Earth exists under extremely diverse conditions, extracting energy through a number of different mechanisms.  That fact encourages us to speculate that carbon-based life might be rather widespread throughout the universe.  But another factor might be the ease or difficulty of life beginning <i>ex nihilo</i> where no life existed previously.    </p>
<p>So the question which interests me most right now is whether life on Earth began only once or whether it had at least two completely independent beginnings.  If all our diverse biospheres evolved from the same beginning, then life may be a very rare occurrence despite its ability to evolve and adapt once initiated.  I hope I have made myself clear, and I would welcome input from Caleb or anyone else.</p>
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		<title>By: caleb</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120052</link>
		<dc:creator>caleb</dc:creator>
		<pubDate>Thu, 06 May 2010 22:34:05 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120052</guid>
		<description>Let me respond to a couple of those points. The term &#039;core planetary gene set&#039; is the one used in the paper by Falkowski et al, published in Science in 2008, in this case it&#039;s really just trying to emphasize that there are a surprisingly small number of known genes (about 1500) that seem to code for all the molecular machinery needed to perform metabolism (which encompasses the ten or so known metabolic pathways - photosynthesis, methanogenesis, o2 respiration, sulphate reduction etc.). So, &#039;core&#039; means an essentially irreducible set, take any of these away and life and the planet changes significantly if not disastrously. You&#039;re right that &#039;metabolic gene set&#039; would be more specific sounding, but again, the point was I think to emphasize how critical these genes are. I don&#039;t think anyone is trying to say that this is a universal truth applicable to all planets - but it sure is intriguing.

What is deep about this (specific)  truth? Well, it&#039;s the result of extensive research by many, many people, it&#039;s not an answer that just fell out of the sky, it&#039;s a carefully considered, examined, partially tested, idea that no one had come to just on the basis of applying evolutionary theory and/or horizontal gene transfer. In retrospect I completely agree that it makes a lot of sense...most of the best scientific ideas do, with hindsight.

As for poor old (new ?) astrobiology. Well, it may surprise you that I actually agree that &#039;astrobiology&#039; is not so much a unique discipline, but that it&#039;s a convenient way of labeling an array of research done in different classical disciplines, all of which nonetheless is tackling the common questions of &#039;life in the universe&#039;.  For example, I do not call myself an astrobiologist - I&#039;m an astrophysicist by trade, who happens to work on exoplanets and the questions relating to how we can go look for life beyond the Earth. One of the reasons we use the term &#039;astrobiology&#039; is because historically it has been hard to get people in different classical scientific disciplines to talk to each other, beyond casual bar room fare. Consider it an experiment to attach this label in the hope that people  feel less embarrassed to admit that they&#039;re interested in &#039;aliens&#039;. The fact is though that within the classical disciplines (and yes, under the label of astrobiology) there have been amazing advances in understanding extremophilic organisms on Earth - often motivated *precisely* because of what might be happening on Mars or Europa or elsewhere. In astronomy the big drive is to find the terrestrial type planets (NASA&#039;s Kepler mission is designed to provide a statistical measurement of how many such planets exist) - why ? Because the idea of finding a planet like the Earth, that could harbor life is so compelling and interesting. Does this need to be called astrobiology ? No, but that is what it is....</description>
		<content:encoded><![CDATA[<p>Let me respond to a couple of those points. The term &#8216;core planetary gene set&#8217; is the one used in the paper by Falkowski et al, published in Science in 2008, in this case it&#8217;s really just trying to emphasize that there are a surprisingly small number of known genes (about 1500) that seem to code for all the molecular machinery needed to perform metabolism (which encompasses the ten or so known metabolic pathways &#8211; photosynthesis, methanogenesis, o2 respiration, sulphate reduction etc.). So, &#8216;core&#8217; means an essentially irreducible set, take any of these away and life and the planet changes significantly if not disastrously. You&#8217;re right that &#8216;metabolic gene set&#8217; would be more specific sounding, but again, the point was I think to emphasize how critical these genes are. I don&#8217;t think anyone is trying to say that this is a universal truth applicable to all planets &#8211; but it sure is intriguing.</p>
<p>What is deep about this (specific)  truth? Well, it&#8217;s the result of extensive research by many, many people, it&#8217;s not an answer that just fell out of the sky, it&#8217;s a carefully considered, examined, partially tested, idea that no one had come to just on the basis of applying evolutionary theory and/or horizontal gene transfer. In retrospect I completely agree that it makes a lot of sense&#8230;most of the best scientific ideas do, with hindsight.</p>
<p>As for poor old (new ?) astrobiology. Well, it may surprise you that I actually agree that &#8216;astrobiology&#8217; is not so much a unique discipline, but that it&#8217;s a convenient way of labeling an array of research done in different classical disciplines, all of which nonetheless is tackling the common questions of &#8216;life in the universe&#8217;.  For example, I do not call myself an astrobiologist &#8211; I&#8217;m an astrophysicist by trade, who happens to work on exoplanets and the questions relating to how we can go look for life beyond the Earth. One of the reasons we use the term &#8216;astrobiology&#8217; is because historically it has been hard to get people in different classical scientific disciplines to talk to each other, beyond casual bar room fare. Consider it an experiment to attach this label in the hope that people  feel less embarrassed to admit that they&#8217;re interested in &#8216;aliens&#8217;. The fact is though that within the classical disciplines (and yes, under the label of astrobiology) there have been amazing advances in understanding extremophilic organisms on Earth &#8211; often motivated *precisely* because of what might be happening on Mars or Europa or elsewhere. In astronomy the big drive is to find the terrestrial type planets (NASA&#8217;s Kepler mission is designed to provide a statistical measurement of how many such planets exist) &#8211; why ? Because the idea of finding a planet like the Earth, that could harbor life is so compelling and interesting. Does this need to be called astrobiology ? No, but that is what it is&#8230;.</p>
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		<title>By: Mantis</title>
		<link>http://blogs.discovermagazine.com/cosmicvariance/2010/05/06/guest-post-caleb-scharf-on-the-shadow-biosphere/comment-page-1/#comment-120050</link>
		<dc:creator>Mantis</dc:creator>
		<pubDate>Thu, 06 May 2010 21:32:36 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/cosmicvariance/?p=4796#comment-120050</guid>
		<description>Personally I don&#039;t see the need for astrobiology and would love to read a post explaining why such a discipline is warranted and what astrobiologists have achieved so far.

Caleb: &quot;A truly wonderful paper was published a couple of years ago in which Falkowski, Fenchel and Delong laid out the big picture for life on Earth. In essence, they argue that single-celled microbial life is the manifestation of an even deeper truth; the core planetary gene set. This is the set of recipes for metabolism, or how to harvest a planet for energy, and we all rely on them.&quot;

What exactly is so deep about this truth? It seems like a pretty straightforward consequence of the theory of evolution and abundance of horizontal gene transfer.

And why call it &quot;the core planetary gene set&quot;? To make it sound more astrobiologish? The adjective planetary makes little sense, we don&#039;t know for example lunar or comet gene sets, yes, the genes in question are specific to Earth but they are not specific to planets in general. 
The &quot;core&quot; also makes no sense, what core? There are plenty of alternative routes to generate energy, there is no core set of such genes present in every organism.  
Finally we should distinguish the gene set in question from many others not involved in harvesting energy like those who carry out anabolism or replication. 
Taking all this into account a much better description would be &quot;the metabolic gene set.&quot;</description>
		<content:encoded><![CDATA[<p>Personally I don&#8217;t see the need for astrobiology and would love to read a post explaining why such a discipline is warranted and what astrobiologists have achieved so far.</p>
<p>Caleb: &#8220;A truly wonderful paper was published a couple of years ago in which Falkowski, Fenchel and Delong laid out the big picture for life on Earth. In essence, they argue that single-celled microbial life is the manifestation of an even deeper truth; the core planetary gene set. This is the set of recipes for metabolism, or how to harvest a planet for energy, and we all rely on them.&#8221;</p>
<p>What exactly is so deep about this truth? It seems like a pretty straightforward consequence of the theory of evolution and abundance of horizontal gene transfer.</p>
<p>And why call it &#8220;the core planetary gene set&#8221;? To make it sound more astrobiologish? The adjective planetary makes little sense, we don&#8217;t know for example lunar or comet gene sets, yes, the genes in question are specific to Earth but they are not specific to planets in general.<br />
The &#8220;core&#8221; also makes no sense, what core? There are plenty of alternative routes to generate energy, there is no core set of such genes present in every organism.<br />
Finally we should distinguish the gene set in question from many others not involved in harvesting energy like those who carry out anabolism or replication.<br />
Taking all this into account a much better description would be &#8220;the metabolic gene set.&#8221;</p>
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