<article>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#article10_01_26_2143251</id>
	<title>Darwinian Evolution Considered As a Phase</title>
	<author>kdawson</author>
	<datestamp>1264505220000</datestamp>
	<htmltext>LucidBeast tips a mind-bending report at New Scientist on the latest paradigm-breaking work of Carl Woese, one of whose earlier discoveries was the third branch of life on Earth, the Archaea. Woese and physicist Nigel Goldenfeld argue that, even in its sophisticated modern form, Darwin's theory of evolution by natural selection applies only to a recent phase of life on Earth. Woese and Goldenfeld believe that <a href="http://www.newscientist.com/article/mg20527441.500-horizontal-and-vertical-the-evolution-of-evolution.html?full=true&amp;print=true">horizontal evolution led to the rise of the genetic code itself</a>. <i>"At the root of this idea is overwhelming recent evidence for horizontal gene transfer &mdash; in which organisms acquire genetic material 'horizontally' from other organisms around them, rather than vertically from their parents or ancestors. The donor organisms may not even be the same species. This mechanism is already known to play a huge role in the evolution of microbial genomes, but its consequences have hardly been explored. According to Woese and Goldenfeld, they are profound, and horizontal gene transfer alters the evolutionary process itself."</i></htmltext>
<tokenext>LucidBeast tips a mind-bending report at New Scientist on the latest paradigm-breaking work of Carl Woese , one of whose earlier discoveries was the third branch of life on Earth , the Archaea .
Woese and physicist Nigel Goldenfeld argue that , even in its sophisticated modern form , Darwin 's theory of evolution by natural selection applies only to a recent phase of life on Earth .
Woese and Goldenfeld believe that horizontal evolution led to the rise of the genetic code itself .
" At the root of this idea is overwhelming recent evidence for horizontal gene transfer    in which organisms acquire genetic material 'horizontally ' from other organisms around them , rather than vertically from their parents or ancestors .
The donor organisms may not even be the same species .
This mechanism is already known to play a huge role in the evolution of microbial genomes , but its consequences have hardly been explored .
According to Woese and Goldenfeld , they are profound , and horizontal gene transfer alters the evolutionary process itself .
"</tokentext>
<sentencetext>LucidBeast tips a mind-bending report at New Scientist on the latest paradigm-breaking work of Carl Woese, one of whose earlier discoveries was the third branch of life on Earth, the Archaea.
Woese and physicist Nigel Goldenfeld argue that, even in its sophisticated modern form, Darwin's theory of evolution by natural selection applies only to a recent phase of life on Earth.
Woese and Goldenfeld believe that horizontal evolution led to the rise of the genetic code itself.
"At the root of this idea is overwhelming recent evidence for horizontal gene transfer — in which organisms acquire genetic material 'horizontally' from other organisms around them, rather than vertically from their parents or ancestors.
The donor organisms may not even be the same species.
This mechanism is already known to play a huge role in the evolution of microbial genomes, but its consequences have hardly been explored.
According to Woese and Goldenfeld, they are profound, and horizontal gene transfer alters the evolutionary process itself.
"</sentencetext>
</article>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911832</id>
	<title>Bestiality?</title>
	<author>Anonymous</author>
	<datestamp>1264510440000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext>Cross-species genetic transfer? Like on Avatar, right?</htmltext>
<tokenext>Cross-species genetic transfer ?
Like on Avatar , right ?</tokentext>
<sentencetext>Cross-species genetic transfer?
Like on Avatar, right?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912478</id>
	<title>Re:It's still natural selection</title>
	<author>Anonymous</author>
	<datestamp>1264515180000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>3</modscore>
	<htmltext><p>Not the individual's genes, the individual gene. In all plants and animals it is reproduction combined with mutation and recombination that is driving evolution.</p><p>Social animals posses genetic traits which promote social or herd behaviour. In these animals the trait survives because for these animals in the environment in which the trait emerged it increases the chance of survival and reproduction. The gene promotes itself.</p><p>Worker ants are infertile. They share common genetic information with the queen. To protect the nest and the queen increases the chance of propagation of their genes even though they do not reproduce themselves. There's probably a gene for that.</p><p>I have no idea about infanticide but I do recall hearing of a study recently which observed that homosexual men frequently have one or more close female relatives who are unusually fecund. I can't find the link and the research may have since been debunked but the idea is interesting as it suggests the possibility of a gene which increases the reproductive fitness of one individual while reducing the reproductive fitness of another.</p><p>Of course that assumes that being homosexual reduces your chance of reproduction.</p></htmltext>
<tokenext>Not the individual 's genes , the individual gene .
In all plants and animals it is reproduction combined with mutation and recombination that is driving evolution.Social animals posses genetic traits which promote social or herd behaviour .
In these animals the trait survives because for these animals in the environment in which the trait emerged it increases the chance of survival and reproduction .
The gene promotes itself.Worker ants are infertile .
They share common genetic information with the queen .
To protect the nest and the queen increases the chance of propagation of their genes even though they do not reproduce themselves .
There 's probably a gene for that.I have no idea about infanticide but I do recall hearing of a study recently which observed that homosexual men frequently have one or more close female relatives who are unusually fecund .
I ca n't find the link and the research may have since been debunked but the idea is interesting as it suggests the possibility of a gene which increases the reproductive fitness of one individual while reducing the reproductive fitness of another.Of course that assumes that being homosexual reduces your chance of reproduction .</tokentext>
<sentencetext>Not the individual's genes, the individual gene.
In all plants and animals it is reproduction combined with mutation and recombination that is driving evolution.Social animals posses genetic traits which promote social or herd behaviour.
In these animals the trait survives because for these animals in the environment in which the trait emerged it increases the chance of survival and reproduction.
The gene promotes itself.Worker ants are infertile.
They share common genetic information with the queen.
To protect the nest and the queen increases the chance of propagation of their genes even though they do not reproduce themselves.
There's probably a gene for that.I have no idea about infanticide but I do recall hearing of a study recently which observed that homosexual men frequently have one or more close female relatives who are unusually fecund.
I can't find the link and the research may have since been debunked but the idea is interesting as it suggests the possibility of a gene which increases the reproductive fitness of one individual while reducing the reproductive fitness of another.Of course that assumes that being homosexual reduces your chance of reproduction.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911836</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911980</id>
	<title>Viruses</title>
	<author>Arancaytar</author>
	<datestamp>1264511580000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>4</modscore>
	<htmltext><p>Horizontal transfer isn't really over, either - we still have retroviruses.</p></htmltext>
<tokenext>Horizontal transfer is n't really over , either - we still have retroviruses .</tokentext>
<sentencetext>Horizontal transfer isn't really over, either - we still have retroviruses.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913470</id>
	<title>Re:It's what's for dinner.</title>
	<author>aqk</author>
	<datestamp>1264525860000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext>Sounds good. <br>
 <br>
Can you bring a bottle of Pinot? <br>
I promise.  We'll just watch PBS.  Or whatever you want, big boy.  I'm easy.
<br>
<br>
   <br>
    <br>
  <br>
And I  do make a magnificent Fettucini Vongole!</htmltext>
<tokenext>Sounds good .
Can you bring a bottle of Pinot ?
I promise .
We 'll just watch PBS .
Or whatever you want , big boy .
I 'm easy .
And I do make a magnificent Fettucini Vongole !</tokentext>
<sentencetext>Sounds good.
Can you bring a bottle of Pinot?
I promise.
We'll just watch PBS.
Or whatever you want, big boy.
I'm easy.
And I  do make a magnificent Fettucini Vongole!</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911776</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913096</id>
	<title>Re:Capitalism?</title>
	<author>ppanon</author>
	<datestamp>1264521480000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>3</modscore>
	<htmltext><blockquote><div><p>Which is a good point. Though really, as far as what affects us and other sexually reproducing creatures, Darwinian evolution is still 'it' more or less. The real importance of this breakthrough is in studying how the evolutionary mechanisms themselves evolved -- evolution is of course not immune to evolution.<nobr> <wbr></nobr>;) This is going to be a powerful way of thinking about how early aspects of DNA came to be.</p></div></blockquote><p>I'm not so sure about that. Endo-retro viruses might still be a major factor for more complex organisms and even chordates. I've been wondering about whether super-retro viruses that can cross-infect multiple species while carrying secondary genetic payloads would be a possible agent for punctuated equilibrium. </p><p>It's interesting that there are people with varying degrees of immunity to retro-viruses like AIDS. While AIDS is not very contagious, other retroviruses could be much more easily transmitted, so you would think that retro-viral resistance would be a very beneficial and common mutation, however it appears to be quite rare.  Why?  Well, it's possible that such mutations have drawbacks that are more frequently a disadvantage than the immunity advantage (as a parallel, sickle-cell and Thalassemia resistance to malaria), it also might be because susceptibility to retro viruses provides a significant evolutionary advantage in the Red Queen's race for complex organisms just as horizontal DNA exchange does for bacteria.</p></div>
	</htmltext>
<tokenext>Which is a good point .
Though really , as far as what affects us and other sexually reproducing creatures , Darwinian evolution is still 'it ' more or less .
The real importance of this breakthrough is in studying how the evolutionary mechanisms themselves evolved -- evolution is of course not immune to evolution .
; ) This is going to be a powerful way of thinking about how early aspects of DNA came to be.I 'm not so sure about that .
Endo-retro viruses might still be a major factor for more complex organisms and even chordates .
I 've been wondering about whether super-retro viruses that can cross-infect multiple species while carrying secondary genetic payloads would be a possible agent for punctuated equilibrium .
It 's interesting that there are people with varying degrees of immunity to retro-viruses like AIDS .
While AIDS is not very contagious , other retroviruses could be much more easily transmitted , so you would think that retro-viral resistance would be a very beneficial and common mutation , however it appears to be quite rare .
Why ? Well , it 's possible that such mutations have drawbacks that are more frequently a disadvantage than the immunity advantage ( as a parallel , sickle-cell and Thalassemia resistance to malaria ) , it also might be because susceptibility to retro viruses provides a significant evolutionary advantage in the Red Queen 's race for complex organisms just as horizontal DNA exchange does for bacteria .</tokentext>
<sentencetext>Which is a good point.
Though really, as far as what affects us and other sexually reproducing creatures, Darwinian evolution is still 'it' more or less.
The real importance of this breakthrough is in studying how the evolutionary mechanisms themselves evolved -- evolution is of course not immune to evolution.
;) This is going to be a powerful way of thinking about how early aspects of DNA came to be.I'm not so sure about that.
Endo-retro viruses might still be a major factor for more complex organisms and even chordates.
I've been wondering about whether super-retro viruses that can cross-infect multiple species while carrying secondary genetic payloads would be a possible agent for punctuated equilibrium.
It's interesting that there are people with varying degrees of immunity to retro-viruses like AIDS.
While AIDS is not very contagious, other retroviruses could be much more easily transmitted, so you would think that retro-viral resistance would be a very beneficial and common mutation, however it appears to be quite rare.
Why?  Well, it's possible that such mutations have drawbacks that are more frequently a disadvantage than the immunity advantage (as a parallel, sickle-cell and Thalassemia resistance to malaria), it also might be because susceptibility to retro viruses provides a significant evolutionary advantage in the Red Queen's race for complex organisms just as horizontal DNA exchange does for bacteria.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911936</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30915042</id>
	<title>Re:Here's A Tip, Folks</title>
	<author>Avnerus</author>
	<datestamp>1264591620000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>Have you read TFA?
From what I understand, the breakthrough in this research is not the discovery of horizontal gene transfer in microbes, but of the fact it may have been, according to their simulations, the \_primary\_ factor in the evolution of the genetic code. That means that the idea of natural selection, in the development of the genetic code, is not the regular notion of survival of the fittest individual which passes its traits vertically, but rather the joined survival of a group of organisms based on their ability to share their genetic code horizontally.</htmltext>
<tokenext>Have you read TFA ?
From what I understand , the breakthrough in this research is not the discovery of horizontal gene transfer in microbes , but of the fact it may have been , according to their simulations , the \ _primary \ _ factor in the evolution of the genetic code .
That means that the idea of natural selection , in the development of the genetic code , is not the regular notion of survival of the fittest individual which passes its traits vertically , but rather the joined survival of a group of organisms based on their ability to share their genetic code horizontally .</tokentext>
<sentencetext>Have you read TFA?
From what I understand, the breakthrough in this research is not the discovery of horizontal gene transfer in microbes, but of the fact it may have been, according to their simulations, the \_primary\_ factor in the evolution of the genetic code.
That means that the idea of natural selection, in the development of the genetic code, is not the regular notion of survival of the fittest individual which passes its traits vertically, but rather the joined survival of a group of organisms based on their ability to share their genetic code horizontally.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911972</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912290</id>
	<title>Re:It's still natural selection</title>
	<author>feepness</author>
	<datestamp>1264513980000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><div class="quote"><p>In social animals, it is the survival of the group that is driving evolution, not the survival of individual or their genes.</p></div><p>The question then becomes... <i>which group</i>.</p></div>
	</htmltext>
<tokenext>In social animals , it is the survival of the group that is driving evolution , not the survival of individual or their genes.The question then becomes... which group .</tokentext>
<sentencetext>In social animals, it is the survival of the group that is driving evolution, not the survival of individual or their genes.The question then becomes... which group.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911836</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913874</id>
	<title>Herpes</title>
	<author>Xaduurv</author>
	<datestamp>1264530120000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>A choc-chip cookie to whoever put in the herpes tag</htmltext>
<tokenext>A choc-chip cookie to whoever put in the herpes tag</tokentext>
<sentencetext>A choc-chip cookie to whoever put in the herpes tag</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911614</id>
	<title>Proven example:</title>
	<author>Monkeedude1212</author>
	<datestamp>1264509060000</datestamp>
	<modclass>Funny</modclass>
	<modscore>5</modscore>
	<htmltext><p>The first 2 parts of Spore are like Horizontal Evolution, and the later parts are all vertical.</p><p>It makes perfect sense. Clearly Will Wright is a genius.</p></htmltext>
<tokenext>The first 2 parts of Spore are like Horizontal Evolution , and the later parts are all vertical.It makes perfect sense .
Clearly Will Wright is a genius .</tokentext>
<sentencetext>The first 2 parts of Spore are like Horizontal Evolution, and the later parts are all vertical.It makes perfect sense.
Clearly Will Wright is a genius.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912826</id>
	<title>Re:Here's A Tip, Folks</title>
	<author>syousef</author>
	<datestamp>1264518660000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>3</modscore>
	<htmltext><p><i>Here's a tip, folks. The minute you see some science journalist use the word "paradigm", as in "paradigm shift" or "paradigm breaking" you can be quite certain that what follows will be neither.</i></p><p>Thank goodness! Relativity and Quantum Mechanics make my head hurt. With this wonderful insight you've provided I can crawl back into my Newtonian clockwork universe shell and ignore them!<nobr> <wbr></nobr>;-)</p><p>More seriously. Pardigms do "shift" and get "broken". It's just that almost every journalist wants to sensationalise their news piece to sell it. That doesn't mean there aren't genuine breakthroughs. Just that you can't trust a journalist to tell you about them.</p></htmltext>
<tokenext>Here 's a tip , folks .
The minute you see some science journalist use the word " paradigm " , as in " paradigm shift " or " paradigm breaking " you can be quite certain that what follows will be neither.Thank goodness !
Relativity and Quantum Mechanics make my head hurt .
With this wonderful insight you 've provided I can crawl back into my Newtonian clockwork universe shell and ignore them !
; - ) More seriously .
Pardigms do " shift " and get " broken " .
It 's just that almost every journalist wants to sensationalise their news piece to sell it .
That does n't mean there are n't genuine breakthroughs .
Just that you ca n't trust a journalist to tell you about them .</tokentext>
<sentencetext>Here's a tip, folks.
The minute you see some science journalist use the word "paradigm", as in "paradigm shift" or "paradigm breaking" you can be quite certain that what follows will be neither.Thank goodness!
Relativity and Quantum Mechanics make my head hurt.
With this wonderful insight you've provided I can crawl back into my Newtonian clockwork universe shell and ignore them!
;-)More seriously.
Pardigms do "shift" and get "broken".
It's just that almost every journalist wants to sensationalise their news piece to sell it.
That doesn't mean there aren't genuine breakthroughs.
Just that you can't trust a journalist to tell you about them.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911972</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911776</id>
	<title>It's what's for dinner.</title>
	<author>Anonymous</author>
	<datestamp>1264509960000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>3</modscore>
	<htmltext><p>I am going to come over there and take all your stuff and I'm going to kill you and take your weapons and use them for myself!!!</p><p>If you're really nice and sweet I'll beat the crap out of you and then stick you in my kitchen to make food for me.</p><p>The second is referring to mitochondria not kitchen bitches.</p></htmltext>
<tokenext>I am going to come over there and take all your stuff and I 'm going to kill you and take your weapons and use them for myself ! !
! If you 're really nice and sweet I 'll beat the crap out of you and then stick you in my kitchen to make food for me.The second is referring to mitochondria not kitchen bitches .</tokentext>
<sentencetext>I am going to come over there and take all your stuff and I'm going to kill you and take your weapons and use them for myself!!
!If you're really nice and sweet I'll beat the crap out of you and then stick you in my kitchen to make food for me.The second is referring to mitochondria not kitchen bitches.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911636</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912882</id>
	<title>Re:I realize scientists need a breakthrough</title>
	<author>Anonymous</author>
	<datestamp>1264519200000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>1</modscore>
	<htmltext><p><div class="quote"><p>The idea that some genetic material might actually be passed from ourselves to these bacteria, or the other way around, seemed to make sense. I'm not talking about large chunks of DNA, but rather a codon or two every dozen generations, or something to that effect. Given that mutations/variations are more likely to occur in two species, as opposed to one, that symbiotic relationship might have accelerated genetic changes in either, or both, species. Who knows, maybe our ability to digest some specific foodstuff (a foodstuff that we previously relied on a bacteria in our gut to help us digest/process) was derived from genetic material that originally came from a bacteria that had the ability but was passed on to us a codon at a time. Just an example.</p></div><p>Actually, this does not make sense and I can't believe this was modded insightful. Other than the fact that the structure of genes in eukaryotes (with a complex intron/exon structure) versus prokaryotes (that usually have genes structured in operons) would prevent horizontal gene transfer from occurring, passing DNA codon by codon would never work in a probabilistic sense. The hope that moving small (i.e. 3 nucleotides) piece of DNA from one organism to another would land in a gene (which is less than 2\% of the human genome) and then even land in a portion of that gene to cause a functional change (much less a positive functional change) is so infinitesimal it is absurd. Moreover, for these changes to be inherited, they would need to occur in the germ lines of a human, not in somatic cells. The location of germ line cells is kept bacteria-free under normal conditions, so no possibility of horizontal transfer.</p><p>Plus, any time you study an eukaryotic organism that has a unique ability to digest a non-typical food source (e.g. termites), it is the result of a symbiotic relationship with gut bacteria that produce enzymes (via their own genes) to digest the materials, not by DNA transfer.</p><p><div class="quote"><p>This leads me to the question of whether or not our preoccupation with sanitization/sterilization of our own bodies might be having some detrimental effect on our EVOLUTION. Is our wiping out species, to the point of extinction, actually limiting the evolutionary process, in essence limiting variation in the exchange of genetic material?</p></div><p>No. At worst it creates open niches for infectious bacteria to inhabit, but no DNA transferring is lost.</p></div>
	</htmltext>
<tokenext>The idea that some genetic material might actually be passed from ourselves to these bacteria , or the other way around , seemed to make sense .
I 'm not talking about large chunks of DNA , but rather a codon or two every dozen generations , or something to that effect .
Given that mutations/variations are more likely to occur in two species , as opposed to one , that symbiotic relationship might have accelerated genetic changes in either , or both , species .
Who knows , maybe our ability to digest some specific foodstuff ( a foodstuff that we previously relied on a bacteria in our gut to help us digest/process ) was derived from genetic material that originally came from a bacteria that had the ability but was passed on to us a codon at a time .
Just an example.Actually , this does not make sense and I ca n't believe this was modded insightful .
Other than the fact that the structure of genes in eukaryotes ( with a complex intron/exon structure ) versus prokaryotes ( that usually have genes structured in operons ) would prevent horizontal gene transfer from occurring , passing DNA codon by codon would never work in a probabilistic sense .
The hope that moving small ( i.e .
3 nucleotides ) piece of DNA from one organism to another would land in a gene ( which is less than 2 \ % of the human genome ) and then even land in a portion of that gene to cause a functional change ( much less a positive functional change ) is so infinitesimal it is absurd .
Moreover , for these changes to be inherited , they would need to occur in the germ lines of a human , not in somatic cells .
The location of germ line cells is kept bacteria-free under normal conditions , so no possibility of horizontal transfer.Plus , any time you study an eukaryotic organism that has a unique ability to digest a non-typical food source ( e.g .
termites ) , it is the result of a symbiotic relationship with gut bacteria that produce enzymes ( via their own genes ) to digest the materials , not by DNA transfer.This leads me to the question of whether or not our preoccupation with sanitization/sterilization of our own bodies might be having some detrimental effect on our EVOLUTION .
Is our wiping out species , to the point of extinction , actually limiting the evolutionary process , in essence limiting variation in the exchange of genetic material ? No .
At worst it creates open niches for infectious bacteria to inhabit , but no DNA transferring is lost .</tokentext>
<sentencetext>The idea that some genetic material might actually be passed from ourselves to these bacteria, or the other way around, seemed to make sense.
I'm not talking about large chunks of DNA, but rather a codon or two every dozen generations, or something to that effect.
Given that mutations/variations are more likely to occur in two species, as opposed to one, that symbiotic relationship might have accelerated genetic changes in either, or both, species.
Who knows, maybe our ability to digest some specific foodstuff (a foodstuff that we previously relied on a bacteria in our gut to help us digest/process) was derived from genetic material that originally came from a bacteria that had the ability but was passed on to us a codon at a time.
Just an example.Actually, this does not make sense and I can't believe this was modded insightful.
Other than the fact that the structure of genes in eukaryotes (with a complex intron/exon structure) versus prokaryotes (that usually have genes structured in operons) would prevent horizontal gene transfer from occurring, passing DNA codon by codon would never work in a probabilistic sense.
The hope that moving small (i.e.
3 nucleotides) piece of DNA from one organism to another would land in a gene (which is less than 2\% of the human genome) and then even land in a portion of that gene to cause a functional change (much less a positive functional change) is so infinitesimal it is absurd.
Moreover, for these changes to be inherited, they would need to occur in the germ lines of a human, not in somatic cells.
The location of germ line cells is kept bacteria-free under normal conditions, so no possibility of horizontal transfer.Plus, any time you study an eukaryotic organism that has a unique ability to digest a non-typical food source (e.g.
termites), it is the result of a symbiotic relationship with gut bacteria that produce enzymes (via their own genes) to digest the materials, not by DNA transfer.This leads me to the question of whether or not our preoccupation with sanitization/sterilization of our own bodies might be having some detrimental effect on our EVOLUTION.
Is our wiping out species, to the point of extinction, actually limiting the evolutionary process, in essence limiting variation in the exchange of genetic material?No.
At worst it creates open niches for infectious bacteria to inhabit, but no DNA transferring is lost.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912030</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912220</id>
	<title>Re:Original paper on arXiv</title>
	<author>radtea</author>
	<datestamp>1264513440000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>3</modscore>
	<htmltext><p><i>http://arxiv.org/abs/q-bio/0702015 [arxiv.org]</i></p><p>Ok, I've read the original paper now, and it is almost as moronic as the New Sensationalist makes it out to be.</p><p>Their argument is analogous to the following claim:</p><p>I can stand on dry land, or I can swim in the water, but there is the broad swath of territory that is neither dry land nor water so deep I can do nothing but swim in it.  Therefore, the concept of "land" (or "water") may actually be completely useless!  Aren't we clever?</p><p>Scientists have a tendency toward various kinds of conceptual realism, where they think that there is exactly one way to properly understand the universe, and the entities picked out by that way are "real" and no others are.  When they find a case that they can't crisply classify under the existing concepts there are two moves:  the smart one, that refines existing concepts and introduces new ones to deal with the boundary cases; and the idiotic one, that claims that since the existing concepts don't deal well with the new case, they must not pick out anything "real" after all and should be thrown away.</p><p>That the biological species concept fails in various ways has been known for a long time.  They are now pointing out that certain criteria that would normally be used to delineate individuals might also fail under some circumstances.  To this I say:  big deal.  The biological species concept, like the concept of Newtonian mass, is still incredibly useful in understanding reality under a wide range of circumstances, which is all a scientist can hope for.  If their new concepts--which they don't really offer--transform smoothly into the biological species concept in the appropriate circumstances I'll be interested.  Otherwise, they're just gabbling.</p></htmltext>
<tokenext>http : //arxiv.org/abs/q-bio/0702015 [ arxiv.org ] Ok , I 've read the original paper now , and it is almost as moronic as the New Sensationalist makes it out to be.Their argument is analogous to the following claim : I can stand on dry land , or I can swim in the water , but there is the broad swath of territory that is neither dry land nor water so deep I can do nothing but swim in it .
Therefore , the concept of " land " ( or " water " ) may actually be completely useless !
Are n't we clever ? Scientists have a tendency toward various kinds of conceptual realism , where they think that there is exactly one way to properly understand the universe , and the entities picked out by that way are " real " and no others are .
When they find a case that they ca n't crisply classify under the existing concepts there are two moves : the smart one , that refines existing concepts and introduces new ones to deal with the boundary cases ; and the idiotic one , that claims that since the existing concepts do n't deal well with the new case , they must not pick out anything " real " after all and should be thrown away.That the biological species concept fails in various ways has been known for a long time .
They are now pointing out that certain criteria that would normally be used to delineate individuals might also fail under some circumstances .
To this I say : big deal .
The biological species concept , like the concept of Newtonian mass , is still incredibly useful in understanding reality under a wide range of circumstances , which is all a scientist can hope for .
If their new concepts--which they do n't really offer--transform smoothly into the biological species concept in the appropriate circumstances I 'll be interested .
Otherwise , they 're just gabbling .</tokentext>
<sentencetext>http://arxiv.org/abs/q-bio/0702015 [arxiv.org]Ok, I've read the original paper now, and it is almost as moronic as the New Sensationalist makes it out to be.Their argument is analogous to the following claim:I can stand on dry land, or I can swim in the water, but there is the broad swath of territory that is neither dry land nor water so deep I can do nothing but swim in it.
Therefore, the concept of "land" (or "water") may actually be completely useless!
Aren't we clever?Scientists have a tendency toward various kinds of conceptual realism, where they think that there is exactly one way to properly understand the universe, and the entities picked out by that way are "real" and no others are.
When they find a case that they can't crisply classify under the existing concepts there are two moves:  the smart one, that refines existing concepts and introduces new ones to deal with the boundary cases; and the idiotic one, that claims that since the existing concepts don't deal well with the new case, they must not pick out anything "real" after all and should be thrown away.That the biological species concept fails in various ways has been known for a long time.
They are now pointing out that certain criteria that would normally be used to delineate individuals might also fail under some circumstances.
To this I say:  big deal.
The biological species concept, like the concept of Newtonian mass, is still incredibly useful in understanding reality under a wide range of circumstances, which is all a scientist can hope for.
If their new concepts--which they don't really offer--transform smoothly into the biological species concept in the appropriate circumstances I'll be interested.
Otherwise, they're just gabbling.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911928</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914986</id>
	<title>What we need is a paradigm shift.</title>
	<author>MrMr</author>
	<datestamp>1264591080000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>Away from paradigms and towards an evolutionary theory of the development of science.<br>
Btw, Horizontal gene transfer is only different from 'standard' evolution if you think all evolution occurs at the organism level instead of at the gene level.
<br>I could recommend an excellent book on that subject.</htmltext>
<tokenext>Away from paradigms and towards an evolutionary theory of the development of science .
Btw , Horizontal gene transfer is only different from 'standard ' evolution if you think all evolution occurs at the organism level instead of at the gene level .
I could recommend an excellent book on that subject .</tokentext>
<sentencetext>Away from paradigms and towards an evolutionary theory of the development of science.
Btw, Horizontal gene transfer is only different from 'standard' evolution if you think all evolution occurs at the organism level instead of at the gene level.
I could recommend an excellent book on that subject.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912032</id>
	<title>Genetic Manipulation?</title>
	<author>Anonymous</author>
	<datestamp>1264511940000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>yes, but not really surprising looking at jumping genes: http://en.wikipedia.org/wiki/Jumping\_genes</p><p>for me: GM might be more complicated than often thought....and maybe more dangerous.<br>do we really know what we are doing?<br>it seems there are more mechanism involved in genetics than: parent passes genes to offspring.</p></htmltext>
<tokenext>yes , but not really surprising looking at jumping genes : http : //en.wikipedia.org/wiki/Jumping \ _genesfor me : GM might be more complicated than often thought....and maybe more dangerous.do we really know what we are doing ? it seems there are more mechanism involved in genetics than : parent passes genes to offspring .</tokentext>
<sentencetext>yes, but not really surprising looking at jumping genes: http://en.wikipedia.org/wiki/Jumping\_genesfor me: GM might be more complicated than often thought....and maybe more dangerous.do we really know what we are doing?it seems there are more mechanism involved in genetics than: parent passes genes to offspring.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911786</id>
	<title>I've suspected this all along</title>
	<author>Locke2005</author>
	<datestamp>1264510020000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>I've always felt that viruses might be the driving force in evolution; they are very good at taking genes from one organism and splicing them into another. Also, one of the first traits that would have evolved after the split into two sexes would have been the ability to choose mates with traits complementary to your own, thus for higher species there is actually some intelligence driving evolution forward.</htmltext>
<tokenext>I 've always felt that viruses might be the driving force in evolution ; they are very good at taking genes from one organism and splicing them into another .
Also , one of the first traits that would have evolved after the split into two sexes would have been the ability to choose mates with traits complementary to your own , thus for higher species there is actually some intelligence driving evolution forward .</tokentext>
<sentencetext>I've always felt that viruses might be the driving force in evolution; they are very good at taking genes from one organism and splicing them into another.
Also, one of the first traits that would have evolved after the split into two sexes would have been the ability to choose mates with traits complementary to your own, thus for higher species there is actually some intelligence driving evolution forward.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912720</id>
	<title>Like mullets and backtalk...</title>
	<author>PinchDuck</author>
	<datestamp>1264517160000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>You'll grow out of it.</p></htmltext>
<tokenext>You 'll grow out of it .</tokentext>
<sentencetext>You'll grow out of it.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913722</id>
	<title>Earth is an organism</title>
	<author>Anonymous</author>
	<datestamp>1264528560000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>Its better to consider all life on Earth as part of a single organism. Makes one wonder what happens with the decimation of biodiversity.</p></htmltext>
<tokenext>Its better to consider all life on Earth as part of a single organism .
Makes one wonder what happens with the decimation of biodiversity .</tokentext>
<sentencetext>Its better to consider all life on Earth as part of a single organism.
Makes one wonder what happens with the decimation of biodiversity.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914162</id>
	<title>Re:I realize scientists need a breakthrough</title>
	<author>ajlisows</author>
	<datestamp>1264533660000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>It has been awhile, but I was once a Biochemist working in a gene therapy lab.  We encased DNA in a polymer that had proteins that would cause the package to be delivered to the desired organ attached to the polymer with PEG.  Once the package bonded to its target, the polymer had to be weak enough that it would break apart and release the DNA (of course, it had to be strong enough to get there....a very delicate balance that made this tricky.)  We would pass it off where it was administered to lab rats and expression would be measured.</p><p>I may not be precise in my numbers here, but they are close enough to illustrate the point.  Our target uptake percentage that would ensure expression was 5\%, meaning if we could deliver to the target organ and have the DNA incorporate it into the lab animal's DNA in the target organ it would be sufficient for gene therapy to be successful.  I did not highly research that number myself, but it was generally accepted to be the magic number. Anyway, to give a baseline, they periodically did control tests, where the lab rat would be administered just free floating DNA.  This is where I reach my point.  The expression in these control subjects was nearly 1\%!  Although this was under unrealistic circumstances (large quantities of a single gene injected into the target) it does go to show that the uptake of free floating DNA is probably quite common.</p></htmltext>
<tokenext>It has been awhile , but I was once a Biochemist working in a gene therapy lab .
We encased DNA in a polymer that had proteins that would cause the package to be delivered to the desired organ attached to the polymer with PEG .
Once the package bonded to its target , the polymer had to be weak enough that it would break apart and release the DNA ( of course , it had to be strong enough to get there....a very delicate balance that made this tricky .
) We would pass it off where it was administered to lab rats and expression would be measured.I may not be precise in my numbers here , but they are close enough to illustrate the point .
Our target uptake percentage that would ensure expression was 5 \ % , meaning if we could deliver to the target organ and have the DNA incorporate it into the lab animal 's DNA in the target organ it would be sufficient for gene therapy to be successful .
I did not highly research that number myself , but it was generally accepted to be the magic number .
Anyway , to give a baseline , they periodically did control tests , where the lab rat would be administered just free floating DNA .
This is where I reach my point .
The expression in these control subjects was nearly 1 \ % !
Although this was under unrealistic circumstances ( large quantities of a single gene injected into the target ) it does go to show that the uptake of free floating DNA is probably quite common .</tokentext>
<sentencetext>It has been awhile, but I was once a Biochemist working in a gene therapy lab.
We encased DNA in a polymer that had proteins that would cause the package to be delivered to the desired organ attached to the polymer with PEG.
Once the package bonded to its target, the polymer had to be weak enough that it would break apart and release the DNA (of course, it had to be strong enough to get there....a very delicate balance that made this tricky.
)  We would pass it off where it was administered to lab rats and expression would be measured.I may not be precise in my numbers here, but they are close enough to illustrate the point.
Our target uptake percentage that would ensure expression was 5\%, meaning if we could deliver to the target organ and have the DNA incorporate it into the lab animal's DNA in the target organ it would be sufficient for gene therapy to be successful.
I did not highly research that number myself, but it was generally accepted to be the magic number.
Anyway, to give a baseline, they periodically did control tests, where the lab rat would be administered just free floating DNA.
This is where I reach my point.
The expression in these control subjects was nearly 1\%!
Although this was under unrealistic circumstances (large quantities of a single gene injected into the target) it does go to show that the uptake of free floating DNA is probably quite common.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912030</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913432</id>
	<title>Swamp Thing.</title>
	<author>Somecallmechief</author>
	<datestamp>1264525260000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>His genetic heritage "selected" him for survival.  As millions of scientists simultaneously exposed themselves to vast arrays of chemicals in lab environments (with either no regard for common knowledge safety recommendations or that basic distrust of other scientists exhibiting the occasional evil laugh) and produced offspring; it was a matter of when, not if, Alex would be born.  Naturally selected to survive both explosion and immersion in a primordial stew of chemicals, he then received the genetic code of the swamp "horizontally", as it were, thus simultaneously being the fittest and taking the fittest.

I think Swamp Thing has a lesson for us all.</htmltext>
<tokenext>His genetic heritage " selected " him for survival .
As millions of scientists simultaneously exposed themselves to vast arrays of chemicals in lab environments ( with either no regard for common knowledge safety recommendations or that basic distrust of other scientists exhibiting the occasional evil laugh ) and produced offspring ; it was a matter of when , not if , Alex would be born .
Naturally selected to survive both explosion and immersion in a primordial stew of chemicals , he then received the genetic code of the swamp " horizontally " , as it were , thus simultaneously being the fittest and taking the fittest .
I think Swamp Thing has a lesson for us all .</tokentext>
<sentencetext>His genetic heritage "selected" him for survival.
As millions of scientists simultaneously exposed themselves to vast arrays of chemicals in lab environments (with either no regard for common knowledge safety recommendations or that basic distrust of other scientists exhibiting the occasional evil laugh) and produced offspring; it was a matter of when, not if, Alex would be born.
Naturally selected to survive both explosion and immersion in a primordial stew of chemicals, he then received the genetic code of the swamp "horizontally", as it were, thus simultaneously being the fittest and taking the fittest.
I think Swamp Thing has a lesson for us all.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911600</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30917222</id>
	<title>Lateral Transfer In Humans?</title>
	<author>Anonymous</author>
	<datestamp>1264607400000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>Proposed gene therapy technologies (directly inserting new/effective copies of genes into human genomes for therapeutic reasons) would amount to a - albeit engineered - form of lateral gene transfer.<br>We (humans) would then be subject to a complex and currently unpredictable hybrid of horizontal and vertical evolution.</p></htmltext>
<tokenext>Proposed gene therapy technologies ( directly inserting new/effective copies of genes into human genomes for therapeutic reasons ) would amount to a - albeit engineered - form of lateral gene transfer.We ( humans ) would then be subject to a complex and currently unpredictable hybrid of horizontal and vertical evolution .</tokentext>
<sentencetext>Proposed gene therapy technologies (directly inserting new/effective copies of genes into human genomes for therapeutic reasons) would amount to a - albeit engineered - form of lateral gene transfer.We (humans) would then be subject to a complex and currently unpredictable hybrid of horizontal and vertical evolution.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912744</id>
	<title>Re:Gene Synthesis</title>
	<author>brit74</author>
	<datestamp>1264517520000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>4</modscore>
	<htmltext><blockquote><div><p>It's not like one protein that catalyzes one reaction can simply mutate into a different protein that catalyzes a different reaction. It's more of an all or nothing thing. It doesn't seem like you would ever see transitional "evolutionary" forms of proteins for that reason.</p></div></blockquote><p>
There are instances of proteins evolving into something that does something different.
<br> <br>
"Biologists have shown that independent but similar molecular changes turned a harmless digestive enzyme into a toxin in two unrelated species -- a shrew and a lizard -- giving each a venomous bite."<br>
<a href="http://www.sciencedaily.com/releases/2009/10/091029125532.htm" title="sciencedaily.com">http://www.sciencedaily.com/releases/2009/10/091029125532.htm</a> [sciencedaily.com]
<br> <br>
Generally, what happens in these cases (where a protein evolved into a different protein with a different function) is that the original DNA sequence gets duplicated, and then one of the duplicates starts evolving (and the other copy continues to serve the same original function that it had earlier).  One of the things that evolutionary biologists do is look at protein sequences and find similar sequences within the same organism.  Very often, there's a tree-like structure showing multiple variations on a single protein within an organism.  For example, humans have multiple copies/variations on the hemoglobin gene.  They're either inactive or active at different phases in a person's life.  Example:
<br> <br>
"Fetal hemoglobin, or foetal haemoglobin, (also hemoglobin F or HbF) is the main oxygen transport protein in the fetus during the last seven months of development in the uterus and in the newborn until roughly 6 months old. Functionally, fetal hemoglobin differs most from adult hemoglobin in that it is able to bind oxygen with greater affinity than the adult form, giving the developing fetus better access to oxygen from the mother's bloodstream."<br>
<a href="http://en.wikipedia.org/wiki/Hemoglobin\_F" title="wikipedia.org">http://en.wikipedia.org/wiki/Hemoglobin\_F</a> [wikipedia.org] <br>
<a href="http://en.wikipedia.org/wiki/Hemoglobin#Types\_in\_humans" title="wikipedia.org">http://en.wikipedia.org/wiki/Hemoglobin#Types\_in\_humans</a> [wikipedia.org]
<br> <br>
There's also the case of the fish antifreeze that evolved from non-protein-coding DNA:
<br>
"Scientists at the University of Illinois have discovered an antifreeze-protein gene in cod that has evolved from non-coding or 'junk' DNA."<br>
<a href="http://www.sciencedaily.com/releases/2006/04/060404090831.htm" title="sciencedaily.com">http://www.sciencedaily.com/releases/2006/04/060404090831.htm</a> [sciencedaily.com]</p></div>
	</htmltext>
<tokenext>It 's not like one protein that catalyzes one reaction can simply mutate into a different protein that catalyzes a different reaction .
It 's more of an all or nothing thing .
It does n't seem like you would ever see transitional " evolutionary " forms of proteins for that reason .
There are instances of proteins evolving into something that does something different .
" Biologists have shown that independent but similar molecular changes turned a harmless digestive enzyme into a toxin in two unrelated species -- a shrew and a lizard -- giving each a venomous bite .
" http : //www.sciencedaily.com/releases/2009/10/091029125532.htm [ sciencedaily.com ] Generally , what happens in these cases ( where a protein evolved into a different protein with a different function ) is that the original DNA sequence gets duplicated , and then one of the duplicates starts evolving ( and the other copy continues to serve the same original function that it had earlier ) .
One of the things that evolutionary biologists do is look at protein sequences and find similar sequences within the same organism .
Very often , there 's a tree-like structure showing multiple variations on a single protein within an organism .
For example , humans have multiple copies/variations on the hemoglobin gene .
They 're either inactive or active at different phases in a person 's life .
Example : " Fetal hemoglobin , or foetal haemoglobin , ( also hemoglobin F or HbF ) is the main oxygen transport protein in the fetus during the last seven months of development in the uterus and in the newborn until roughly 6 months old .
Functionally , fetal hemoglobin differs most from adult hemoglobin in that it is able to bind oxygen with greater affinity than the adult form , giving the developing fetus better access to oxygen from the mother 's bloodstream .
" http : //en.wikipedia.org/wiki/Hemoglobin \ _F [ wikipedia.org ] http : //en.wikipedia.org/wiki/Hemoglobin # Types \ _in \ _humans [ wikipedia.org ] There 's also the case of the fish antifreeze that evolved from non-protein-coding DNA : " Scientists at the University of Illinois have discovered an antifreeze-protein gene in cod that has evolved from non-coding or 'junk ' DNA .
" http : //www.sciencedaily.com/releases/2006/04/060404090831.htm [ sciencedaily.com ]</tokentext>
<sentencetext>It's not like one protein that catalyzes one reaction can simply mutate into a different protein that catalyzes a different reaction.
It's more of an all or nothing thing.
It doesn't seem like you would ever see transitional "evolutionary" forms of proteins for that reason.
There are instances of proteins evolving into something that does something different.
"Biologists have shown that independent but similar molecular changes turned a harmless digestive enzyme into a toxin in two unrelated species -- a shrew and a lizard -- giving each a venomous bite.
"
http://www.sciencedaily.com/releases/2009/10/091029125532.htm [sciencedaily.com]
 
Generally, what happens in these cases (where a protein evolved into a different protein with a different function) is that the original DNA sequence gets duplicated, and then one of the duplicates starts evolving (and the other copy continues to serve the same original function that it had earlier).
One of the things that evolutionary biologists do is look at protein sequences and find similar sequences within the same organism.
Very often, there's a tree-like structure showing multiple variations on a single protein within an organism.
For example, humans have multiple copies/variations on the hemoglobin gene.
They're either inactive or active at different phases in a person's life.
Example:
 
"Fetal hemoglobin, or foetal haemoglobin, (also hemoglobin F or HbF) is the main oxygen transport protein in the fetus during the last seven months of development in the uterus and in the newborn until roughly 6 months old.
Functionally, fetal hemoglobin differs most from adult hemoglobin in that it is able to bind oxygen with greater affinity than the adult form, giving the developing fetus better access to oxygen from the mother's bloodstream.
"
http://en.wikipedia.org/wiki/Hemoglobin\_F [wikipedia.org] 
http://en.wikipedia.org/wiki/Hemoglobin#Types\_in\_humans [wikipedia.org]
 
There's also the case of the fish antifreeze that evolved from non-protein-coding DNA:

"Scientists at the University of Illinois have discovered an antifreeze-protein gene in cod that has evolved from non-coding or 'junk' DNA.
"
http://www.sciencedaily.com/releases/2006/04/060404090831.htm [sciencedaily.com]
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912130</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914924</id>
	<title>Re:It's what's for dinner.</title>
	<author>stifler9999</author>
	<datestamp>1264589760000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>But the Mitochlorides in me will win, Obi Wan.</htmltext>
<tokenext>But the Mitochlorides in me will win , Obi Wan .</tokentext>
<sentencetext>But the Mitochlorides in me will win, Obi Wan.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911776</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911962</id>
	<title>So how does the FSM fit into all of this?</title>
	<author>davidwr</author>
	<datestamp>1264511460000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>I mean, explain <a href="http://en.wikipedia.org/wiki/File:Touched\_by\_His\_Noodly\_Appendage.jpg" title="wikipedia.org" rel="nofollow">this</a> [wikipedia.org].</p></htmltext>
<tokenext>I mean , explain this [ wikipedia.org ] .</tokentext>
<sentencetext>I mean, explain this [wikipedia.org].</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912830</id>
	<title>Re:Gene Synthesis</title>
	<author>Anonymous</author>
	<datestamp>1264518660000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>This is one of the key issues with the origin of life. Basic life processes are made up of so many inter-connected and inter-regulating components that it creates a catch-22 in figuring out which cam first.</p><p>If I recall though, many of life's building blocks have been observed in self-replication. I do believe ssRNA had been observed self-annealed and self-propagating/self-elongating. Not sure about proteins.</p><p>One major important factor to consider is that life had all the time it needed to form, it didn't have a deadline. So if one kind of component wasn't ready, the others could just exist (dynamically) for a while until it was ready. Proto-life may have been very incomplete, and the first "cell(s)" may have "lived" for a very long time until they became able to perform metabolically at a reasonable rate, reproduce, etc.</p><p>I don't know if we'll ever be able to know what proto-life was like on Earth (assuming life originated on this planet and didn't arrive), as all the innovations of the genetic and metabolic machinery would obsolete any "lifeforms" that would just 'leave it to chance' for things to react.</p><p>It would be amazing if we found life on other celestial bodies, but it would be equally to find proto-life, assuming we could distinguish it from a pile of carbon goo.</p></htmltext>
<tokenext>This is one of the key issues with the origin of life .
Basic life processes are made up of so many inter-connected and inter-regulating components that it creates a catch-22 in figuring out which cam first.If I recall though , many of life 's building blocks have been observed in self-replication .
I do believe ssRNA had been observed self-annealed and self-propagating/self-elongating .
Not sure about proteins.One major important factor to consider is that life had all the time it needed to form , it did n't have a deadline .
So if one kind of component was n't ready , the others could just exist ( dynamically ) for a while until it was ready .
Proto-life may have been very incomplete , and the first " cell ( s ) " may have " lived " for a very long time until they became able to perform metabolically at a reasonable rate , reproduce , etc.I do n't know if we 'll ever be able to know what proto-life was like on Earth ( assuming life originated on this planet and did n't arrive ) , as all the innovations of the genetic and metabolic machinery would obsolete any " lifeforms " that would just 'leave it to chance ' for things to react.It would be amazing if we found life on other celestial bodies , but it would be equally to find proto-life , assuming we could distinguish it from a pile of carbon goo .</tokentext>
<sentencetext>This is one of the key issues with the origin of life.
Basic life processes are made up of so many inter-connected and inter-regulating components that it creates a catch-22 in figuring out which cam first.If I recall though, many of life's building blocks have been observed in self-replication.
I do believe ssRNA had been observed self-annealed and self-propagating/self-elongating.
Not sure about proteins.One major important factor to consider is that life had all the time it needed to form, it didn't have a deadline.
So if one kind of component wasn't ready, the others could just exist (dynamically) for a while until it was ready.
Proto-life may have been very incomplete, and the first "cell(s)" may have "lived" for a very long time until they became able to perform metabolically at a reasonable rate, reproduce, etc.I don't know if we'll ever be able to know what proto-life was like on Earth (assuming life originated on this planet and didn't arrive), as all the innovations of the genetic and metabolic machinery would obsolete any "lifeforms" that would just 'leave it to chance' for things to react.It would be amazing if we found life on other celestial bodies, but it would be equally to find proto-life, assuming we could distinguish it from a pile of carbon goo.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912130</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912130</id>
	<title>Gene Synthesis</title>
	<author>Anonymous</author>
	<datestamp>1264512600000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>3</modscore>
	<htmltext>One of the big difficulties I have in understanding evolution is the process of gene syntheses.  It seems reasonable that over time certain combinations of genes can win out over others, and certainly in bacteria you see this horizontal gene transfer happen all the time.  You even see it in plants now thanks to genetic engineering, and before that you saw it in a more limited way thanks to viruses and cross-pollination and things like that.  But all these things have to do with the transfer of genetic information between life-forms.<br><br>The question in my mind is where did all the genes come from in the first place.  Proteins are complex macro-molecules.  It's not like one protein that catalyzes one reaction can simply mutate into a different protein that catalyzes a different reaction.  It's more of an all or nothing thing.  It doesn't seem like you would ever see transitional "evolutionary" forms of proteins for that reason.  Worse still, you can't (as far as we know) start with a working a protein and reverse-transcribe from it into a strand of DNA or RNA that could code for it.<br><br>What do you think?</htmltext>
<tokenext>One of the big difficulties I have in understanding evolution is the process of gene syntheses .
It seems reasonable that over time certain combinations of genes can win out over others , and certainly in bacteria you see this horizontal gene transfer happen all the time .
You even see it in plants now thanks to genetic engineering , and before that you saw it in a more limited way thanks to viruses and cross-pollination and things like that .
But all these things have to do with the transfer of genetic information between life-forms.The question in my mind is where did all the genes come from in the first place .
Proteins are complex macro-molecules .
It 's not like one protein that catalyzes one reaction can simply mutate into a different protein that catalyzes a different reaction .
It 's more of an all or nothing thing .
It does n't seem like you would ever see transitional " evolutionary " forms of proteins for that reason .
Worse still , you ca n't ( as far as we know ) start with a working a protein and reverse-transcribe from it into a strand of DNA or RNA that could code for it.What do you think ?</tokentext>
<sentencetext>One of the big difficulties I have in understanding evolution is the process of gene syntheses.
It seems reasonable that over time certain combinations of genes can win out over others, and certainly in bacteria you see this horizontal gene transfer happen all the time.
You even see it in plants now thanks to genetic engineering, and before that you saw it in a more limited way thanks to viruses and cross-pollination and things like that.
But all these things have to do with the transfer of genetic information between life-forms.The question in my mind is where did all the genes come from in the first place.
Proteins are complex macro-molecules.
It's not like one protein that catalyzes one reaction can simply mutate into a different protein that catalyzes a different reaction.
It's more of an all or nothing thing.
It doesn't seem like you would ever see transitional "evolutionary" forms of proteins for that reason.
Worse still, you can't (as far as we know) start with a working a protein and reverse-transcribe from it into a strand of DNA or RNA that could code for it.What do you think?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912276</id>
	<title>Hey wait, does this mean...</title>
	<author>Redon</author>
	<datestamp>1264513800000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>...early life was open-source?!<nobr> <wbr></nobr>:D</htmltext>
<tokenext>...early life was open-source ? !
: D</tokentext>
<sentencetext>...early life was open-source?!
:D</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911666</id>
	<title>Capitalism?</title>
	<author>Anonymous</author>
	<datestamp>1264509360000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>2</modscore>
	<htmltext><p>So, would this "horizontal gene transfer" be like capitalism?
Does it become a battle to see who can acquire the most and/or
the best genes?  Do you end up with winners for a while, until the
losers get disgusted and start sparking genetic revolutions?
Would Darwinian revolution be a happy meritocracy that arose
as a kind of "compromise"?</p><p>However, I've always read Darwinian evolution as "survival of the fittest",
with no qualifier as to how you go about surviving.  It always
implied to me that the organisms (as defined by its genetic code) were
what did the surviving.  If organisms enhance their survival by
acquiring genes through means other than sex, this doesn't seem non
Darwinian to me.  It just seems like a deeper understanding of evolution.</p><p>The more intriguing possibility, with serious impliations for us humans,
is "intentional evolution".  In other words, organisms purposefully manipulating
their own genes.  That actually might be considered a radical enough change
to give it a new name:  Recursive Evolution.</p></htmltext>
<tokenext>So , would this " horizontal gene transfer " be like capitalism ?
Does it become a battle to see who can acquire the most and/or the best genes ?
Do you end up with winners for a while , until the losers get disgusted and start sparking genetic revolutions ?
Would Darwinian revolution be a happy meritocracy that arose as a kind of " compromise " ? However , I 've always read Darwinian evolution as " survival of the fittest " , with no qualifier as to how you go about surviving .
It always implied to me that the organisms ( as defined by its genetic code ) were what did the surviving .
If organisms enhance their survival by acquiring genes through means other than sex , this does n't seem non Darwinian to me .
It just seems like a deeper understanding of evolution.The more intriguing possibility , with serious impliations for us humans , is " intentional evolution " .
In other words , organisms purposefully manipulating their own genes .
That actually might be considered a radical enough change to give it a new name : Recursive Evolution .</tokentext>
<sentencetext>So, would this "horizontal gene transfer" be like capitalism?
Does it become a battle to see who can acquire the most and/or
the best genes?
Do you end up with winners for a while, until the
losers get disgusted and start sparking genetic revolutions?
Would Darwinian revolution be a happy meritocracy that arose
as a kind of "compromise"?However, I've always read Darwinian evolution as "survival of the fittest",
with no qualifier as to how you go about surviving.
It always
implied to me that the organisms (as defined by its genetic code) were
what did the surviving.
If organisms enhance their survival by
acquiring genes through means other than sex, this doesn't seem non
Darwinian to me.
It just seems like a deeper understanding of evolution.The more intriguing possibility, with serious impliations for us humans,
is "intentional evolution".
In other words, organisms purposefully manipulating
their own genes.
That actually might be considered a radical enough change
to give it a new name:  Recursive Evolution.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913674</id>
	<title>Re:Here's A Tip, Folks</title>
	<author>Anonymous</author>
	<datestamp>1264528020000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>1</modscore>
	<htmltext><p>Another way of thinking about horizontal gene transfer is that it's exactly like Darwinian evolution, but with the evolutionary units competing amongst themselves being the genes rather than the organisms.  This is nothing new - this viewpoint was promulgated by Dawkins in "The Selfish Gene" back in the 70s.</p></htmltext>
<tokenext>Another way of thinking about horizontal gene transfer is that it 's exactly like Darwinian evolution , but with the evolutionary units competing amongst themselves being the genes rather than the organisms .
This is nothing new - this viewpoint was promulgated by Dawkins in " The Selfish Gene " back in the 70s .</tokentext>
<sentencetext>Another way of thinking about horizontal gene transfer is that it's exactly like Darwinian evolution, but with the evolutionary units competing amongst themselves being the genes rather than the organisms.
This is nothing new - this viewpoint was promulgated by Dawkins in "The Selfish Gene" back in the 70s.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912132</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912878</id>
	<title>Re:It's still natural selection</title>
	<author>Anonymous</author>
	<datestamp>1264519200000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>This is a common misconception, there is no group selection in current evolutionary theory. Altruism is not valuable for the individual because there is only one copy of each, but it's valuable for a gene because it might be copied several times in other  individuals. In other words, when you sacrifice yourself to save 8 of your cousins you might be saving an average of 2 copies of your genes, which is all natural selection cares about. It's still survival of the fittest gene, not of one particular copy of the gene, but of the gene as a unit of information that can be replicated in several individuals.</p></htmltext>
<tokenext>This is a common misconception , there is no group selection in current evolutionary theory .
Altruism is not valuable for the individual because there is only one copy of each , but it 's valuable for a gene because it might be copied several times in other individuals .
In other words , when you sacrifice yourself to save 8 of your cousins you might be saving an average of 2 copies of your genes , which is all natural selection cares about .
It 's still survival of the fittest gene , not of one particular copy of the gene , but of the gene as a unit of information that can be replicated in several individuals .</tokentext>
<sentencetext>This is a common misconception, there is no group selection in current evolutionary theory.
Altruism is not valuable for the individual because there is only one copy of each, but it's valuable for a gene because it might be copied several times in other  individuals.
In other words, when you sacrifice yourself to save 8 of your cousins you might be saving an average of 2 copies of your genes, which is all natural selection cares about.
It's still survival of the fittest gene, not of one particular copy of the gene, but of the gene as a unit of information that can be replicated in several individuals.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911836</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912038</id>
	<title>darwinism doesn't even support evolution....</title>
	<author>scrout</author>
	<datestamp>1264512000000</datestamp>
	<modclass>None</modclass>
	<modscore>-1</modscore>
	<htmltext>Finches beaks evolve depending on environmental factors = one species evolves to another...NOT.
Since proving something as complex as DNA evolved is somewhat problematic, especially to mathematicians, something new will have to be proposed....</htmltext>
<tokenext>Finches beaks evolve depending on environmental factors = one species evolves to another...NOT .
Since proving something as complex as DNA evolved is somewhat problematic , especially to mathematicians , something new will have to be proposed... .</tokentext>
<sentencetext>Finches beaks evolve depending on environmental factors = one species evolves to another...NOT.
Since proving something as complex as DNA evolved is somewhat problematic, especially to mathematicians, something new will have to be proposed....</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912398</id>
	<title>Re:Gene Synthesis</title>
	<author>maxume</author>
	<datestamp>1264514700000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>I think you are overestimating your ability to cope with several billion years.</p><p>(I'm not insisting that I am any better at it, but I am willing to believe that lots of things can happen in 1 billion years, no matter how improbable)</p></htmltext>
<tokenext>I think you are overestimating your ability to cope with several billion years .
( I 'm not insisting that I am any better at it , but I am willing to believe that lots of things can happen in 1 billion years , no matter how improbable )</tokentext>
<sentencetext>I think you are overestimating your ability to cope with several billion years.
(I'm not insisting that I am any better at it, but I am willing to believe that lots of things can happen in 1 billion years, no matter how improbable)</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912130</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912102</id>
	<title>Objectors vs. Occurs in nature</title>
	<author>DragonWriter</author>
	<datestamp>1264512420000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><blockquote><div><p>As a side note... I wonder if the fact this occurs in nature will silence some of the people objecting to genetic splicing?</p></div></blockquote><p>Has the fact that miscarriage occurs in nature silenced the people objecting to induced abortion?</p><p>Has the fact that death occurs in nature silenced the people objecting to murder?</p><p>Has the fact that group conflicts over territory occur in nature silenced the people objecting to war?</p><p>Has the fact that climate changes occur in nature silenced the people objecting to human actions which contribute to climate change?</p><p>In general "<i>X</i> occurs in nature" does not silence people who object to humans choosing actions which use or result in <i>X</i> or something very much like it.</p></div>
	</htmltext>
<tokenext>As a side note... I wonder if the fact this occurs in nature will silence some of the people objecting to genetic splicing ? Has the fact that miscarriage occurs in nature silenced the people objecting to induced abortion ? Has the fact that death occurs in nature silenced the people objecting to murder ? Has the fact that group conflicts over territory occur in nature silenced the people objecting to war ? Has the fact that climate changes occur in nature silenced the people objecting to human actions which contribute to climate change ? In general " X occurs in nature " does not silence people who object to humans choosing actions which use or result in X or something very much like it .</tokentext>
<sentencetext>As a side note... I wonder if the fact this occurs in nature will silence some of the people objecting to genetic splicing?Has the fact that miscarriage occurs in nature silenced the people objecting to induced abortion?Has the fact that death occurs in nature silenced the people objecting to murder?Has the fact that group conflicts over territory occur in nature silenced the people objecting to war?Has the fact that climate changes occur in nature silenced the people objecting to human actions which contribute to climate change?In general "X occurs in nature" does not silence people who object to humans choosing actions which use or result in X or something very much like it.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911784</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913028</id>
	<title>They are the same in the beginning</title>
	<author>copponex</author>
	<datestamp>1264520580000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext><p>You're right - religion and science are the same in one sense. They are guesses at what reality is.</p><p>The largest difference is that science acknowledges that it is a guess. A very educated guess, which yes yielded modern life as we know it. Religion tries to claim that it is the truth, and the only truth, and expects it's adherents to doggedly follow it's rules and values way beyond their useful context. To give you an example, a slashdot poster recently gave a ridiculously long opinion on whether pig meat cultivated in a lab would be kosher or not.</p><p>Now, religion in it's early days claimed to heal the sick, to make the blind see, and to allow the lame to walk again. It has never done any of these things. Science, on the other hand, has done all of these things and much more. I'll stick with the continued results of the scientific method. You can keep your bronze age mysticism.</p></htmltext>
<tokenext>You 're right - religion and science are the same in one sense .
They are guesses at what reality is.The largest difference is that science acknowledges that it is a guess .
A very educated guess , which yes yielded modern life as we know it .
Religion tries to claim that it is the truth , and the only truth , and expects it 's adherents to doggedly follow it 's rules and values way beyond their useful context .
To give you an example , a slashdot poster recently gave a ridiculously long opinion on whether pig meat cultivated in a lab would be kosher or not.Now , religion in it 's early days claimed to heal the sick , to make the blind see , and to allow the lame to walk again .
It has never done any of these things .
Science , on the other hand , has done all of these things and much more .
I 'll stick with the continued results of the scientific method .
You can keep your bronze age mysticism .</tokentext>
<sentencetext>You're right - religion and science are the same in one sense.
They are guesses at what reality is.The largest difference is that science acknowledges that it is a guess.
A very educated guess, which yes yielded modern life as we know it.
Religion tries to claim that it is the truth, and the only truth, and expects it's adherents to doggedly follow it's rules and values way beyond their useful context.
To give you an example, a slashdot poster recently gave a ridiculously long opinion on whether pig meat cultivated in a lab would be kosher or not.Now, religion in it's early days claimed to heal the sick, to make the blind see, and to allow the lame to walk again.
It has never done any of these things.
Science, on the other hand, has done all of these things and much more.
I'll stick with the continued results of the scientific method.
You can keep your bronze age mysticism.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912246</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30916856</id>
	<title>Creationists are reading this article</title>
	<author>jmbeck15</author>
	<datestamp>1264605840000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext>...to see if this news bodes well for them, and then reading these comments, to see if someone here can spin it to fit.</htmltext>
<tokenext>...to see if this news bodes well for them , and then reading these comments , to see if someone here can spin it to fit .</tokentext>
<sentencetext>...to see if this news bodes well for them, and then reading these comments, to see if someone here can spin it to fit.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911878</id>
	<title>Re:I dunno...</title>
	<author>girlintraining</author>
	<datestamp>1264510800000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><div class="quote"><p>I pass on my genes horizontally</p></div><p>Roses are red, genes are blue,<br>their mistakes are small, and very rare,<br>as long as you discount, Dupple's hair.<br>*cough*<br>Anyway, I don't care what's in your genes as long as you stay out of mine.<nobr> <wbr></nobr>:P</p></div>
	</htmltext>
<tokenext>I pass on my genes horizontallyRoses are red , genes are blue,their mistakes are small , and very rare,as long as you discount , Dupple 's hair .
* cough * Anyway , I do n't care what 's in your genes as long as you stay out of mine .
: P</tokentext>
<sentencetext>I pass on my genes horizontallyRoses are red, genes are blue,their mistakes are small, and very rare,as long as you discount, Dupple's hair.
*cough*Anyway, I don't care what's in your genes as long as you stay out of mine.
:P
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911712</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30916842</id>
	<title>Re:Here's A Tip, Folks</title>
	<author>Anonymous</author>
	<datestamp>1264605720000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>no, you're wrong. it's definitely jesus.</p></htmltext>
<tokenext>no , you 're wrong .
it 's definitely jesus .</tokentext>
<sentencetext>no, you're wrong.
it's definitely jesus.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911972</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30918538</id>
	<title>Programming Consequences</title>
	<author>Anonymous</author>
	<datestamp>1264612320000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>Time to dump OOP inheritance hierarchies and all those cute little animal training examples and replace it with set theory. No wonder my classes grew so messy over time. In the real world, features are promiscuous.</p></htmltext>
<tokenext>Time to dump OOP inheritance hierarchies and all those cute little animal training examples and replace it with set theory .
No wonder my classes grew so messy over time .
In the real world , features are promiscuous .</tokentext>
<sentencetext>Time to dump OOP inheritance hierarchies and all those cute little animal training examples and replace it with set theory.
No wonder my classes grew so messy over time.
In the real world, features are promiscuous.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913800</id>
	<title>I have a theory</title>
	<author>JimboFBX</author>
	<datestamp>1264529280000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>I have a theory that "genetic momentum", for lack of a better term, exists. Its where you have genes that dictate what your children will have, sort of like code that writes its own code. This kind of phenomena would allow for, for example, giraffes to evolve fairly quickly because there would be a gene that gives their children a longer neck than themselves. This could be the function of what is known as "junk" DNA. Of course, I would like to know if anyone else has heard of something like this, and if it has been proven to exist or not.</htmltext>
<tokenext>I have a theory that " genetic momentum " , for lack of a better term , exists .
Its where you have genes that dictate what your children will have , sort of like code that writes its own code .
This kind of phenomena would allow for , for example , giraffes to evolve fairly quickly because there would be a gene that gives their children a longer neck than themselves .
This could be the function of what is known as " junk " DNA .
Of course , I would like to know if anyone else has heard of something like this , and if it has been proven to exist or not .</tokentext>
<sentencetext>I have a theory that "genetic momentum", for lack of a better term, exists.
Its where you have genes that dictate what your children will have, sort of like code that writes its own code.
This kind of phenomena would allow for, for example, giraffes to evolve fairly quickly because there would be a gene that gives their children a longer neck than themselves.
This could be the function of what is known as "junk" DNA.
Of course, I would like to know if anyone else has heard of something like this, and if it has been proven to exist or not.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912504</id>
	<title>Recent evidence for horizontal gene transfer</title>
	<author>ther.geek</author>
	<datestamp>1264515360000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>Spider-man and Batman are the proof of horizontal gene transfer theory.</htmltext>
<tokenext>Spider-man and Batman are the proof of horizontal gene transfer theory .</tokentext>
<sentencetext>Spider-man and Batman are the proof of horizontal gene transfer theory.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911704</id>
	<title>Once again</title>
	<author>copponex</author>
	<datestamp>1264509600000</datestamp>
	<modclass>Funny</modclass>
	<modscore>5</modscore>
	<htmltext><p>You know, scientists just keep reforming their ideas until it conforms to observable reality. How can they expect anyone to believe what they say when they're just going to keep changing their minds?</p><p>I prefer my religion. It allows me to conform reality to my ideas.</p></htmltext>
<tokenext>You know , scientists just keep reforming their ideas until it conforms to observable reality .
How can they expect anyone to believe what they say when they 're just going to keep changing their minds ? I prefer my religion .
It allows me to conform reality to my ideas .</tokentext>
<sentencetext>You know, scientists just keep reforming their ideas until it conforms to observable reality.
How can they expect anyone to believe what they say when they're just going to keep changing their minds?I prefer my religion.
It allows me to conform reality to my ideas.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913274</id>
	<title>I don't know about horizontal evolution but...</title>
	<author>lindseyp</author>
	<datestamp>1264523400000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>it was certainly horizontal gymnastics that led to my kid's genetic code being built.</p></htmltext>
<tokenext>it was certainly horizontal gymnastics that led to my kid 's genetic code being built .</tokentext>
<sentencetext>it was certainly horizontal gymnastics that led to my kid's genetic code being built.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912436</id>
	<title>Its still evolution virtical or horizontal.</title>
	<author>Anonymous</author>
	<datestamp>1264514880000</datestamp>
	<modclass>Flamebait</modclass>
	<modscore>-1</modscore>
	<htmltext><p>Just one more bullet in the killing of gods.</p></htmltext>
<tokenext>Just one more bullet in the killing of gods .</tokentext>
<sentencetext>Just one more bullet in the killing of gods.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912514</id>
	<title>Darwinian Evolution Considered As a Phase</title>
	<author>Phizzle</author>
	<datestamp>1264515420000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>between Creationism and Global Warming!!! OMGZ</htmltext>
<tokenext>between Creationism and Global Warming ! ! !
OMGZ</tokentext>
<sentencetext>between Creationism and Global Warming!!!
OMGZ</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911700</id>
	<title>You Need the Right Tools</title>
	<author>Favonius Cornelius</author>
	<datestamp>1264509540000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext>I guess you could push horizontal genetic flow with viruses in the higher organisms, like us. In general however, horizontal genetic flow occurs between plants and bacteria because they have the molecular mechanisims for it.


If anything it would suggest horizontal genetic flow was the first stage of evolution, with classic evolution taking over more so as time moved forward since higher organisms have a higher need to maintain genetic continuity due to specific and more complicated form.


For instance you have chromosomal ploidy in plants because they follow a different evolutionary strategy: stay in place, but grow as much as possible to aquire resources. In this case genetic diversity may help. In the ambultory mammal however, it wants to retain a very specific morphology to keep doing what it does, therefore it maintains a more rigid genetic control and linear evolution.</htmltext>
<tokenext>I guess you could push horizontal genetic flow with viruses in the higher organisms , like us .
In general however , horizontal genetic flow occurs between plants and bacteria because they have the molecular mechanisims for it .
If anything it would suggest horizontal genetic flow was the first stage of evolution , with classic evolution taking over more so as time moved forward since higher organisms have a higher need to maintain genetic continuity due to specific and more complicated form .
For instance you have chromosomal ploidy in plants because they follow a different evolutionary strategy : stay in place , but grow as much as possible to aquire resources .
In this case genetic diversity may help .
In the ambultory mammal however , it wants to retain a very specific morphology to keep doing what it does , therefore it maintains a more rigid genetic control and linear evolution .</tokentext>
<sentencetext>I guess you could push horizontal genetic flow with viruses in the higher organisms, like us.
In general however, horizontal genetic flow occurs between plants and bacteria because they have the molecular mechanisims for it.
If anything it would suggest horizontal genetic flow was the first stage of evolution, with classic evolution taking over more so as time moved forward since higher organisms have a higher need to maintain genetic continuity due to specific and more complicated form.
For instance you have chromosomal ploidy in plants because they follow a different evolutionary strategy: stay in place, but grow as much as possible to aquire resources.
In this case genetic diversity may help.
In the ambultory mammal however, it wants to retain a very specific morphology to keep doing what it does, therefore it maintains a more rigid genetic control and linear evolution.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30918068</id>
	<title>Re:Here's A Tip, Folks</title>
	<author>omfglearntoplay</author>
	<datestamp>1264610640000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>It all reminds me of Alien 4: resurrection, when Ripley's clones have her genes mixed with the alien genes. So if you could pick, what organism would you want to borrow some genes from? I'm thinking a dragon... half-dragon characters in DnD seem pretty well off.<nobr> <wbr></nobr>:)</p></htmltext>
<tokenext>It all reminds me of Alien 4 : resurrection , when Ripley 's clones have her genes mixed with the alien genes .
So if you could pick , what organism would you want to borrow some genes from ?
I 'm thinking a dragon... half-dragon characters in DnD seem pretty well off .
: )</tokentext>
<sentencetext>It all reminds me of Alien 4: resurrection, when Ripley's clones have her genes mixed with the alien genes.
So if you could pick, what organism would you want to borrow some genes from?
I'm thinking a dragon... half-dragon characters in DnD seem pretty well off.
:)</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911972</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911804</id>
	<title>I've heard of this</title>
	<author>Beerdood</author>
	<datestamp>1264510200000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext>From TFA :
<i> Suppose that a process he never wrote about, and never even imagined, has been controlling the evolution of life throughout most of the Earth's history</i>
<br> <br>
Intelligent Design?</htmltext>
<tokenext>From TFA : Suppose that a process he never wrote about , and never even imagined , has been controlling the evolution of life throughout most of the Earth 's history Intelligent Design ?</tokentext>
<sentencetext>From TFA :
 Suppose that a process he never wrote about, and never even imagined, has been controlling the evolution of life throughout most of the Earth's history
 
Intelligent Design?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912768</id>
	<title>Re:Once again</title>
	<author>Opportunist</author>
	<datestamp>1264517700000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>You conform reality to your ideas? You change reality by the power of your will?</p><p>Yo're practicing witchcraft! WITCH! BURN IT!</p></htmltext>
<tokenext>You conform reality to your ideas ?
You change reality by the power of your will ? Yo 're practicing witchcraft !
WITCH ! BURN IT !</tokentext>
<sentencetext>You conform reality to your ideas?
You change reality by the power of your will?Yo're practicing witchcraft!
WITCH! BURN IT!</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911704</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911724</id>
	<title>It's still natural selection</title>
	<author>BenBoy</author>
	<datestamp>1264509660000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>4</modscore>
	<htmltext>This really isn't entirely new; Dawkins' book <a href="http://www.amazon.com/Selfish-Gene-Anniversary-Introduction/dp/0199291152/ref=sr\_1\_1?ie=UTF8&amp;s=books&amp;qid=1264549144&amp;sr=8-1" title="amazon.com" rel="nofollow">The Selfish Gene</a> [amazon.com] is based around the idea that it's individual <b>genes</b> that are selected for, not organisms.</htmltext>
<tokenext>This really is n't entirely new ; Dawkins ' book The Selfish Gene [ amazon.com ] is based around the idea that it 's individual genes that are selected for , not organisms .</tokentext>
<sentencetext>This really isn't entirely new; Dawkins' book The Selfish Gene [amazon.com] is based around the idea that it's individual genes that are selected for, not organisms.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913194</id>
	<title>Jumpin' Genes, Grandma!</title>
	<author>thomst</author>
	<datestamp>1264522500000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>Does this remind anyone else of Greg Bear's Darwin's Radio/Darwin's Children duology? 'Cause it sure reminds <b>me</b> of them!</htmltext>
<tokenext>Does this remind anyone else of Greg Bear 's Darwin 's Radio/Darwin 's Children duology ?
'Cause it sure reminds me of them !</tokentext>
<sentencetext>Does this remind anyone else of Greg Bear's Darwin's Radio/Darwin's Children duology?
'Cause it sure reminds me of them!</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912264</id>
	<title>Re:I realize scientists need a breakthrough</title>
	<author>Anonymous</author>
	<datestamp>1264513740000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>All I know is the story I heard when I was still a little kid, that chlorophyll wasn't originally a part of plants.</p><p>It was somewhat like the "horizontal transfer" thingy, and got merged into the plant's genetic code.</p></htmltext>
<tokenext>All I know is the story I heard when I was still a little kid , that chlorophyll was n't originally a part of plants.It was somewhat like the " horizontal transfer " thingy , and got merged into the plant 's genetic code .</tokentext>
<sentencetext>All I know is the story I heard when I was still a little kid, that chlorophyll wasn't originally a part of plants.It was somewhat like the "horizontal transfer" thingy, and got merged into the plant's genetic code.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911600</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913040</id>
	<title>Re:Well duh?</title>
	<author>claar</author>
	<datestamp>1264520640000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><div class="quote"><p>the religious nuts</p></div><p>Completely unnecessary.  While I may personally be a bit nutty, I never cease to be amazed at how the "tolerant left" is anything but.</p></div>
	</htmltext>
<tokenext>the religious nutsCompletely unnecessary .
While I may personally be a bit nutty , I never cease to be amazed at how the " tolerant left " is anything but .</tokentext>
<sentencetext>the religious nutsCompletely unnecessary.
While I may personally be a bit nutty, I never cease to be amazed at how the "tolerant left" is anything but.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911636</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912778</id>
	<title>The funny thing is</title>
	<author>WindBourne</author>
	<datestamp>1264517880000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>That I have been saying that here for the last 8 years. And this was talked at in the CDC lab that I worked at back in 1981. IOW, this is not a new theory. All you have to do is pay attention to how things are jumping. It has everything to do with bio density of population and how fast virus mutates. It also has to do with the blood transfusions in which we transfer these virus.
<br> <br>My guess is that a number of asymptomatic virus exists that are slowly able to move from species to species. Those will increase our evolution. Oddly, it means that it will allow us to pick up diseases that take decades to show. My guess is that when we have a colony on Mars, we will get to see evolution difference show up.</htmltext>
<tokenext>That I have been saying that here for the last 8 years .
And this was talked at in the CDC lab that I worked at back in 1981 .
IOW , this is not a new theory .
All you have to do is pay attention to how things are jumping .
It has everything to do with bio density of population and how fast virus mutates .
It also has to do with the blood transfusions in which we transfer these virus .
My guess is that a number of asymptomatic virus exists that are slowly able to move from species to species .
Those will increase our evolution .
Oddly , it means that it will allow us to pick up diseases that take decades to show .
My guess is that when we have a colony on Mars , we will get to see evolution difference show up .</tokentext>
<sentencetext>That I have been saying that here for the last 8 years.
And this was talked at in the CDC lab that I worked at back in 1981.
IOW, this is not a new theory.
All you have to do is pay attention to how things are jumping.
It has everything to do with bio density of population and how fast virus mutates.
It also has to do with the blood transfusions in which we transfer these virus.
My guess is that a number of asymptomatic virus exists that are slowly able to move from species to species.
Those will increase our evolution.
Oddly, it means that it will allow us to pick up diseases that take decades to show.
My guess is that when we have a colony on Mars, we will get to see evolution difference show up.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914182</id>
	<title>gene modification is not evolution</title>
	<author>Nowhere.Men</author>
	<datestamp>1264533960000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>How the individuals changes ( horizontal or vertical gene modification, OGM) is separate from the selection effects that drives evolution.</p><p>In his lab, a scientist may come up with lot of gene modification but only the one he will be able to sell (one selection effect, Darwin may not have though about)) will go into the fields where they can breed with the wild flora.</p></htmltext>
<tokenext>How the individuals changes ( horizontal or vertical gene modification , OGM ) is separate from the selection effects that drives evolution.In his lab , a scientist may come up with lot of gene modification but only the one he will be able to sell ( one selection effect , Darwin may not have though about ) ) will go into the fields where they can breed with the wild flora .</tokentext>
<sentencetext>How the individuals changes ( horizontal or vertical gene modification, OGM) is separate from the selection effects that drives evolution.In his lab, a scientist may come up with lot of gene modification but only the one he will be able to sell (one selection effect, Darwin may not have though about)) will go into the fields where they can breed with the wild flora.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911600</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911810</id>
	<title>Only horizontally? How quaint</title>
	<author>Anonymous</author>
	<datestamp>1264510260000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>You're not nearly adventurous enough, young lad!</p><p>Then again.. I've always thought the guy who's getting it on standing upright in his Corvette convertible is destined for a Darwin Award, so there might be something to this story</p></htmltext>
<tokenext>You 're not nearly adventurous enough , young lad ! Then again.. I 've always thought the guy who 's getting it on standing upright in his Corvette convertible is destined for a Darwin Award , so there might be something to this story</tokentext>
<sentencetext>You're not nearly adventurous enough, young lad!Then again.. I've always thought the guy who's getting it on standing upright in his Corvette convertible is destined for a Darwin Award, so there might be something to this story</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911712</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911972</id>
	<title>Here's A Tip, Folks</title>
	<author>MightyMartian</author>
	<datestamp>1264511460000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>4</modscore>
	<htmltext><p>Here's a tip, folks.  The minute you see some science journalist use the word "paradigm", as in "paradigm shift" or "paradigm breaking" you can be quite certain that what follows will be neither.</p><p>Horizontal gene transfer has been known about for decades, and the notion that the root of the tree of life is more a tangle of interconnecting branches has pretty much been accepted for some time now.  We know that particularly with prokaryotes, horizontal transfer happens, and that while more difficult with eukaryotes, can still happen (ie. endo-retroviral insertions).  It is yet another facet of evolution, not some independent force.</p></htmltext>
<tokenext>Here 's a tip , folks .
The minute you see some science journalist use the word " paradigm " , as in " paradigm shift " or " paradigm breaking " you can be quite certain that what follows will be neither.Horizontal gene transfer has been known about for decades , and the notion that the root of the tree of life is more a tangle of interconnecting branches has pretty much been accepted for some time now .
We know that particularly with prokaryotes , horizontal transfer happens , and that while more difficult with eukaryotes , can still happen ( ie .
endo-retroviral insertions ) .
It is yet another facet of evolution , not some independent force .</tokentext>
<sentencetext>Here's a tip, folks.
The minute you see some science journalist use the word "paradigm", as in "paradigm shift" or "paradigm breaking" you can be quite certain that what follows will be neither.Horizontal gene transfer has been known about for decades, and the notion that the root of the tree of life is more a tangle of interconnecting branches has pretty much been accepted for some time now.
We know that particularly with prokaryotes, horizontal transfer happens, and that while more difficult with eukaryotes, can still happen (ie.
endo-retroviral insertions).
It is yet another facet of evolution, not some independent force.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911600</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30916322</id>
	<title>Re:I realize scientists need a breakthrough</title>
	<author>hesaigo999ca</author>
	<datestamp>1264603200000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Yes, as well, one bacteria originating from one source affects another...so let's say a dog has a virus that spreads to humans, and makes the humans susceptible or immune to that virus, but leaves a trace that mutates in the genes further generations down the line...this is what I am thinking they mean, cross species barriers being bypassed....and ending up mutating due to evolution.</p></htmltext>
<tokenext>Yes , as well , one bacteria originating from one source affects another...so let 's say a dog has a virus that spreads to humans , and makes the humans susceptible or immune to that virus , but leaves a trace that mutates in the genes further generations down the line...this is what I am thinking they mean , cross species barriers being bypassed....and ending up mutating due to evolution .</tokentext>
<sentencetext>Yes, as well, one bacteria originating from one source affects another...so let's say a dog has a virus that spreads to humans, and makes the humans susceptible or immune to that virus, but leaves a trace that mutates in the genes further generations down the line...this is what I am thinking they mean, cross species barriers being bypassed....and ending up mutating due to evolution.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911600</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912150</id>
	<title>Let me explain...</title>
	<author>denzacar</author>
	<datestamp>1264512840000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>3</modscore>
	<htmltext><p><div class="quote"><p>Just why is it that ultra-conservative rants about God or racial superiority or anti-socialism are instantly modded off-topic, troll, and/or flamebait until they sink beneath the thresh hold and yet completely off-topic attacks on Creationism in every story even vaguely connected with biology or evolution get modded +5 insightful?</p></div><p>Same reason why at least someone will look favorably on the fact that you may have served pizza for desert, while you will be forever banished from the kitchen (and other places) if you serve up a pile of dung.</p><p>Both are off-topic, but while one still satisfies the basic requirements - the other is a pile of shit.</p><p>In the case of pizza - it is still food; in case of pointing out the errors of creationism - it is still a discussion about evolutionary theories, it only digresses towards pointing out the wrong ones.<br>Creationism and a plate full of dung - a pile of shit.</p></div>
	</htmltext>
<tokenext>Just why is it that ultra-conservative rants about God or racial superiority or anti-socialism are instantly modded off-topic , troll , and/or flamebait until they sink beneath the thresh hold and yet completely off-topic attacks on Creationism in every story even vaguely connected with biology or evolution get modded + 5 insightful ? Same reason why at least someone will look favorably on the fact that you may have served pizza for desert , while you will be forever banished from the kitchen ( and other places ) if you serve up a pile of dung.Both are off-topic , but while one still satisfies the basic requirements - the other is a pile of shit.In the case of pizza - it is still food ; in case of pointing out the errors of creationism - it is still a discussion about evolutionary theories , it only digresses towards pointing out the wrong ones.Creationism and a plate full of dung - a pile of shit .</tokentext>
<sentencetext>Just why is it that ultra-conservative rants about God or racial superiority or anti-socialism are instantly modded off-topic, troll, and/or flamebait until they sink beneath the thresh hold and yet completely off-topic attacks on Creationism in every story even vaguely connected with biology or evolution get modded +5 insightful?Same reason why at least someone will look favorably on the fact that you may have served pizza for desert, while you will be forever banished from the kitchen (and other places) if you serve up a pile of dung.Both are off-topic, but while one still satisfies the basic requirements - the other is a pile of shit.In the case of pizza - it is still food; in case of pointing out the errors of creationism - it is still a discussion about evolutionary theories, it only digresses towards pointing out the wrong ones.Creationism and a plate full of dung - a pile of shit.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912010</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911996</id>
	<title>hopefully faggots are only a phase</title>
	<author>Anonymous</author>
	<datestamp>1264511640000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext>i hope they all die out forever</htmltext>
<tokenext>i hope they all die out forever</tokentext>
<sentencetext>i hope they all die out forever</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912002</id>
	<title>Fascinating</title>
	<author>koan</author>
	<datestamp>1264511700000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>As to the vector for horizontal transmission of genetic material how about viruses?</p></htmltext>
<tokenext>As to the vector for horizontal transmission of genetic material how about viruses ?</tokentext>
<sentencetext>As to the vector for horizontal transmission of genetic material how about viruses?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913852</id>
	<title>Evolution cannot explain error-resistant DNA</title>
	<author>davide marney</author>
	<datestamp>1264529820000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>From the article:</p><blockquote><div><p>Though [the genetic code] was discovered in the 1960s, no one had been able to explain how evolution could have made it so exquisitely tuned to resisting errors. Mutations happen in DNA coding all the time, and yet the proteins it produces often remain unaffected by these glitches. Darwinian evolution simply cannot explain how such a code could arise. But horizontal gene transfer can, say Woese and Goldenfeld.</p></div></blockquote><p>Interesting.</p></div>
	</htmltext>
<tokenext>From the article : Though [ the genetic code ] was discovered in the 1960s , no one had been able to explain how evolution could have made it so exquisitely tuned to resisting errors .
Mutations happen in DNA coding all the time , and yet the proteins it produces often remain unaffected by these glitches .
Darwinian evolution simply can not explain how such a code could arise .
But horizontal gene transfer can , say Woese and Goldenfeld.Interesting .</tokentext>
<sentencetext>From the article:Though [the genetic code] was discovered in the 1960s, no one had been able to explain how evolution could have made it so exquisitely tuned to resisting errors.
Mutations happen in DNA coding all the time, and yet the proteins it produces often remain unaffected by these glitches.
Darwinian evolution simply cannot explain how such a code could arise.
But horizontal gene transfer can, say Woese and Goldenfeld.Interesting.
	</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913684</id>
	<title>Re:darwin didn't know the details? shocking!</title>
	<author>Artifakt</author>
	<datestamp>1264528140000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>It's not that this 'undermines' Darwin, or that Darwin was 'wrong' about genes, but Evolutionary theory is a hybred. It combines Darwin's insight that natural pressures can select a subset of each generation to differentially reproduce, and Mendel's genetics. When Darwin proposed Natural Selection, he made predictions, such as that whatever mechanisms Heredity used, those mechanisms could not allow for unlimited blending of traits. Mendel's experiments showed how there could be non-blendable control mechanisms at the heart of the reproductive process. It's not just that mutation is a requirement along side natural selection to have the whole theory of Evolution, but that one of Darwin's conditions is the code being occasionally mutated must be a code that doesn't allow more than, at most, very limited blending. So, a non-Mendelian form of genetic transfer doesn't necessarily support Darwin's idea of how selection can work to produce long term changes, and if it doesn't, you can't (or shouldn't) call what's happening in such cases 'evolution'.</p></htmltext>
<tokenext>It 's not that this 'undermines ' Darwin , or that Darwin was 'wrong ' about genes , but Evolutionary theory is a hybred .
It combines Darwin 's insight that natural pressures can select a subset of each generation to differentially reproduce , and Mendel 's genetics .
When Darwin proposed Natural Selection , he made predictions , such as that whatever mechanisms Heredity used , those mechanisms could not allow for unlimited blending of traits .
Mendel 's experiments showed how there could be non-blendable control mechanisms at the heart of the reproductive process .
It 's not just that mutation is a requirement along side natural selection to have the whole theory of Evolution , but that one of Darwin 's conditions is the code being occasionally mutated must be a code that does n't allow more than , at most , very limited blending .
So , a non-Mendelian form of genetic transfer does n't necessarily support Darwin 's idea of how selection can work to produce long term changes , and if it does n't , you ca n't ( or should n't ) call what 's happening in such cases 'evolution' .</tokentext>
<sentencetext>It's not that this 'undermines' Darwin, or that Darwin was 'wrong' about genes, but Evolutionary theory is a hybred.
It combines Darwin's insight that natural pressures can select a subset of each generation to differentially reproduce, and Mendel's genetics.
When Darwin proposed Natural Selection, he made predictions, such as that whatever mechanisms Heredity used, those mechanisms could not allow for unlimited blending of traits.
Mendel's experiments showed how there could be non-blendable control mechanisms at the heart of the reproductive process.
It's not just that mutation is a requirement along side natural selection to have the whole theory of Evolution, but that one of Darwin's conditions is the code being occasionally mutated must be a code that doesn't allow more than, at most, very limited blending.
So, a non-Mendelian form of genetic transfer doesn't necessarily support Darwin's idea of how selection can work to produce long term changes, and if it doesn't, you can't (or shouldn't) call what's happening in such cases 'evolution'.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912194</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30919666</id>
	<title>Re:It's still natural selection</title>
	<author>mcgrew</author>
	<datestamp>1264616700000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><i>Of course that assumes that being homosexual reduces your chance of reproduction.<br></i><br>I don't see how it wouldn't. One has to be attracted to the opposite sex (and be attractive to them) to reproduce.</p></htmltext>
<tokenext>Of course that assumes that being homosexual reduces your chance of reproduction.I do n't see how it would n't .
One has to be attracted to the opposite sex ( and be attractive to them ) to reproduce .</tokentext>
<sentencetext>Of course that assumes that being homosexual reduces your chance of reproduction.I don't see how it wouldn't.
One has to be attracted to the opposite sex (and be attractive to them) to reproduce.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912478</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914030</id>
	<title>Re:Gene Synthesis</title>
	<author>Anonymous</author>
	<datestamp>1264531980000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>Occasionally, large portions of DNA are copied, potentially resulting in two copies of a gene. This leaves the gene free to evolve without needing to maintain its critical functionality, since the other copy can do so. Hence, you get a fully functional new gene, though at the start its function is identical to that of another. But having the backup copy means that it can evolve to take a different role, whether slightly different or very different.</p></htmltext>
<tokenext>Occasionally , large portions of DNA are copied , potentially resulting in two copies of a gene .
This leaves the gene free to evolve without needing to maintain its critical functionality , since the other copy can do so .
Hence , you get a fully functional new gene , though at the start its function is identical to that of another .
But having the backup copy means that it can evolve to take a different role , whether slightly different or very different .</tokentext>
<sentencetext>Occasionally, large portions of DNA are copied, potentially resulting in two copies of a gene.
This leaves the gene free to evolve without needing to maintain its critical functionality, since the other copy can do so.
Hence, you get a fully functional new gene, though at the start its function is identical to that of another.
But having the backup copy means that it can evolve to take a different role, whether slightly different or very different.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912130</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30915044</id>
	<title>Re:Still natural selection</title>
	<author>MrMr</author>
	<datestamp>1264591620000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>I find it surprising that the auhors seem to think that Darwinian selection only happens to organisms, but not to the genes that are being spliced.<br>Perhaps the only paradigm they need to shift is their misconception of what exactly evolves in evolution.</htmltext>
<tokenext>I find it surprising that the auhors seem to think that Darwinian selection only happens to organisms , but not to the genes that are being spliced.Perhaps the only paradigm they need to shift is their misconception of what exactly evolves in evolution .</tokentext>
<sentencetext>I find it surprising that the auhors seem to think that Darwinian selection only happens to organisms, but not to the genes that are being spliced.Perhaps the only paradigm they need to shift is their misconception of what exactly evolves in evolution.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911784</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912010</id>
	<title>Re:Well duh?</title>
	<author>RobinEggs</author>
	<datestamp>1264511760000</datestamp>
	<modclass>Offtopic</modclass>
	<modscore>-1</modscore>
	<htmltext>The very first thing I wondered when I saw the word Darwinian in the headline was "How many seconds will it take the slashdotters to slip in a blithe attack on creationism, even though no creationists will have attacked the theory or even responded?"<br> <br>
Turns out it was roughly five.
 <br> <br>Just why is it that ultra-conservative rants about God or racial superiority or anti-socialism are instantly modded off-topic, troll, and/or flamebait until they sink beneath the thresh hold and yet completely off-topic attacks on Creationism in every story even vaguely connected with biology or evolution get modded +5 insightful?</htmltext>
<tokenext>The very first thing I wondered when I saw the word Darwinian in the headline was " How many seconds will it take the slashdotters to slip in a blithe attack on creationism , even though no creationists will have attacked the theory or even responded ?
" Turns out it was roughly five .
Just why is it that ultra-conservative rants about God or racial superiority or anti-socialism are instantly modded off-topic , troll , and/or flamebait until they sink beneath the thresh hold and yet completely off-topic attacks on Creationism in every story even vaguely connected with biology or evolution get modded + 5 insightful ?</tokentext>
<sentencetext>The very first thing I wondered when I saw the word Darwinian in the headline was "How many seconds will it take the slashdotters to slip in a blithe attack on creationism, even though no creationists will have attacked the theory or even responded?
" 
Turns out it was roughly five.
Just why is it that ultra-conservative rants about God or racial superiority or anti-socialism are instantly modded off-topic, troll, and/or flamebait until they sink beneath the thresh hold and yet completely off-topic attacks on Creationism in every story even vaguely connected with biology or evolution get modded +5 insightful?</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911636</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913480</id>
	<title>Re:Well duh?</title>
	<author>Tomfrh</author>
	<datestamp>1264526040000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><i>To be precise, there is no theory that says your grandfather was a monkey.</i></p><p>Exactly. We haven't been monkeys for at least 100 generations. Heck, maybe even 200...</p></htmltext>
<tokenext>To be precise , there is no theory that says your grandfather was a monkey.Exactly .
We have n't been monkeys for at least 100 generations .
Heck , maybe even 200.. .</tokentext>
<sentencetext>To be precise, there is no theory that says your grandfather was a monkey.Exactly.
We haven't been monkeys for at least 100 generations.
Heck, maybe even 200...</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911964</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914988</id>
	<title>One of the most interesting things I've read</title>
	<author>Asterra</author>
	<datestamp>1264591080000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>One of the most interesting things I've read in a while.</p><p>Like Carl Sagan said, science is self-correcting.  He also said you have to back up big statements with big evidence.  So best of luck to this theory, in that respect.</p></htmltext>
<tokenext>One of the most interesting things I 've read in a while.Like Carl Sagan said , science is self-correcting .
He also said you have to back up big statements with big evidence .
So best of luck to this theory , in that respect .</tokentext>
<sentencetext>One of the most interesting things I've read in a while.Like Carl Sagan said, science is self-correcting.
He also said you have to back up big statements with big evidence.
So best of luck to this theory, in that respect.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912644</id>
	<title>Re:Here's A Tip, Folks</title>
	<author>camperdave</author>
	<datestamp>1264516380000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>5</modscore>
	<htmltext>In other words, the tree of life is a <a href="http://upload.wikimedia.org/wikipedia/commons/thumb/d/dc/Banyan\_tree\_Old\_Lee\_County\_Courthouse.jpg/800px-Banyan\_tree\_Old\_Lee\_County\_Courthouse.jpg" title="wikimedia.org">banyan</a> [wikimedia.org] tree.</htmltext>
<tokenext>In other words , the tree of life is a banyan [ wikimedia.org ] tree .</tokentext>
<sentencetext>In other words, the tree of life is a banyan [wikimedia.org] tree.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911972</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913700</id>
	<title>Asari?</title>
	<author>Anonymous</author>
	<datestamp>1264528260000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Did anyone else read the summary and suddenly think some scientist has gone an actually elevated the status of the Asari in Mass Effect from a horndog trope to sledgehammer blue alien lesbians into hard sci-fi...into the realm of 'egads!-it-could-happen?-ism'....??? </p></htmltext>
<tokenext>Did anyone else read the summary and suddenly think some scientist has gone an actually elevated the status of the Asari in Mass Effect from a horndog trope to sledgehammer blue alien lesbians into hard sci-fi...into the realm of 'egads ! -it-could-happen ? -ism'.... ? ?
?</tokentext>
<sentencetext>Did anyone else read the summary and suddenly think some scientist has gone an actually elevated the status of the Asari in Mass Effect from a horndog trope to sledgehammer blue alien lesbians into hard sci-fi...into the realm of 'egads!-it-could-happen?-ism'....??
? </sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30918878</id>
	<title>blasphemy!</title>
	<author>steak</author>
	<datestamp>1264613640000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>the word of darwin is set in stone and is a sacrosanct theroy. any work that seeks to alter the theroy of evolution is a violation of holy science.</p><p>troll out</p></htmltext>
<tokenext>the word of darwin is set in stone and is a sacrosanct theroy .
any work that seeks to alter the theroy of evolution is a violation of holy science.troll out</tokentext>
<sentencetext>the word of darwin is set in stone and is a sacrosanct theroy.
any work that seeks to alter the theroy of evolution is a violation of holy science.troll out</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912246</id>
	<title>Re:Once again</title>
	<author>BitZtream</author>
	<datestamp>1264513620000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>3</modscore>
	<htmltext><p>Most people treat what they call science as a religion.  They go wild that someone reads a book and believes the far fetched ideas in it, yet they have no problem reading something off wikipedia and assuming its fact.</p><p>The claim is that you CAN test and confirm it, but they don't, they just blindly assume because someone else wrote it down and some others agree with them.</p><p>I really don't see any difference in the way most nutjobs treat science compared/contrasted to the way religions nutjobs treat religion.</p></htmltext>
<tokenext>Most people treat what they call science as a religion .
They go wild that someone reads a book and believes the far fetched ideas in it , yet they have no problem reading something off wikipedia and assuming its fact.The claim is that you CAN test and confirm it , but they do n't , they just blindly assume because someone else wrote it down and some others agree with them.I really do n't see any difference in the way most nutjobs treat science compared/contrasted to the way religions nutjobs treat religion .</tokentext>
<sentencetext>Most people treat what they call science as a religion.
They go wild that someone reads a book and believes the far fetched ideas in it, yet they have no problem reading something off wikipedia and assuming its fact.The claim is that you CAN test and confirm it, but they don't, they just blindly assume because someone else wrote it down and some others agree with them.I really don't see any difference in the way most nutjobs treat science compared/contrasted to the way religions nutjobs treat religion.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911704</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912030</id>
	<title>Re:I realize scientists need a breakthrough</title>
	<author>Anachragnome</author>
	<datestamp>1264511940000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext><p>I agree.</p><p>It always seemed a little odd that evolutionists minimized such interactions as the bacteria that lives on, and IN, us as little more then a symbiotic relationship.</p><p>The idea that some genetic material might actually be passed from ourselves to these bacteria, or the other way around, seemed to make sense. I'm not talking about large chunks of DNA, but rather a codon or two every dozen generations, or something to that effect. Given that mutations/variations are more likely to occur in two species, as opposed to one, that symbiotic relationship might have accelerated genetic changes in either, or both, species. Who knows, maybe our ability to digest some specific foodstuff (a foodstuff that we previously relied on a bacteria in our gut to help us digest/process) was derived from genetic material that originally came from a bacteria that had the ability but was passed on to us a codon at a time. Just an example.</p><p>This leads me to the question of whether or not our preoccupation with sanitization/sterilization of our own bodies might be having some detrimental effect on our EVOLUTION. Is our wiping out species, to the point of extinction, actually limiting the evolutionary process, in essence limiting variation in the exchange of genetic material?</p></htmltext>
<tokenext>I agree.It always seemed a little odd that evolutionists minimized such interactions as the bacteria that lives on , and IN , us as little more then a symbiotic relationship.The idea that some genetic material might actually be passed from ourselves to these bacteria , or the other way around , seemed to make sense .
I 'm not talking about large chunks of DNA , but rather a codon or two every dozen generations , or something to that effect .
Given that mutations/variations are more likely to occur in two species , as opposed to one , that symbiotic relationship might have accelerated genetic changes in either , or both , species .
Who knows , maybe our ability to digest some specific foodstuff ( a foodstuff that we previously relied on a bacteria in our gut to help us digest/process ) was derived from genetic material that originally came from a bacteria that had the ability but was passed on to us a codon at a time .
Just an example.This leads me to the question of whether or not our preoccupation with sanitization/sterilization of our own bodies might be having some detrimental effect on our EVOLUTION .
Is our wiping out species , to the point of extinction , actually limiting the evolutionary process , in essence limiting variation in the exchange of genetic material ?</tokentext>
<sentencetext>I agree.It always seemed a little odd that evolutionists minimized such interactions as the bacteria that lives on, and IN, us as little more then a symbiotic relationship.The idea that some genetic material might actually be passed from ourselves to these bacteria, or the other way around, seemed to make sense.
I'm not talking about large chunks of DNA, but rather a codon or two every dozen generations, or something to that effect.
Given that mutations/variations are more likely to occur in two species, as opposed to one, that symbiotic relationship might have accelerated genetic changes in either, or both, species.
Who knows, maybe our ability to digest some specific foodstuff (a foodstuff that we previously relied on a bacteria in our gut to help us digest/process) was derived from genetic material that originally came from a bacteria that had the ability but was passed on to us a codon at a time.
Just an example.This leads me to the question of whether or not our preoccupation with sanitization/sterilization of our own bodies might be having some detrimental effect on our EVOLUTION.
Is our wiping out species, to the point of extinction, actually limiting the evolutionary process, in essence limiting variation in the exchange of genetic material?</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911600</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911930</id>
	<title>I wrote about this a while ago</title>
	<author>presidenteloco</author>
	<datestamp>1264511040000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>3</modscore>
	<htmltext><p>The notion that life probably started by weak, stochastic replication of families of similar molecules.</p><p>By weak, is meant that the replication of the molecule/structure is more imperfect from generation to generation<br>than in present day life, and so a class of similar molecules (life codes) is being continued through time<br>rather than a singular particular molecule (same genome).</p><p>If this origin theory were true, we would expect the replication capability (continued recreation of imperfect but still somewhat replication-capable molecules)<br>to be robust to change of DNA/RNA even today.</p><p>By stochastic, is meant that such imperfect replication is likely to only be stochastically successful in a huge population of the<br>initially highly approximate (i.e. weak) replicator molecules.</p><p>In other words, we would not expect this proto-life to be as reliable at being able to continue (or to always reliably grow by recruiting<br>surrounding matter into high-fidelity copies.)</p><p>So we might expect these proto-life molecule soups to initially just contain in some regions higher than expected probabilities,<br>stochastically, from time to time, of weak-replicator molecule classes.</p><p>Perhaps there is a binary threshold of replication probability and fidelity at which the process self-sustains reliably in the<br>generality of environment it finds itself in. Life catches fire, and cannot easily be stopped at its matter and energy recruitment<br>game from that point on.</p></htmltext>
<tokenext>The notion that life probably started by weak , stochastic replication of families of similar molecules.By weak , is meant that the replication of the molecule/structure is more imperfect from generation to generationthan in present day life , and so a class of similar molecules ( life codes ) is being continued through timerather than a singular particular molecule ( same genome ) .If this origin theory were true , we would expect the replication capability ( continued recreation of imperfect but still somewhat replication-capable molecules ) to be robust to change of DNA/RNA even today.By stochastic , is meant that such imperfect replication is likely to only be stochastically successful in a huge population of theinitially highly approximate ( i.e .
weak ) replicator molecules.In other words , we would not expect this proto-life to be as reliable at being able to continue ( or to always reliably grow by recruitingsurrounding matter into high-fidelity copies .
) So we might expect these proto-life molecule soups to initially just contain in some regions higher than expected probabilities,stochastically , from time to time , of weak-replicator molecule classes.Perhaps there is a binary threshold of replication probability and fidelity at which the process self-sustains reliably in thegenerality of environment it finds itself in .
Life catches fire , and can not easily be stopped at its matter and energy recruitmentgame from that point on .</tokentext>
<sentencetext>The notion that life probably started by weak, stochastic replication of families of similar molecules.By weak, is meant that the replication of the molecule/structure is more imperfect from generation to generationthan in present day life, and so a class of similar molecules (life codes) is being continued through timerather than a singular particular molecule (same genome).If this origin theory were true, we would expect the replication capability (continued recreation of imperfect but still somewhat replication-capable molecules)to be robust to change of DNA/RNA even today.By stochastic, is meant that such imperfect replication is likely to only be stochastically successful in a huge population of theinitially highly approximate (i.e.
weak) replicator molecules.In other words, we would not expect this proto-life to be as reliable at being able to continue (or to always reliably grow by recruitingsurrounding matter into high-fidelity copies.
)So we might expect these proto-life molecule soups to initially just contain in some regions higher than expected probabilities,stochastically, from time to time, of weak-replicator molecule classes.Perhaps there is a binary threshold of replication probability and fidelity at which the process self-sustains reliably in thegenerality of environment it finds itself in.
Life catches fire, and cannot easily be stopped at its matter and energy recruitmentgame from that point on.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912058</id>
	<title>Has anyone added this to a GA yet?</title>
	<author>John Hasler</author>
	<datestamp>1264512180000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>n/t</p></htmltext>
<tokenext>n/t</tokentext>
<sentencetext>n/t</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914584</id>
	<title>Re:I realize scientists need a breakthrough</title>
	<author>Anonymous</author>
	<datestamp>1264584000000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p><div class="quote"><p>Is our wiping out species, to the point of extinction, actually limiting the evolutionary process, in essence limiting variation in the exchange of genetic material?</p></div><p> Have no fear! There is always the herpes simplex to lean on.</p></div>
	</htmltext>
<tokenext>Is our wiping out species , to the point of extinction , actually limiting the evolutionary process , in essence limiting variation in the exchange of genetic material ?
Have no fear !
There is always the herpes simplex to lean on .</tokentext>
<sentencetext>Is our wiping out species, to the point of extinction, actually limiting the evolutionary process, in essence limiting variation in the exchange of genetic material?
Have no fear!
There is always the herpes simplex to lean on.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912030</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30917778</id>
	<title>What is non-Darwinian about this?</title>
	<author>tgibbs</author>
	<datestamp>1264609560000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Darwin never specified how inheritable traits arise. He knew nothing of genes, other than that his theory required the units of inheritance to be discrete. So whether or not genes are transferred horizontally has nothing to do with whether it is Darwinian evolution. The key issue is whether organisms that acquired the trait tended to propagate more successfully and pass the trait onto their descendants, thereby increasing the frequency of that trait in the population. If that is the case, then it is Darwinian evolution.</p><p>It's certainly true that many modern scientists have tended to assume that the major source of genetic generation of diversity was spontaneous mutations in an organisms DNA, but the idea of a contribution from gene transfer is not itself particularly novel.</p></htmltext>
<tokenext>Darwin never specified how inheritable traits arise .
He knew nothing of genes , other than that his theory required the units of inheritance to be discrete .
So whether or not genes are transferred horizontally has nothing to do with whether it is Darwinian evolution .
The key issue is whether organisms that acquired the trait tended to propagate more successfully and pass the trait onto their descendants , thereby increasing the frequency of that trait in the population .
If that is the case , then it is Darwinian evolution.It 's certainly true that many modern scientists have tended to assume that the major source of genetic generation of diversity was spontaneous mutations in an organisms DNA , but the idea of a contribution from gene transfer is not itself particularly novel .</tokentext>
<sentencetext>Darwin never specified how inheritable traits arise.
He knew nothing of genes, other than that his theory required the units of inheritance to be discrete.
So whether or not genes are transferred horizontally has nothing to do with whether it is Darwinian evolution.
The key issue is whether organisms that acquired the trait tended to propagate more successfully and pass the trait onto their descendants, thereby increasing the frequency of that trait in the population.
If that is the case, then it is Darwinian evolution.It's certainly true that many modern scientists have tended to assume that the major source of genetic generation of diversity was spontaneous mutations in an organisms DNA, but the idea of a contribution from gene transfer is not itself particularly novel.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912054</id>
	<title>Re:It's still natural selection</title>
	<author>franoreilly</author>
	<datestamp>1264512120000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>There's nothing fundamentally different being mooted here.</p><p>We are talking  about the very early stages of life when I imagine that the boundary between separate organisms itself was probably very poorly defined compared to today's life forms; so in that sort of environment, a different horizontal mechanism of gene propagation could well have been the primary one.</p><p>The mechanism may be somewhat different to most of what happens today, but the core concept of Dawkins' "selfish gene" is unchanged, where the propagation of the gene, not the type of organism, is selected for,</p></htmltext>
<tokenext>There 's nothing fundamentally different being mooted here.We are talking about the very early stages of life when I imagine that the boundary between separate organisms itself was probably very poorly defined compared to today 's life forms ; so in that sort of environment , a different horizontal mechanism of gene propagation could well have been the primary one.The mechanism may be somewhat different to most of what happens today , but the core concept of Dawkins ' " selfish gene " is unchanged , where the propagation of the gene , not the type of organism , is selected for,</tokentext>
<sentencetext>There's nothing fundamentally different being mooted here.We are talking  about the very early stages of life when I imagine that the boundary between separate organisms itself was probably very poorly defined compared to today's life forms; so in that sort of environment, a different horizontal mechanism of gene propagation could well have been the primary one.The mechanism may be somewhat different to most of what happens today, but the core concept of Dawkins' "selfish gene" is unchanged, where the propagation of the gene, not the type of organism, is selected for,</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911724</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913356</id>
	<title>Re:Here's A Tip, Folks</title>
	<author>liquidpele</author>
	<datestamp>1264524180000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>You would do well to read this book.  The man actually coined the term you just dismissed.

<a href="http://en.wikipedia.org/wiki/The\_Structure\_of\_Scientific\_Revolutions" title="wikipedia.org">http://en.wikipedia.org/wiki/The\_Structure\_of\_Scientific\_Revolutions</a> [wikipedia.org]</htmltext>
<tokenext>You would do well to read this book .
The man actually coined the term you just dismissed .
http : //en.wikipedia.org/wiki/The \ _Structure \ _of \ _Scientific \ _Revolutions [ wikipedia.org ]</tokentext>
<sentencetext>You would do well to read this book.
The man actually coined the term you just dismissed.
http://en.wikipedia.org/wiki/The\_Structure\_of\_Scientific\_Revolutions [wikipedia.org]</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911972</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911600</id>
	<title>I realize scientists need a breakthrough</title>
	<author>Blappo</author>
	<datestamp>1264509000000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>3</modscore>
	<htmltext><p>I strongly suspect it isn't, nor was it ever, one type of evolution over the other, but a complex interaction between many environmental pressures where both types of evolution played a role.</p></htmltext>
<tokenext>I strongly suspect it is n't , nor was it ever , one type of evolution over the other , but a complex interaction between many environmental pressures where both types of evolution played a role .</tokentext>
<sentencetext>I strongly suspect it isn't, nor was it ever, one type of evolution over the other, but a complex interaction between many environmental pressures where both types of evolution played a role.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912490</id>
	<title>Re:It's still natural selection</title>
	<author>SoftwareArtist</author>
	<datestamp>1264515240000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>3</modscore>
	<htmltext>Exactly.  Evolution is a fundamental mathematical process that applies to <i>information</i>, not <i>organisms</i>.  To get evolution, you only need two elements:
<br> <br>
1. An information storage medium.
<br> <br>
2. A mechanism for reproducing that information such that certain pieces of information are more likely to get reproduced than others.
<br> <br>
Once you have those, everything else follows, and it doesn't matter what the precise storage mechanism or copying mechanism is.  Horizontal gene transfer is just another way for genetic information to reproduce.</htmltext>
<tokenext>Exactly .
Evolution is a fundamental mathematical process that applies to information , not organisms .
To get evolution , you only need two elements : 1 .
An information storage medium .
2. A mechanism for reproducing that information such that certain pieces of information are more likely to get reproduced than others .
Once you have those , everything else follows , and it does n't matter what the precise storage mechanism or copying mechanism is .
Horizontal gene transfer is just another way for genetic information to reproduce .</tokentext>
<sentencetext>Exactly.
Evolution is a fundamental mathematical process that applies to information, not organisms.
To get evolution, you only need two elements:
 
1.
An information storage medium.
2. A mechanism for reproducing that information such that certain pieces of information are more likely to get reproduced than others.
Once you have those, everything else follows, and it doesn't matter what the precise storage mechanism or copying mechanism is.
Horizontal gene transfer is just another way for genetic information to reproduce.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911724</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913880</id>
	<title>Re:Here's A Tip, Folks</title>
	<author>khallow</author>
	<datestamp>1264530180000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><div class="quote"><p>Further it has nothing at all to do with Darwinism.</p></div><p>This is wrong. Darwinism isn't natural selection. It's more than that:<br> <br>

1) Traits are inherited.<br>

2) Traits affect the survivability of the organism.<br>

3) There is natural selection. That is, there's some process or events by which some organisms fail to reproduce.<br> <br>

It's worth noting here that natural selection is only one point of three. The first point is the one that is changed by horizontal gene transfer. Darwinism assumes inheritance as the form of trait transfer. If you have other modes of transfer of traits (for example, Lamarckism), then the dynamics of biology can be substantially different than evolution. Another example is human learning. There's more information in a person's brain than in their DNA. The means by which a person learns is vastly different from evolution. While we learn a lot from our caregivers (who need not be related to us), we also can learn from anyone or anything we meet and observe. We also learn from activities.<br> <br>

Hence, learning is not best described by evolution even though part can be modeled ok by evolutionary models (namely, the stuff kids learn from parents).</p></div>
	</htmltext>
<tokenext>Further it has nothing at all to do with Darwinism.This is wrong .
Darwinism is n't natural selection .
It 's more than that : 1 ) Traits are inherited .
2 ) Traits affect the survivability of the organism .
3 ) There is natural selection .
That is , there 's some process or events by which some organisms fail to reproduce .
It 's worth noting here that natural selection is only one point of three .
The first point is the one that is changed by horizontal gene transfer .
Darwinism assumes inheritance as the form of trait transfer .
If you have other modes of transfer of traits ( for example , Lamarckism ) , then the dynamics of biology can be substantially different than evolution .
Another example is human learning .
There 's more information in a person 's brain than in their DNA .
The means by which a person learns is vastly different from evolution .
While we learn a lot from our caregivers ( who need not be related to us ) , we also can learn from anyone or anything we meet and observe .
We also learn from activities .
Hence , learning is not best described by evolution even though part can be modeled ok by evolutionary models ( namely , the stuff kids learn from parents ) .</tokentext>
<sentencetext>Further it has nothing at all to do with Darwinism.This is wrong.
Darwinism isn't natural selection.
It's more than that: 

1) Traits are inherited.
2) Traits affect the survivability of the organism.
3) There is natural selection.
That is, there's some process or events by which some organisms fail to reproduce.
It's worth noting here that natural selection is only one point of three.
The first point is the one that is changed by horizontal gene transfer.
Darwinism assumes inheritance as the form of trait transfer.
If you have other modes of transfer of traits (for example, Lamarckism), then the dynamics of biology can be substantially different than evolution.
Another example is human learning.
There's more information in a person's brain than in their DNA.
The means by which a person learns is vastly different from evolution.
While we learn a lot from our caregivers (who need not be related to us), we also can learn from anyone or anything we meet and observe.
We also learn from activities.
Hence, learning is not best described by evolution even though part can be modeled ok by evolutionary models (namely, the stuff kids learn from parents).
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912132</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911964</id>
	<title>Re:Well duh?</title>
	<author>Arancaytar</author>
	<datestamp>1264511460000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>2</modscore>
	<htmltext><p>To be precise, there is no theory that says your grandfather was a monkey. The religious nuts made that straw-man up all on their own.<nobr> <wbr></nobr>:P</p></htmltext>
<tokenext>To be precise , there is no theory that says your grandfather was a monkey .
The religious nuts made that straw-man up all on their own .
: P</tokentext>
<sentencetext>To be precise, there is no theory that says your grandfather was a monkey.
The religious nuts made that straw-man up all on their own.
:P</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911636</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912132</id>
	<title>Re:Here's A Tip, Folks</title>
	<author>icebike</author>
	<datestamp>1264512600000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>5</modscore>
	<htmltext><p><div class="quote"><p>Horizontal gene transfer has been known about for decades, and the notion that the root of the tree of life is more a tangle of interconnecting branches has pretty much been accepted for some time now.</p> </div><p>Further it has nothing at all to do with Darwinism.</p><p>A mechanism of gene transfer plays no role in the "Survival of the Fittest" (a phrase coined not by Darwin, but rather by Spencer), or natural selection.  Its not germane.</p><p>Natural Selection is a winnowing process, and a mutation amplifying force, but says nothing about the acquisition or dispersion of said mutations.  It was never meant to.</p></div>
	</htmltext>
<tokenext>Horizontal gene transfer has been known about for decades , and the notion that the root of the tree of life is more a tangle of interconnecting branches has pretty much been accepted for some time now .
Further it has nothing at all to do with Darwinism.A mechanism of gene transfer plays no role in the " Survival of the Fittest " ( a phrase coined not by Darwin , but rather by Spencer ) , or natural selection .
Its not germane.Natural Selection is a winnowing process , and a mutation amplifying force , but says nothing about the acquisition or dispersion of said mutations .
It was never meant to .</tokentext>
<sentencetext>Horizontal gene transfer has been known about for decades, and the notion that the root of the tree of life is more a tangle of interconnecting branches has pretty much been accepted for some time now.
Further it has nothing at all to do with Darwinism.A mechanism of gene transfer plays no role in the "Survival of the Fittest" (a phrase coined not by Darwin, but rather by Spencer), or natural selection.
Its not germane.Natural Selection is a winnowing process, and a mutation amplifying force, but says nothing about the acquisition or dispersion of said mutations.
It was never meant to.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911972</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914662</id>
	<title>nothing mind-bending about it</title>
	<author>pydev</author>
	<datestamp>1264585620000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Horizontal gene transfer has been known for a long time, as has its influence on bacterial evolution.  So, there is really little fundamentally new insight in this paper.</p></htmltext>
<tokenext>Horizontal gene transfer has been known for a long time , as has its influence on bacterial evolution .
So , there is really little fundamentally new insight in this paper .</tokentext>
<sentencetext>Horizontal gene transfer has been known for a long time, as has its influence on bacterial evolution.
So, there is really little fundamentally new insight in this paper.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30915672</id>
	<title>Re:darwin didn't know the details? shocking!</title>
	<author>Kynde</author>
	<datestamp>1264598700000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><i>I mean, was Jesus wrong about genes, too?</i></p><p>Well, I don't know quite how to put it, but yes.</p></htmltext>
<tokenext>I mean , was Jesus wrong about genes , too ? Well , I do n't know quite how to put it , but yes .</tokentext>
<sentencetext>I mean, was Jesus wrong about genes, too?Well, I don't know quite how to put it, but yes.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912194</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912524</id>
	<title>Outstanding point</title>
	<author>sgt\_doom</author>
	<datestamp>1264515420000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Outstanding concept - and correct, of course!</p><p>Of course, it is great research, but also quite obvious to the rest of us as viral transfer of DNA material has been known for quite some time, and numerous research grants were submitted in the late '70s and early '80s --- unfortunately that was the time of the anti-science of Reagan and the first wave of neocons.</p></htmltext>
<tokenext>Outstanding concept - and correct , of course ! Of course , it is great research , but also quite obvious to the rest of us as viral transfer of DNA material has been known for quite some time , and numerous research grants were submitted in the late '70s and early '80s --- unfortunately that was the time of the anti-science of Reagan and the first wave of neocons .</tokentext>
<sentencetext>Outstanding concept - and correct, of course!Of course, it is great research, but also quite obvious to the rest of us as viral transfer of DNA material has been known for quite some time, and numerous research grants were submitted in the late '70s and early '80s --- unfortunately that was the time of the anti-science of Reagan and the first wave of neocons.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911972</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914430</id>
	<title>Re:Once again</title>
	<author>repapetilto</author>
	<datestamp>1264624260000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>The problem is that it takes so much specialized knowledge to be able to really judge how a scientist has interpreted their data due to all the background info needed to take it in the correct context. But thats just how it is... the world is complex... you arent going to get anything more than a superficial understanding of what goes on inside cells from an NPR episode because you have to consider the model (in vitro... cell type, buffer, concentrations of various ions, source of the cells, etc) or in vivo (what did they have to do to manipulate the organism to have to study it, what other systems are regulating that one, possibly vice versa at the same time...) My point is to really know whats going on take specialized knowledge that you just cant incorperate into your worldview properly by reading one article plus looking up what you dont know at wikipedia/google/whatever. It really is literally impossible to explain it fully to someone in a time period measured in less than years. People have other things to do and need to sleep to consolidate the knowledge.</p></htmltext>
<tokenext>The problem is that it takes so much specialized knowledge to be able to really judge how a scientist has interpreted their data due to all the background info needed to take it in the correct context .
But thats just how it is... the world is complex... you arent going to get anything more than a superficial understanding of what goes on inside cells from an NPR episode because you have to consider the model ( in vitro... cell type , buffer , concentrations of various ions , source of the cells , etc ) or in vivo ( what did they have to do to manipulate the organism to have to study it , what other systems are regulating that one , possibly vice versa at the same time... ) My point is to really know whats going on take specialized knowledge that you just cant incorperate into your worldview properly by reading one article plus looking up what you dont know at wikipedia/google/whatever .
It really is literally impossible to explain it fully to someone in a time period measured in less than years .
People have other things to do and need to sleep to consolidate the knowledge .</tokentext>
<sentencetext>The problem is that it takes so much specialized knowledge to be able to really judge how a scientist has interpreted their data due to all the background info needed to take it in the correct context.
But thats just how it is... the world is complex... you arent going to get anything more than a superficial understanding of what goes on inside cells from an NPR episode because you have to consider the model (in vitro... cell type, buffer, concentrations of various ions, source of the cells, etc) or in vivo (what did they have to do to manipulate the organism to have to study it, what other systems are regulating that one, possibly vice versa at the same time...) My point is to really know whats going on take specialized knowledge that you just cant incorperate into your worldview properly by reading one article plus looking up what you dont know at wikipedia/google/whatever.
It really is literally impossible to explain it fully to someone in a time period measured in less than years.
People have other things to do and need to sleep to consolidate the knowledge.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912246</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914706</id>
	<title>Re:Gene Synthesis</title>
	<author>presidenteloco</author>
	<datestamp>1264586460000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>First, take all the alternative molecules that can be formed by a given RNA-like molecule (call that molecular structure b, for reasons<br>that may shortly become obvious) with only one or very few<br>point mutations or section permutations. If we make the (rather strong) analogy of the RNA-like molecule<br>to a particular construction-program-representing bitstring value, then we are considering the set of alternative bitstring values<br>which have low relative Kolmogorov complexity compared to the original bitstring value.<br>Consider the set of molecules(bitstrings) which can be produced by only a few simple and probable/feasible-by-chance-or-thermodynamics<br>physical process steps, (i.e. by a few local program steps), given the original molecule(bitstring) as a starting point.<br>Call that set of molecules/bitstrings Sb.</p><p>Now consider the subset of Sb, S'b which codes for structures/processes which, in the context of the surrounding structures/processes<br>that Sb codes for, and additionally in the context of the prevailing set of probable environmental states C, will do no harm to the continuation<br>of the whole homeostatic and replicating structure/process.</p><p>Now consider the subset of S'b, S''b, which codes for structures/processes that have an adaptive (survival probability) advantage in<br>the prevailing environment C.</p><p>Evolution of any currently extant (ergo successful) structure-construction program-encoding molecule b will tend to<br>proceed at each step from b to a b'' which is found in S''b.</p><p>A more complex picture would see a mix of moves from b to b' (in S'b) (harmless,useless mutations) as well as moves straight<br>from b, or through any b', to b'' or to b''', but roughly, the end-effect is moves from b to a b'', repeat ad nauseum.</p><p>There are two constraints operating here. The first is that the program code evolution must be probable and feasible.<br>The second is that the work-product variation caused by the program code variation must be at least<br>non-destructive (so it can hang around as fodder for usefulness should the environment C change), or must be<br>adaptive i.e. MTBF(b'',C) &gt; MTBF(b,C), where F, failure, is defined as loss of any existence/embodiment of the molecular<br>structure/bitstring b in that (causally connected) spacetime region.</p><p>That is, pseudo-mathematically speaking, the direction that evolution will tend to take.</p><p>But it leaves the question of how simple the simplest reliably surviving b + b-replicating context/machine<br>(i.e. the simplest self-creating Turing machine) was, and what it would have been like, chemically, and how that<br>worked, exactly.</p></htmltext>
<tokenext>First , take all the alternative molecules that can be formed by a given RNA-like molecule ( call that molecular structure b , for reasonsthat may shortly become obvious ) with only one or very fewpoint mutations or section permutations .
If we make the ( rather strong ) analogy of the RNA-like moleculeto a particular construction-program-representing bitstring value , then we are considering the set of alternative bitstring valueswhich have low relative Kolmogorov complexity compared to the original bitstring value.Consider the set of molecules ( bitstrings ) which can be produced by only a few simple and probable/feasible-by-chance-or-thermodynamicsphysical process steps , ( i.e .
by a few local program steps ) , given the original molecule ( bitstring ) as a starting point.Call that set of molecules/bitstrings Sb.Now consider the subset of Sb , S'b which codes for structures/processes which , in the context of the surrounding structures/processesthat Sb codes for , and additionally in the context of the prevailing set of probable environmental states C , will do no harm to the continuationof the whole homeostatic and replicating structure/process.Now consider the subset of S'b , S''b , which codes for structures/processes that have an adaptive ( survival probability ) advantage inthe prevailing environment C.Evolution of any currently extant ( ergo successful ) structure-construction program-encoding molecule b will tend toproceed at each step from b to a b' ' which is found in S''b.A more complex picture would see a mix of moves from b to b ' ( in S'b ) ( harmless,useless mutations ) as well as moves straightfrom b , or through any b ' , to b' ' or to b'' ' , but roughly , the end-effect is moves from b to a b' ' , repeat ad nauseum.There are two constraints operating here .
The first is that the program code evolution must be probable and feasible.The second is that the work-product variation caused by the program code variation must be at leastnon-destructive ( so it can hang around as fodder for usefulness should the environment C change ) , or must beadaptive i.e .
MTBF ( b'',C ) &gt; MTBF ( b,C ) , where F , failure , is defined as loss of any existence/embodiment of the molecularstructure/bitstring b in that ( causally connected ) spacetime region.That is , pseudo-mathematically speaking , the direction that evolution will tend to take.But it leaves the question of how simple the simplest reliably surviving b + b-replicating context/machine ( i.e .
the simplest self-creating Turing machine ) was , and what it would have been like , chemically , and how thatworked , exactly .</tokentext>
<sentencetext>First, take all the alternative molecules that can be formed by a given RNA-like molecule (call that molecular structure b, for reasonsthat may shortly become obvious) with only one or very fewpoint mutations or section permutations.
If we make the (rather strong) analogy of the RNA-like moleculeto a particular construction-program-representing bitstring value, then we are considering the set of alternative bitstring valueswhich have low relative Kolmogorov complexity compared to the original bitstring value.Consider the set of molecules(bitstrings) which can be produced by only a few simple and probable/feasible-by-chance-or-thermodynamicsphysical process steps, (i.e.
by a few local program steps), given the original molecule(bitstring) as a starting point.Call that set of molecules/bitstrings Sb.Now consider the subset of Sb, S'b which codes for structures/processes which, in the context of the surrounding structures/processesthat Sb codes for, and additionally in the context of the prevailing set of probable environmental states C, will do no harm to the continuationof the whole homeostatic and replicating structure/process.Now consider the subset of S'b, S''b, which codes for structures/processes that have an adaptive (survival probability) advantage inthe prevailing environment C.Evolution of any currently extant (ergo successful) structure-construction program-encoding molecule b will tend toproceed at each step from b to a b'' which is found in S''b.A more complex picture would see a mix of moves from b to b' (in S'b) (harmless,useless mutations) as well as moves straightfrom b, or through any b', to b'' or to b''', but roughly, the end-effect is moves from b to a b'', repeat ad nauseum.There are two constraints operating here.
The first is that the program code evolution must be probable and feasible.The second is that the work-product variation caused by the program code variation must be at leastnon-destructive (so it can hang around as fodder for usefulness should the environment C change), or must beadaptive i.e.
MTBF(b'',C) &gt; MTBF(b,C), where F, failure, is defined as loss of any existence/embodiment of the molecularstructure/bitstring b in that (causally connected) spacetime region.That is, pseudo-mathematically speaking, the direction that evolution will tend to take.But it leaves the question of how simple the simplest reliably surviving b + b-replicating context/machine(i.e.
the simplest self-creating Turing machine) was, and what it would have been like, chemically, and how thatworked, exactly.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912130</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914864</id>
	<title>Re:Gene Synthesis</title>
	<author>Anonymous</author>
	<datestamp>1264588800000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>New proteins usually emerge through mutations in gene sequences that are already present. If you want to get a new protein and still retain the old protein from which it is derived, the<br>gene has to be duplicated first, after which mutations can change the function of one (or both...) of the two copies. Gene duplication happens regularly "by chance" and would usually be<br>considered DNA damage, but in fact pretty much all proteins start out like that: As identical copies of previously existing proteins. Since there are then two copies of the gene in the genome, one<br>of the copies has become redundant and can accumulate mutations as long as they have a neutral effect on overall fitness. This might lead to functional changes over time, some of which can be beneficial. It's not true that you will not find "intermediate" forms of proteins in nature, if you look at the same gene in different species (that is, a gene that has a common ancestor), all of them will<br>be slightly different. There have been studies done in microbes to try to understand exactly how these very slight differences modify the function of the protein and by extension the fitness of the organism. You need to keep in mind that there are a lot of mutations that you can introduce in a functional protein that will not make the protein unfunctional, but just slightly less or slightly more functional, or change it's function slightly. In that way, a complicated organism such as a eukaryote already has a gigantic amount of functional genes that can be used as scaffolds to build new genes. If you start comparing proteins in an organism, you will find that certain parts of their sequences come up again and again, these are called protein domains. These are like functional building block to a degree, and can be reused after gene duplication.</p></htmltext>
<tokenext>New proteins usually emerge through mutations in gene sequences that are already present .
If you want to get a new protein and still retain the old protein from which it is derived , thegene has to be duplicated first , after which mutations can change the function of one ( or both... ) of the two copies .
Gene duplication happens regularly " by chance " and would usually beconsidered DNA damage , but in fact pretty much all proteins start out like that : As identical copies of previously existing proteins .
Since there are then two copies of the gene in the genome , oneof the copies has become redundant and can accumulate mutations as long as they have a neutral effect on overall fitness .
This might lead to functional changes over time , some of which can be beneficial .
It 's not true that you will not find " intermediate " forms of proteins in nature , if you look at the same gene in different species ( that is , a gene that has a common ancestor ) , all of them willbe slightly different .
There have been studies done in microbes to try to understand exactly how these very slight differences modify the function of the protein and by extension the fitness of the organism .
You need to keep in mind that there are a lot of mutations that you can introduce in a functional protein that will not make the protein unfunctional , but just slightly less or slightly more functional , or change it 's function slightly .
In that way , a complicated organism such as a eukaryote already has a gigantic amount of functional genes that can be used as scaffolds to build new genes .
If you start comparing proteins in an organism , you will find that certain parts of their sequences come up again and again , these are called protein domains .
These are like functional building block to a degree , and can be reused after gene duplication .</tokentext>
<sentencetext>New proteins usually emerge through mutations in gene sequences that are already present.
If you want to get a new protein and still retain the old protein from which it is derived, thegene has to be duplicated first, after which mutations can change the function of one (or both...) of the two copies.
Gene duplication happens regularly "by chance" and would usually beconsidered DNA damage, but in fact pretty much all proteins start out like that: As identical copies of previously existing proteins.
Since there are then two copies of the gene in the genome, oneof the copies has become redundant and can accumulate mutations as long as they have a neutral effect on overall fitness.
This might lead to functional changes over time, some of which can be beneficial.
It's not true that you will not find "intermediate" forms of proteins in nature, if you look at the same gene in different species (that is, a gene that has a common ancestor), all of them willbe slightly different.
There have been studies done in microbes to try to understand exactly how these very slight differences modify the function of the protein and by extension the fitness of the organism.
You need to keep in mind that there are a lot of mutations that you can introduce in a functional protein that will not make the protein unfunctional, but just slightly less or slightly more functional, or change it's function slightly.
In that way, a complicated organism such as a eukaryote already has a gigantic amount of functional genes that can be used as scaffolds to build new genes.
If you start comparing proteins in an organism, you will find that certain parts of their sequences come up again and again, these are called protein domains.
These are like functional building block to a degree, and can be reused after gene duplication.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912130</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30915276</id>
	<title>Re:Capitalism?</title>
	<author>someone1234</author>
	<datestamp>1264594500000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>They still pass these horizontally acquired genes to their 'offspring', don't they?</p></htmltext>
<tokenext>They still pass these horizontally acquired genes to their 'offspring ' , do n't they ?</tokentext>
<sentencetext>They still pass these horizontally acquired genes to their 'offspring', don't they?</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911936</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912714</id>
	<title>I can hear them now....</title>
	<author>elitest</author>
	<datestamp>1264517160000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext>I'm sure when the creationists hear "Parallel Evolution" they think "God did it"</htmltext>
<tokenext>I 'm sure when the creationists hear " Parallel Evolution " they think " God did it "</tokentext>
<sentencetext>I'm sure when the creationists hear "Parallel Evolution" they think "God did it"</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912092</id>
	<title>We've heard this from our mothers for years...</title>
	<author>Ransak</author>
	<datestamp>1264512360000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>"You are what you eat."<br> <br>Cue the toilet humor in 3... 2... 1...</htmltext>
<tokenext>" You are what you eat .
" Cue the toilet humor in 3... 2... 1.. .</tokentext>
<sentencetext>"You are what you eat.
" Cue the toilet humor in 3... 2... 1...</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913150</id>
	<title>Re:I realize scientists need a breakthrough</title>
	<author>tempest69</author>
	<datestamp>1264522140000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>as far as humans getting genes from viruses and bacteria.. it is small change relative to recombination, mutation and gene duplication.  Germline cells are really resistant to alterations in general.  Bacteria and viruses could make some changes here and there, but they need to hit a cell that will create offspring, and not leave it (said offspring) jacked up.  <p>
The much more common event is gene duplication and neofunctionilization,  A normally occuring protien gets duplicated, and is no longer under pressure to work,  eventually they get "fired" or go feral, doing something new that provides an advantage to a creature. Eventually causing their new job to be selected for.
</p><p>
So bacteria giving us proteins is rare in the here and now.  Though hyper sanitary conditions do leave people with some real problems, as we didnt evolve into cleanness.</p></htmltext>
<tokenext>as far as humans getting genes from viruses and bacteria.. it is small change relative to recombination , mutation and gene duplication .
Germline cells are really resistant to alterations in general .
Bacteria and viruses could make some changes here and there , but they need to hit a cell that will create offspring , and not leave it ( said offspring ) jacked up .
The much more common event is gene duplication and neofunctionilization , A normally occuring protien gets duplicated , and is no longer under pressure to work , eventually they get " fired " or go feral , doing something new that provides an advantage to a creature .
Eventually causing their new job to be selected for .
So bacteria giving us proteins is rare in the here and now .
Though hyper sanitary conditions do leave people with some real problems , as we didnt evolve into cleanness .</tokentext>
<sentencetext>as far as humans getting genes from viruses and bacteria.. it is small change relative to recombination, mutation and gene duplication.
Germline cells are really resistant to alterations in general.
Bacteria and viruses could make some changes here and there, but they need to hit a cell that will create offspring, and not leave it (said offspring) jacked up.
The much more common event is gene duplication and neofunctionilization,  A normally occuring protien gets duplicated, and is no longer under pressure to work,  eventually they get "fired" or go feral, doing something new that provides an advantage to a creature.
Eventually causing their new job to be selected for.
So bacteria giving us proteins is rare in the here and now.
Though hyper sanitary conditions do leave people with some real problems, as we didnt evolve into cleanness.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912030</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914210</id>
	<title>Re:I realize scientists need a breakthrough</title>
	<author>fusellovirus</author>
	<datestamp>1264534440000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>2</modscore>
	<htmltext>This is old news, Woses paper "on the evolution of cells" explained this concept 8 years ago <a href="http://www.pnas.org/content/99/13/8742.long" title="pnas.org" rel="nofollow">http://www.pnas.org/content/99/13/8742.long</a> [pnas.org]. Even within the protocell or primordial soup where  horizontal gene transfer is hypothesized to play a dominant role natural selection still takes place. The molecules that replicate best increase in number and those that don't die out. Also, several evolutionary biologists such as Woese himself and many of his collegues have made their careers out of studying this phenomenon, so the suggestion " its consequences have hardly been explored" is a bit disingenuous.</htmltext>
<tokenext>This is old news , Woses paper " on the evolution of cells " explained this concept 8 years ago http : //www.pnas.org/content/99/13/8742.long [ pnas.org ] .
Even within the protocell or primordial soup where horizontal gene transfer is hypothesized to play a dominant role natural selection still takes place .
The molecules that replicate best increase in number and those that do n't die out .
Also , several evolutionary biologists such as Woese himself and many of his collegues have made their careers out of studying this phenomenon , so the suggestion " its consequences have hardly been explored " is a bit disingenuous .</tokentext>
<sentencetext>This is old news, Woses paper "on the evolution of cells" explained this concept 8 years ago http://www.pnas.org/content/99/13/8742.long [pnas.org].
Even within the protocell or primordial soup where  horizontal gene transfer is hypothesized to play a dominant role natural selection still takes place.
The molecules that replicate best increase in number and those that don't die out.
Also, several evolutionary biologists such as Woese himself and many of his collegues have made their careers out of studying this phenomenon, so the suggestion " its consequences have hardly been explored" is a bit disingenuous.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911600</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912818</id>
	<title>Dubious</title>
	<author>Thuktun</author>
	<datestamp>1264518420000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Natural selection describes a process by which beneficial mutations are kept and improve the suitability of a species to its environs.  It does not talk about genetics at all.  Why wouldn't mutations caused by horizontal gene transfer also apply to natural selection?</p></htmltext>
<tokenext>Natural selection describes a process by which beneficial mutations are kept and improve the suitability of a species to its environs .
It does not talk about genetics at all .
Why would n't mutations caused by horizontal gene transfer also apply to natural selection ?</tokentext>
<sentencetext>Natural selection describes a process by which beneficial mutations are kept and improve the suitability of a species to its environs.
It does not talk about genetics at all.
Why wouldn't mutations caused by horizontal gene transfer also apply to natural selection?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913588</id>
	<title>Human Interaction</title>
	<author>smd75</author>
	<datestamp>1264527060000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>I would believe that it could be considered a phase now, because due to human interaction, we've slowed its effectiveness. german engineered cars, selective breeding of animals and plants, Engineering crops to survive in locales that don't support that type of life, Geoengineering to farm in the desert (which I find funny when people complain about a drought IN THE DESERT)</p><p>Humans have taken the darwinism theory and shot it to hell.<br>Yes, at one time, it was a trend, now it has passed.</p></htmltext>
<tokenext>I would believe that it could be considered a phase now , because due to human interaction , we 've slowed its effectiveness .
german engineered cars , selective breeding of animals and plants , Engineering crops to survive in locales that do n't support that type of life , Geoengineering to farm in the desert ( which I find funny when people complain about a drought IN THE DESERT ) Humans have taken the darwinism theory and shot it to hell.Yes , at one time , it was a trend , now it has passed .</tokentext>
<sentencetext>I would believe that it could be considered a phase now, because due to human interaction, we've slowed its effectiveness.
german engineered cars, selective breeding of animals and plants, Engineering crops to survive in locales that don't support that type of life, Geoengineering to farm in the desert (which I find funny when people complain about a drought IN THE DESERT)Humans have taken the darwinism theory and shot it to hell.Yes, at one time, it was a trend, now it has passed.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912194</id>
	<title>darwin didn't know the details?  shocking!</title>
	<author>panthroman</author>
	<datestamp>1264513260000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>4</modscore>
	<htmltext><p>Have Woese and Goldenfeld a brilliant new idea?  All they're saying, I think, is that "parent" and "child" are the appropriate units of selection only when genes are passed vertically: from parent to child.  They're suggesting that horizontal gene transfer is underrated as a historical evolutionary force.</p><p>Agree or not, it hardly undermines Darwin.  Genes weren't known in the 19th century.  Darwin didn't have a clue about genes, so we're gonna knock him for being "wrong" about it?  I mean, was Jesus wrong about genes, too?  It's anachronistic silliness.</p><p>Science is fundamentally dynamic.  Any science that hasn't progressed in 150 years ain't doing too well.  (Dear creationists: stop calling us "Darwinists."  We've moved on.)  I mean, The Origin came out in <em>1859</em>, for crying out loud!  Darwin was more brilliant, more insightful, and rightly more famous than I'll ever be.  But if we both had to take a biology test right now, I'd kill him.</p></htmltext>
<tokenext>Have Woese and Goldenfeld a brilliant new idea ?
All they 're saying , I think , is that " parent " and " child " are the appropriate units of selection only when genes are passed vertically : from parent to child .
They 're suggesting that horizontal gene transfer is underrated as a historical evolutionary force.Agree or not , it hardly undermines Darwin .
Genes were n't known in the 19th century .
Darwin did n't have a clue about genes , so we 're gon na knock him for being " wrong " about it ?
I mean , was Jesus wrong about genes , too ?
It 's anachronistic silliness.Science is fundamentally dynamic .
Any science that has n't progressed in 150 years ai n't doing too well .
( Dear creationists : stop calling us " Darwinists .
" We 've moved on .
) I mean , The Origin came out in 1859 , for crying out loud !
Darwin was more brilliant , more insightful , and rightly more famous than I 'll ever be .
But if we both had to take a biology test right now , I 'd kill him .</tokentext>
<sentencetext>Have Woese and Goldenfeld a brilliant new idea?
All they're saying, I think, is that "parent" and "child" are the appropriate units of selection only when genes are passed vertically: from parent to child.
They're suggesting that horizontal gene transfer is underrated as a historical evolutionary force.Agree or not, it hardly undermines Darwin.
Genes weren't known in the 19th century.
Darwin didn't have a clue about genes, so we're gonna knock him for being "wrong" about it?
I mean, was Jesus wrong about genes, too?
It's anachronistic silliness.Science is fundamentally dynamic.
Any science that hasn't progressed in 150 years ain't doing too well.
(Dear creationists: stop calling us "Darwinists.
"  We've moved on.
)  I mean, The Origin came out in 1859, for crying out loud!
Darwin was more brilliant, more insightful, and rightly more famous than I'll ever be.
But if we both had to take a biology test right now, I'd kill him.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914336</id>
	<title>Re:Once again</title>
	<author>Thaidog</author>
	<datestamp>1264622700000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>But they're not really your ideas are they? I mean, unless you invented the religion chances are you've just have a "time share" on your beliefs.... and I hate timeshares.</p></htmltext>
<tokenext>But they 're not really your ideas are they ?
I mean , unless you invented the religion chances are you 've just have a " time share " on your beliefs.... and I hate timeshares .</tokentext>
<sentencetext>But they're not really your ideas are they?
I mean, unless you invented the religion chances are you've just have a "time share" on your beliefs.... and I hate timeshares.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911704</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30916284</id>
	<title>Really?</title>
	<author>harrytuttle777</author>
	<datestamp>1264603020000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>So, you mean that Uncle Jed, the Pig Fu&amp;*er is on the cutting edge of genetic evolution, and ensuring plenty of 'horizontal gene transfer'?</p></htmltext>
<tokenext>So , you mean that Uncle Jed , the Pig Fu&amp; * er is on the cutting edge of genetic evolution , and ensuring plenty of 'horizontal gene transfer ' ?</tokentext>
<sentencetext>So, you mean that Uncle Jed, the Pig Fu&amp;*er is on the cutting edge of genetic evolution, and ensuring plenty of 'horizontal gene transfer'?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911636</id>
	<title>Well duh?</title>
	<author>tzenes</author>
	<datestamp>1264509180000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>3</modscore>
	<htmltext><p>For anyone familiar with the Red Queen Hypothesis ( <a href="http://en.wikipedia.org/wiki/Red\_Queen" title="wikipedia.org" rel="nofollow">http://en.wikipedia.org/wiki/Red\_Queen</a> [wikipedia.org] ) this should be obvious.</p><p>While direct DNA transfer is not the component usually referred to by this "arms race," it is merely an extension of a known theory.</p><p>No one makes a big hype about this theory, because it doesn't say your grandfather was a monkey and piss off the religious nuts</p></htmltext>
<tokenext>For anyone familiar with the Red Queen Hypothesis ( http : //en.wikipedia.org/wiki/Red \ _Queen [ wikipedia.org ] ) this should be obvious.While direct DNA transfer is not the component usually referred to by this " arms race , " it is merely an extension of a known theory.No one makes a big hype about this theory , because it does n't say your grandfather was a monkey and piss off the religious nuts</tokentext>
<sentencetext>For anyone familiar with the Red Queen Hypothesis ( http://en.wikipedia.org/wiki/Red\_Queen [wikipedia.org] ) this should be obvious.While direct DNA transfer is not the component usually referred to by this "arms race," it is merely an extension of a known theory.No one makes a big hype about this theory, because it doesn't say your grandfather was a monkey and piss off the religious nuts</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912640</id>
	<title>RTFA</title>
	<author>gpronger</author>
	<datestamp>1264516380000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>A key point of the article that seems to have slipped past a fair number here is that the researchers are attempting to explain the robustness of the gene replication:<br> <br>

"Evidence for this lies in the genetic code, say Woese and Goldenfeld. Though it was discovered in the 1960s, no one had been able to explain how evolution could have made it so exquisitely tuned to resisting errors. Mutations happen in DNA coding all the time, and yet the proteins it produces often remain unaffected by these glitches. Darwinian evolution simply cannot explain how such a code could arise. But horizontal gene transfer can, say Woese and Goldenfeld."<br> <br>

And:<br> <br>

"In 1991, geneticists David Haig and Lawrence Hurst at the University of Oxford went further, showing that the code's level of error tolerance is truly remarkable. They studied the error tolerance of an enormous number of hypothetical genetic codes, all built from the same base pairs but with codons associated randomly with amino acids. They found that the actual code is around one in a million in terms of how good it is at error mitigation. "The actual genetic code," says Goldenfeld, "stands out like a sore thumb as being the best possible." That would seem to demand some evolutionary explanation. Yet, until now, no one has found one. The reason, say Woese and Goldenfeld, is that everyone has been thinking in terms of the wrong kind of evolution."<br> <br>

The point is that vertical evolution cant' get all the branches to the same point in the stability of gene coding. Their argument is that the fundamental mechanism that allows the system to move forward needed to evolve via vertical transfer and not horizontal. <br> <br>
It's true that its been known for a while, but the significance of horizontal transfer has not.</htmltext>
<tokenext>A key point of the article that seems to have slipped past a fair number here is that the researchers are attempting to explain the robustness of the gene replication : " Evidence for this lies in the genetic code , say Woese and Goldenfeld .
Though it was discovered in the 1960s , no one had been able to explain how evolution could have made it so exquisitely tuned to resisting errors .
Mutations happen in DNA coding all the time , and yet the proteins it produces often remain unaffected by these glitches .
Darwinian evolution simply can not explain how such a code could arise .
But horizontal gene transfer can , say Woese and Goldenfeld .
" And : " In 1991 , geneticists David Haig and Lawrence Hurst at the University of Oxford went further , showing that the code 's level of error tolerance is truly remarkable .
They studied the error tolerance of an enormous number of hypothetical genetic codes , all built from the same base pairs but with codons associated randomly with amino acids .
They found that the actual code is around one in a million in terms of how good it is at error mitigation .
" The actual genetic code , " says Goldenfeld , " stands out like a sore thumb as being the best possible .
" That would seem to demand some evolutionary explanation .
Yet , until now , no one has found one .
The reason , say Woese and Goldenfeld , is that everyone has been thinking in terms of the wrong kind of evolution .
" The point is that vertical evolution cant ' get all the branches to the same point in the stability of gene coding .
Their argument is that the fundamental mechanism that allows the system to move forward needed to evolve via vertical transfer and not horizontal .
It 's true that its been known for a while , but the significance of horizontal transfer has not .</tokentext>
<sentencetext>A key point of the article that seems to have slipped past a fair number here is that the researchers are attempting to explain the robustness of the gene replication: 

"Evidence for this lies in the genetic code, say Woese and Goldenfeld.
Though it was discovered in the 1960s, no one had been able to explain how evolution could have made it so exquisitely tuned to resisting errors.
Mutations happen in DNA coding all the time, and yet the proteins it produces often remain unaffected by these glitches.
Darwinian evolution simply cannot explain how such a code could arise.
But horizontal gene transfer can, say Woese and Goldenfeld.
" 

And: 

"In 1991, geneticists David Haig and Lawrence Hurst at the University of Oxford went further, showing that the code's level of error tolerance is truly remarkable.
They studied the error tolerance of an enormous number of hypothetical genetic codes, all built from the same base pairs but with codons associated randomly with amino acids.
They found that the actual code is around one in a million in terms of how good it is at error mitigation.
"The actual genetic code," says Goldenfeld, "stands out like a sore thumb as being the best possible.
" That would seem to demand some evolutionary explanation.
Yet, until now, no one has found one.
The reason, say Woese and Goldenfeld, is that everyone has been thinking in terms of the wrong kind of evolution.
" 

The point is that vertical evolution cant' get all the branches to the same point in the stability of gene coding.
Their argument is that the fundamental mechanism that allows the system to move forward needed to evolve via vertical transfer and not horizontal.
It's true that its been known for a while, but the significance of horizontal transfer has not.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30915018</id>
	<title>Re:It's what's for dinner.</title>
	<author>stifler9999</author>
	<datestamp>1264591320000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>Its a ZZ9 Plural Alpha thing, here on earth - its plural.</htmltext>
<tokenext>Its a ZZ9 Plural Alpha thing , here on earth - its plural .</tokentext>
<sentencetext>Its a ZZ9 Plural Alpha thing, here on earth - its plural.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912200</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911784</id>
	<title>Still natural selection</title>
	<author>Toonol</author>
	<datestamp>1264510020000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>3</modscore>
	<htmltext>We've already known that evolution depends on both inheritance of genetic matter and mutation of genetic matter.  This is a third mechanism for generating traits, but it stills falls under the umbrella of natural selection.  If the change is beneficial, and leads to more offspring, the change will be selected for.  Certainly worth study, and we may not have known the full scope of the phenomena, but it doesn't really contradict Darwinian evolution at all.<br> <br>

As a side note... I wonder if the fact this occurs in nature will silence some of the people objecting to genetic splicing?</htmltext>
<tokenext>We 've already known that evolution depends on both inheritance of genetic matter and mutation of genetic matter .
This is a third mechanism for generating traits , but it stills falls under the umbrella of natural selection .
If the change is beneficial , and leads to more offspring , the change will be selected for .
Certainly worth study , and we may not have known the full scope of the phenomena , but it does n't really contradict Darwinian evolution at all .
As a side note... I wonder if the fact this occurs in nature will silence some of the people objecting to genetic splicing ?</tokentext>
<sentencetext>We've already known that evolution depends on both inheritance of genetic matter and mutation of genetic matter.
This is a third mechanism for generating traits, but it stills falls under the umbrella of natural selection.
If the change is beneficial, and leads to more offspring, the change will be selected for.
Certainly worth study, and we may not have known the full scope of the phenomena, but it doesn't really contradict Darwinian evolution at all.
As a side note... I wonder if the fact this occurs in nature will silence some of the people objecting to genetic splicing?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912358</id>
	<title>That's very true</title>
	<author>aflag</author>
	<datestamp>1264514340000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>it's how peter parker got his powers!</htmltext>
<tokenext>it 's how peter parker got his powers !</tokentext>
<sentencetext>it's how peter parker got his powers!</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911884</id>
	<title>Re:Well duh?</title>
	<author>UnknowingFool</author>
	<datestamp>1264510800000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>Also to note, this doesn't supplant Darwinian evolution but adds to it.  I can see that this might be plausible in the early stages of life on this planet where microbes would acquire genes from other microbes.  I'm wondering if the proponents consider the mitochondria as one example of this horizontal evolution?</htmltext>
<tokenext>Also to note , this does n't supplant Darwinian evolution but adds to it .
I can see that this might be plausible in the early stages of life on this planet where microbes would acquire genes from other microbes .
I 'm wondering if the proponents consider the mitochondria as one example of this horizontal evolution ?</tokentext>
<sentencetext>Also to note, this doesn't supplant Darwinian evolution but adds to it.
I can see that this might be plausible in the early stages of life on this planet where microbes would acquire genes from other microbes.
I'm wondering if the proponents consider the mitochondria as one example of this horizontal evolution?</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911636</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913182</id>
	<title>Re:Proven example:</title>
	<author>Anonymous</author>
	<datestamp>1264522380000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>ah, so you are suggesting that such a system requires "genius"?  you're fired.</p></htmltext>
<tokenext>ah , so you are suggesting that such a system requires " genius " ?
you 're fired .</tokentext>
<sentencetext>ah, so you are suggesting that such a system requires "genius"?
you're fired.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911614</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30915230</id>
	<title>Horizontal gene transfer less selective</title>
	<author>Anonymous</author>
	<datestamp>1264593960000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>If you want to explain adaption and the rich variety in nature then a more selective process like vertical gene transfer are probably more relevant.</p><p>I think its a question of relevance rather than ignorance from the evolutionary biologists part.</p></htmltext>
<tokenext>If you want to explain adaption and the rich variety in nature then a more selective process like vertical gene transfer are probably more relevant.I think its a question of relevance rather than ignorance from the evolutionary biologists part .</tokentext>
<sentencetext>If you want to explain adaption and the rich variety in nature then a more selective process like vertical gene transfer are probably more relevant.I think its a question of relevance rather than ignorance from the evolutionary biologists part.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913546</id>
	<title>Maybe this defeats the contradiction...</title>
	<author>WheelDweller</author>
	<datestamp>1264526760000</datestamp>
	<modclass>None</modclass>
	<modscore>-1</modscore>
	<htmltext><p>Remember how atoms bumped into each other to make a protien, then proteins bumped into each other until non-vertabrates were accidentally made?  Millenia go by and eventually here come the vertabrates and eventually tax collectors.</p><p>Except one tiny problem: The trilobite's regarded as the oldest living creature, and it has a spine.</p><p>I have NO PROBLEM with animals changing over time. But clearly the 'out of nowhere' concept has a showstopper of a problem.  Is this the only answer science has?  I mean, Darwin couldn't even look inside the cells at the time....all this time and nothing better has been considered?</p></htmltext>
<tokenext>Remember how atoms bumped into each other to make a protien , then proteins bumped into each other until non-vertabrates were accidentally made ?
Millenia go by and eventually here come the vertabrates and eventually tax collectors.Except one tiny problem : The trilobite 's regarded as the oldest living creature , and it has a spine.I have NO PROBLEM with animals changing over time .
But clearly the 'out of nowhere ' concept has a showstopper of a problem .
Is this the only answer science has ?
I mean , Darwin could n't even look inside the cells at the time....all this time and nothing better has been considered ?</tokentext>
<sentencetext>Remember how atoms bumped into each other to make a protien, then proteins bumped into each other until non-vertabrates were accidentally made?
Millenia go by and eventually here come the vertabrates and eventually tax collectors.Except one tiny problem: The trilobite's regarded as the oldest living creature, and it has a spine.I have NO PROBLEM with animals changing over time.
But clearly the 'out of nowhere' concept has a showstopper of a problem.
Is this the only answer science has?
I mean, Darwin couldn't even look inside the cells at the time....all this time and nothing better has been considered?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30919558</id>
	<title>Re:I realize scientists need a breakthrough</title>
	<author>john8-32</author>
	<datestamp>1264616220000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext>I do not suspect...but I KNOW that neither of these is true. God Himself is the Creator of all that man can see and can not see. The natural and the supernatural. It never ceases to amaze a regular person like me...that you self-important "Scientists"-(FYI Jehovah GOD is the Chief Scientist of all)-grasp desperately at any alternative, OTHER than GOD, that comes down the humanists pike through which the majority of scientific self-inflated "egos" feed off one another.Ever preening before each other. Like Richard Dawkins who clings so desperately to his delusions..no matter what the evidence for Design  and THE super-intelligent, all Powerful Designer is. Stephen Hawkings is the brilliant one in relation to created man--he KNOWS and has stated this fact...that Evidence for a Grand Designer is everywhere.

Truly I feel sorry for all who figure they can do away with God....it's so sad to see. Believe me when I do not say this in any way mockingly..but because I care.

You understand that YOU cannot save anyone-not even yourselves- from what is to come upon this earth..and in God's Perfect Timing, upon all those who reject God's Son, mankind's Savior on the Day of Judgment -before Whose Throne of Holiness and Righteousness the unrepentant will stand.

1 Corinthians 18:25~"For to those who are perishing the message of the cross is foolishness, but to us who are being saved it is God's power.  For it is written:
I will destroy the wisdom of the wise, and I will set aside the understanding of the experts.

Where is the philosopher?  Where is the scholar? Where is the debater of this age?  Hasn't God made the world's wisdom foolish? For since, in God's wisdom, the world did not know God through wisdom, God was pleased to save those who believe through the foolishness of the message preached. For the Jews ask for signs  and the Greeks seek wisdom, but we preach Christ crucified, a stumbling block to the Jews and foolishness to the Gentiles. Yet to those who are called,  both Jews and Greeks, Christ is God's power and God's wisdom, because God's foolishness is wiser than human wisdom, and God's weakness is stronger than human strength.

Romans 1:18-25~" For God's wrath is revealed from heaven against all godlessness and unrighteousness of people who by their unrighteousness suppress the truth,  since what can be known about God is evident among them,  because God has shown it to them. From the creation of the world  His invisible attributes, that is, His eternal power and divine nature, have been clearly seen, being understood through what He has made. As a result, people  are without excuse.  For though they knew God, they did not glorify Him as God or show gratitude. Instead, their thinking became nonsense, and their senseless minds  were darkened. Claiming to be wise, they became fools  and exchanged the glory of the immortal God for images resembling mortal man, birds, four-footed animals, and reptiles.

Therefore God delivered them over in the cravings of their hearts to sexual impurity, so that their bodies were degraded among themselves. They exchanged the truth of God for a lie, and worshiped and served something created instead of the Creator, who is blessed forever. Amen.

Truly He is God Almighty..and there is none other God besides He. I share this with you in the love of Jesus Christ.</htmltext>
<tokenext>I do not suspect...but I KNOW that neither of these is true .
God Himself is the Creator of all that man can see and can not see .
The natural and the supernatural .
It never ceases to amaze a regular person like me...that you self-important " Scientists " - ( FYI Jehovah GOD is the Chief Scientist of all ) -grasp desperately at any alternative , OTHER than GOD , that comes down the humanists pike through which the majority of scientific self-inflated " egos " feed off one another.Ever preening before each other .
Like Richard Dawkins who clings so desperately to his delusions..no matter what the evidence for Design and THE super-intelligent , all Powerful Designer is .
Stephen Hawkings is the brilliant one in relation to created man--he KNOWS and has stated this fact...that Evidence for a Grand Designer is everywhere .
Truly I feel sorry for all who figure they can do away with God....it 's so sad to see .
Believe me when I do not say this in any way mockingly..but because I care .
You understand that YOU can not save anyone-not even yourselves- from what is to come upon this earth..and in God 's Perfect Timing , upon all those who reject God 's Son , mankind 's Savior on the Day of Judgment -before Whose Throne of Holiness and Righteousness the unrepentant will stand .
1 Corinthians 18 : 25 ~ " For to those who are perishing the message of the cross is foolishness , but to us who are being saved it is God 's power .
For it is written : I will destroy the wisdom of the wise , and I will set aside the understanding of the experts .
Where is the philosopher ?
Where is the scholar ?
Where is the debater of this age ?
Has n't God made the world 's wisdom foolish ?
For since , in God 's wisdom , the world did not know God through wisdom , God was pleased to save those who believe through the foolishness of the message preached .
For the Jews ask for signs and the Greeks seek wisdom , but we preach Christ crucified , a stumbling block to the Jews and foolishness to the Gentiles .
Yet to those who are called , both Jews and Greeks , Christ is God 's power and God 's wisdom , because God 's foolishness is wiser than human wisdom , and God 's weakness is stronger than human strength .
Romans 1 : 18-25 ~ " For God 's wrath is revealed from heaven against all godlessness and unrighteousness of people who by their unrighteousness suppress the truth , since what can be known about God is evident among them , because God has shown it to them .
From the creation of the world His invisible attributes , that is , His eternal power and divine nature , have been clearly seen , being understood through what He has made .
As a result , people are without excuse .
For though they knew God , they did not glorify Him as God or show gratitude .
Instead , their thinking became nonsense , and their senseless minds were darkened .
Claiming to be wise , they became fools and exchanged the glory of the immortal God for images resembling mortal man , birds , four-footed animals , and reptiles .
Therefore God delivered them over in the cravings of their hearts to sexual impurity , so that their bodies were degraded among themselves .
They exchanged the truth of God for a lie , and worshiped and served something created instead of the Creator , who is blessed forever .
Amen . Truly He is God Almighty..and there is none other God besides He .
I share this with you in the love of Jesus Christ .</tokentext>
<sentencetext>I do not suspect...but I KNOW that neither of these is true.
God Himself is the Creator of all that man can see and can not see.
The natural and the supernatural.
It never ceases to amaze a regular person like me...that you self-important "Scientists"-(FYI Jehovah GOD is the Chief Scientist of all)-grasp desperately at any alternative, OTHER than GOD, that comes down the humanists pike through which the majority of scientific self-inflated "egos" feed off one another.Ever preening before each other.
Like Richard Dawkins who clings so desperately to his delusions..no matter what the evidence for Design  and THE super-intelligent, all Powerful Designer is.
Stephen Hawkings is the brilliant one in relation to created man--he KNOWS and has stated this fact...that Evidence for a Grand Designer is everywhere.
Truly I feel sorry for all who figure they can do away with God....it's so sad to see.
Believe me when I do not say this in any way mockingly..but because I care.
You understand that YOU cannot save anyone-not even yourselves- from what is to come upon this earth..and in God's Perfect Timing, upon all those who reject God's Son, mankind's Savior on the Day of Judgment -before Whose Throne of Holiness and Righteousness the unrepentant will stand.
1 Corinthians 18:25~"For to those who are perishing the message of the cross is foolishness, but to us who are being saved it is God's power.
For it is written:
I will destroy the wisdom of the wise, and I will set aside the understanding of the experts.
Where is the philosopher?
Where is the scholar?
Where is the debater of this age?
Hasn't God made the world's wisdom foolish?
For since, in God's wisdom, the world did not know God through wisdom, God was pleased to save those who believe through the foolishness of the message preached.
For the Jews ask for signs  and the Greeks seek wisdom, but we preach Christ crucified, a stumbling block to the Jews and foolishness to the Gentiles.
Yet to those who are called,  both Jews and Greeks, Christ is God's power and God's wisdom, because God's foolishness is wiser than human wisdom, and God's weakness is stronger than human strength.
Romans 1:18-25~" For God's wrath is revealed from heaven against all godlessness and unrighteousness of people who by their unrighteousness suppress the truth,  since what can be known about God is evident among them,  because God has shown it to them.
From the creation of the world  His invisible attributes, that is, His eternal power and divine nature, have been clearly seen, being understood through what He has made.
As a result, people  are without excuse.
For though they knew God, they did not glorify Him as God or show gratitude.
Instead, their thinking became nonsense, and their senseless minds  were darkened.
Claiming to be wise, they became fools  and exchanged the glory of the immortal God for images resembling mortal man, birds, four-footed animals, and reptiles.
Therefore God delivered them over in the cravings of their hearts to sexual impurity, so that their bodies were degraded among themselves.
They exchanged the truth of God for a lie, and worshiped and served something created instead of the Creator, who is blessed forever.
Amen.

Truly He is God Almighty..and there is none other God besides He.
I share this with you in the love of Jesus Christ.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911600</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911974</id>
	<title>Viruses</title>
	<author>gedrin</author>
	<datestamp>1264511580000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>It's interesting that infectious viruses may form an essential foundation for our own evolution.  It may even be that viruses are a developed strategy for "importing tallent" from competitors or neighbors.  It has interesting things to say about inerconnection between organisms in a species and between species.  Infectability may be a long term strategy for development.<br> <br>Then again, it could be exactly the other way.  Advanced organisms are just diverse platforms which viruses have evolved as elaborate tools and development shops for their survival and propagation.</htmltext>
<tokenext>It 's interesting that infectious viruses may form an essential foundation for our own evolution .
It may even be that viruses are a developed strategy for " importing tallent " from competitors or neighbors .
It has interesting things to say about inerconnection between organisms in a species and between species .
Infectability may be a long term strategy for development .
Then again , it could be exactly the other way .
Advanced organisms are just diverse platforms which viruses have evolved as elaborate tools and development shops for their survival and propagation .</tokentext>
<sentencetext>It's interesting that infectious viruses may form an essential foundation for our own evolution.
It may even be that viruses are a developed strategy for "importing tallent" from competitors or neighbors.
It has interesting things to say about inerconnection between organisms in a species and between species.
Infectability may be a long term strategy for development.
Then again, it could be exactly the other way.
Advanced organisms are just diverse platforms which viruses have evolved as elaborate tools and development shops for their survival and propagation.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912074</id>
	<title>I know</title>
	<author>Anonymous</author>
	<datestamp>1264512240000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>I already beat it. The next phase has a really hard boss.</p></htmltext>
<tokenext>I already beat it .
The next phase has a really hard boss .</tokentext>
<sentencetext>I already beat it.
The next phase has a really hard boss.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913076</id>
	<title>Re:I realize scientists need a breakthrough</title>
	<author>Anonymous</author>
	<datestamp>1264521240000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>'Both' ? I hope you mean 'many'. 'Natural Selection' is one mechanism of evolution, 'Sexual Selection' is another. 'Horizontal Gene Transfer' is just another. They all work together or separately in driving evolution.</p></htmltext>
<tokenext>'Both ' ?
I hope you mean 'many' .
'Natural Selection ' is one mechanism of evolution , 'Sexual Selection ' is another .
'Horizontal Gene Transfer ' is just another .
They all work together or separately in driving evolution .</tokentext>
<sentencetext>'Both' ?
I hope you mean 'many'.
'Natural Selection' is one mechanism of evolution, 'Sexual Selection' is another.
'Horizontal Gene Transfer' is just another.
They all work together or separately in driving evolution.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911600</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912176</id>
	<title>Explains a lot</title>
	<author>joepress99</author>
	<datestamp>1264513080000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>especially my co-workers</p></htmltext>
<tokenext>especially my co-workers</tokentext>
<sentencetext>especially my co-workers</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30915176</id>
	<title>Attacking Darwin sells issues</title>
	<author>VShael</author>
	<datestamp>1264593420000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext><p>It seems to me that one of the reasons journalism science is so bad, is that they believe (rightly or wrongly) that any article which appears to be saying "DARWIN WAS WRONG!" will sell more copies.</p><p>The article doesn't say that, obviously, but it at a cursory glance it could be perceived as that.</p></htmltext>
<tokenext>It seems to me that one of the reasons journalism science is so bad , is that they believe ( rightly or wrongly ) that any article which appears to be saying " DARWIN WAS WRONG !
" will sell more copies.The article does n't say that , obviously , but it at a cursory glance it could be perceived as that .</tokentext>
<sentencetext>It seems to me that one of the reasons journalism science is so bad, is that they believe (rightly or wrongly) that any article which appears to be saying "DARWIN WAS WRONG!
" will sell more copies.The article doesn't say that, obviously, but it at a cursory glance it could be perceived as that.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30918074</id>
	<title>Re:Capitalism?</title>
	<author>mcgrew</author>
	<datestamp>1264610640000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><i>Would Darwinian revolution be a happy meritocracy that arose as a kind of "compromise"?<br>However, I've always read Darwinian evolution as "survival of the fittest", with no qualifier as to how you go about surviving.</i></p><p>There is an element of luck in both capitalism and evolution, and luck probably plays a bigger part in both than fitness. Of course, obviously a bad or outmoded business plan will cause a business to fail, and a bad mutation will cause an organism to die before it can reproduce, but if there's a slow runner that doesn't get eaten by a tiger, that's pure luck. My uncle became rich, and even though he worked his ass of for it, there were a number of lucky happenstances that had to happen for him to gain his wealth.</p></htmltext>
<tokenext>Would Darwinian revolution be a happy meritocracy that arose as a kind of " compromise " ? However , I 've always read Darwinian evolution as " survival of the fittest " , with no qualifier as to how you go about surviving.There is an element of luck in both capitalism and evolution , and luck probably plays a bigger part in both than fitness .
Of course , obviously a bad or outmoded business plan will cause a business to fail , and a bad mutation will cause an organism to die before it can reproduce , but if there 's a slow runner that does n't get eaten by a tiger , that 's pure luck .
My uncle became rich , and even though he worked his ass of for it , there were a number of lucky happenstances that had to happen for him to gain his wealth .</tokentext>
<sentencetext>Would Darwinian revolution be a happy meritocracy that arose as a kind of "compromise"?However, I've always read Darwinian evolution as "survival of the fittest", with no qualifier as to how you go about surviving.There is an element of luck in both capitalism and evolution, and luck probably plays a bigger part in both than fitness.
Of course, obviously a bad or outmoded business plan will cause a business to fail, and a bad mutation will cause an organism to die before it can reproduce, but if there's a slow runner that doesn't get eaten by a tiger, that's pure luck.
My uncle became rich, and even though he worked his ass of for it, there were a number of lucky happenstances that had to happen for him to gain his wealth.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911666</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913166</id>
	<title>Re:Gene Synthesis</title>
	<author>Anonymous</author>
	<datestamp>1264522260000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>Whilst Proteins have catalytic properties but aren't good for transferring information and DNA is good at storing information but doesn't act as a catalyst RNA can do both. RNA transfers genetic info from DNA out of the nucleus where other RNA structures called ribosomes can translate the code into proteins... But one hypothesis is that RNA could thus form self-replicating strands, some of which adapted over time to polymerise DNA and proteins from their building blocks.</p></htmltext>
<tokenext>Whilst Proteins have catalytic properties but are n't good for transferring information and DNA is good at storing information but does n't act as a catalyst RNA can do both .
RNA transfers genetic info from DNA out of the nucleus where other RNA structures called ribosomes can translate the code into proteins... But one hypothesis is that RNA could thus form self-replicating strands , some of which adapted over time to polymerise DNA and proteins from their building blocks .</tokentext>
<sentencetext>Whilst Proteins have catalytic properties but aren't good for transferring information and DNA is good at storing information but doesn't act as a catalyst RNA can do both.
RNA transfers genetic info from DNA out of the nucleus where other RNA structures called ribosomes can translate the code into proteins... But one hypothesis is that RNA could thus form self-replicating strands, some of which adapted over time to polymerise DNA and proteins from their building blocks.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912130</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912544</id>
	<title>Re:Gene Synthesis</title>
	<author>SpinyNorman</author>
	<datestamp>1264515540000</datestamp>
	<modclass>None</modclass>
	<modscore>2</modscore>
	<htmltext><p>DNA is what evolves - i.e. instructions to make proteins, not proteins themselves. Of course most random changes to the instructions are maladaptive or at best useless, but very occasionally not.</p><p>I think what happens in practice is that it's the "useless" changes (do no harm, but under current conditions do no good) that may play the largest role... these can accumulate in different populations of a species and become a differentiator when the environment changes (which is the real driver of evolution) and previously useless traits become either helpful or harmful.</p></htmltext>
<tokenext>DNA is what evolves - i.e .
instructions to make proteins , not proteins themselves .
Of course most random changes to the instructions are maladaptive or at best useless , but very occasionally not.I think what happens in practice is that it 's the " useless " changes ( do no harm , but under current conditions do no good ) that may play the largest role... these can accumulate in different populations of a species and become a differentiator when the environment changes ( which is the real driver of evolution ) and previously useless traits become either helpful or harmful .</tokentext>
<sentencetext>DNA is what evolves - i.e.
instructions to make proteins, not proteins themselves.
Of course most random changes to the instructions are maladaptive or at best useless, but very occasionally not.I think what happens in practice is that it's the "useless" changes (do no harm, but under current conditions do no good) that may play the largest role... these can accumulate in different populations of a species and become a differentiator when the environment changes (which is the real driver of evolution) and previously useless traits become either helpful or harmful.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912130</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912200</id>
	<title>Re:It's what's for dinner.</title>
	<author>nacturation</author>
	<datestamp>1264513320000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><div class="quote"><p>The second is referring to mitochondria not kitchen bitches.</p></div><p>Where do the midichlorians come into play?</p></div>
	</htmltext>
<tokenext>The second is referring to mitochondria not kitchen bitches.Where do the midichlorians come into play ?</tokentext>
<sentencetext>The second is referring to mitochondria not kitchen bitches.Where do the midichlorians come into play?
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911776</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912012</id>
	<title>Recent discoveries...</title>
	<author>Uncle\_Meataxe</author>
	<datestamp>1264511820000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>2</modscore>
	<htmltext>There have been some other interesting discoveries regarding horizontal gene transfer recently. For example, this PNAS paper looks at sea slugs that can photosynthesize by themselves --  <a href="http://www.pnas.org/content/105/46/17867.full.pdf" title="pnas.org" rel="nofollow">http://www.pnas.org/content/105/46/17867.full.pdf</a> [pnas.org]). The sea slugs photosynthesize through a combination of harvesting chloroplasts from the algae they eat and via horizontal transfer of genes involved in photosynthesis from these same algae. This is a bizarre and amazing discovery which demonstrates how genes can move from plants and be incorporated in an animal genome.</htmltext>
<tokenext>There have been some other interesting discoveries regarding horizontal gene transfer recently .
For example , this PNAS paper looks at sea slugs that can photosynthesize by themselves -- http : //www.pnas.org/content/105/46/17867.full.pdf [ pnas.org ] ) .
The sea slugs photosynthesize through a combination of harvesting chloroplasts from the algae they eat and via horizontal transfer of genes involved in photosynthesis from these same algae .
This is a bizarre and amazing discovery which demonstrates how genes can move from plants and be incorporated in an animal genome .</tokentext>
<sentencetext>There have been some other interesting discoveries regarding horizontal gene transfer recently.
For example, this PNAS paper looks at sea slugs that can photosynthesize by themselves --  http://www.pnas.org/content/105/46/17867.full.pdf [pnas.org]).
The sea slugs photosynthesize through a combination of harvesting chloroplasts from the algae they eat and via horizontal transfer of genes involved in photosynthesis from these same algae.
This is a bizarre and amazing discovery which demonstrates how genes can move from plants and be incorporated in an animal genome.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913482</id>
	<title>Re:I realize scientists need a breakthrough</title>
	<author>Anonymous</author>
	<datestamp>1264526100000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>I highly recommend checking out The Selfish Gene. It's a great book. And between the stuff they leave out in school biology and the mists of time, it's very easy to get confused about the mechanics of how genes propagate.</p><p>Specifically, as another poster already commented: genes don't get passed on sexually reproducing organisms unless they make their way into the act of reproduction.</p><p>Some of our genetic code has been demonstrated to be viral (in particular, the mammalian placenta contains a comparatively large amount of viral code). But what you're talking about (bacteria lending their abilities to our digestive organs and that somehow getting passed on) simply doesn't happen. What *does* happen that's perhaps more interesting is coevolution...we could have evolved in such a way that made our stomachs more hospitable for the bacteria, for instance. There are some really colorful examples of coevolution happening with orchids, check out WP for more. Also, Dawkins' latest book has some nice glossy pictures concerning this.</p></htmltext>
<tokenext>I highly recommend checking out The Selfish Gene .
It 's a great book .
And between the stuff they leave out in school biology and the mists of time , it 's very easy to get confused about the mechanics of how genes propagate.Specifically , as another poster already commented : genes do n't get passed on sexually reproducing organisms unless they make their way into the act of reproduction.Some of our genetic code has been demonstrated to be viral ( in particular , the mammalian placenta contains a comparatively large amount of viral code ) .
But what you 're talking about ( bacteria lending their abilities to our digestive organs and that somehow getting passed on ) simply does n't happen .
What * does * happen that 's perhaps more interesting is coevolution...we could have evolved in such a way that made our stomachs more hospitable for the bacteria , for instance .
There are some really colorful examples of coevolution happening with orchids , check out WP for more .
Also , Dawkins ' latest book has some nice glossy pictures concerning this .</tokentext>
<sentencetext>I highly recommend checking out The Selfish Gene.
It's a great book.
And between the stuff they leave out in school biology and the mists of time, it's very easy to get confused about the mechanics of how genes propagate.Specifically, as another poster already commented: genes don't get passed on sexually reproducing organisms unless they make their way into the act of reproduction.Some of our genetic code has been demonstrated to be viral (in particular, the mammalian placenta contains a comparatively large amount of viral code).
But what you're talking about (bacteria lending their abilities to our digestive organs and that somehow getting passed on) simply doesn't happen.
What *does* happen that's perhaps more interesting is coevolution...we could have evolved in such a way that made our stomachs more hospitable for the bacteria, for instance.
There are some really colorful examples of coevolution happening with orchids, check out WP for more.
Also, Dawkins' latest book has some nice glossy pictures concerning this.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912030</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911936</id>
	<title>Re:Capitalism?</title>
	<author>Chris Burke</author>
	<datestamp>1264511100000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>4</modscore>
	<htmltext><p><i>However, I've always read Darwinian evolution as "survival of the fittest", with no qualifier as to how you go about surviving.</i></p><p>"Survival of the fittest" aka Natural Selection was half of Darwinian evolution.  This was the half about how traits were selected for in the environment.</p><p>The other half was how an organism's traits came about, and his theory was that traits were passed from parents to offspring in the reproductive cells via some biological mechanism that allowed for combination and mutation.  Eventually we discovered DNA, the very biological mechanism in question that had traits like Darwin predicted (though Mendel was the one who really nailed down the probably behavior of this then-unknown mechanism).</p><p>"Horizontal" evolution doesn't fall into that category, though.  So it's not "Darwinian".  Even though natural selection (obviously) still applies to what gene transfers result in successful organisms.</p><p>As the summary mentions, this is well known in micro-organisms.  In fact as far as I can tell they aren't arguing that it applies to anything <i>but</i> microorganisms.  The argument seems more like that because these are the most common life forms on earth and also the oldest, Darwinian evolution is not the most common or dominant form of evolution.</p><p>Which is a good point.  Though really, as far as what affects <i>us</i> and other sexually reproducing creatures, Darwinian evolution is still 'it' more or less.  The real importance of this breakthrough is in studying how the evolutionary mechanisms themselves evolved -- evolution is of course not immune to evolution.<nobr> <wbr></nobr>;)  This is going to be a powerful way of thinking about how early aspects of DNA came to be.</p><p>But just to be clear -- if someone says that this proves Darwin was wrong, evolution is a sham, and therefore their beliefs are probably right, go ahead and slap them.<nobr> <wbr></nobr>:)  All this means is that evolution is even more complicated and powerful than previously thought.</p></htmltext>
<tokenext>However , I 've always read Darwinian evolution as " survival of the fittest " , with no qualifier as to how you go about surviving .
" Survival of the fittest " aka Natural Selection was half of Darwinian evolution .
This was the half about how traits were selected for in the environment.The other half was how an organism 's traits came about , and his theory was that traits were passed from parents to offspring in the reproductive cells via some biological mechanism that allowed for combination and mutation .
Eventually we discovered DNA , the very biological mechanism in question that had traits like Darwin predicted ( though Mendel was the one who really nailed down the probably behavior of this then-unknown mechanism ) .
" Horizontal " evolution does n't fall into that category , though .
So it 's not " Darwinian " .
Even though natural selection ( obviously ) still applies to what gene transfers result in successful organisms.As the summary mentions , this is well known in micro-organisms .
In fact as far as I can tell they are n't arguing that it applies to anything but microorganisms .
The argument seems more like that because these are the most common life forms on earth and also the oldest , Darwinian evolution is not the most common or dominant form of evolution.Which is a good point .
Though really , as far as what affects us and other sexually reproducing creatures , Darwinian evolution is still 'it ' more or less .
The real importance of this breakthrough is in studying how the evolutionary mechanisms themselves evolved -- evolution is of course not immune to evolution .
; ) This is going to be a powerful way of thinking about how early aspects of DNA came to be.But just to be clear -- if someone says that this proves Darwin was wrong , evolution is a sham , and therefore their beliefs are probably right , go ahead and slap them .
: ) All this means is that evolution is even more complicated and powerful than previously thought .</tokentext>
<sentencetext>However, I've always read Darwinian evolution as "survival of the fittest", with no qualifier as to how you go about surviving.
"Survival of the fittest" aka Natural Selection was half of Darwinian evolution.
This was the half about how traits were selected for in the environment.The other half was how an organism's traits came about, and his theory was that traits were passed from parents to offspring in the reproductive cells via some biological mechanism that allowed for combination and mutation.
Eventually we discovered DNA, the very biological mechanism in question that had traits like Darwin predicted (though Mendel was the one who really nailed down the probably behavior of this then-unknown mechanism).
"Horizontal" evolution doesn't fall into that category, though.
So it's not "Darwinian".
Even though natural selection (obviously) still applies to what gene transfers result in successful organisms.As the summary mentions, this is well known in micro-organisms.
In fact as far as I can tell they aren't arguing that it applies to anything but microorganisms.
The argument seems more like that because these are the most common life forms on earth and also the oldest, Darwinian evolution is not the most common or dominant form of evolution.Which is a good point.
Though really, as far as what affects us and other sexually reproducing creatures, Darwinian evolution is still 'it' more or less.
The real importance of this breakthrough is in studying how the evolutionary mechanisms themselves evolved -- evolution is of course not immune to evolution.
;)  This is going to be a powerful way of thinking about how early aspects of DNA came to be.But just to be clear -- if someone says that this proves Darwin was wrong, evolution is a sham, and therefore their beliefs are probably right, go ahead and slap them.
:)  All this means is that evolution is even more complicated and powerful than previously thought.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911666</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913178</id>
	<title>Re:I realize scientists need a breakthrough</title>
	<author>Ihmhi</author>
	<datestamp>1264522380000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>What's the kinda of evolution where you wave around a crystal to turn one Pok&#233;mon into another? I'm more in favor of that one. Crystalian evolution.</p></htmltext>
<tokenext>What 's the kinda of evolution where you wave around a crystal to turn one Pok   mon into another ?
I 'm more in favor of that one .
Crystalian evolution .</tokentext>
<sentencetext>What's the kinda of evolution where you wave around a crystal to turn one Pokémon into another?
I'm more in favor of that one.
Crystalian evolution.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911600</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30916352</id>
	<title>Example of this</title>
	<author>JTsyo</author>
	<datestamp>1264603320000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><a href="http://www.msnbc.msn.com/id/34824610/ns/technology\_and\_science-science/?GT1=43001" title="msn.com" rel="nofollow">http://www.msnbc.msn.com/id/34824610/ns/technology\_and\_science-science/?GT1=43001</a> [msn.com] <br>

The sneaky slugs seem to have stolen the genes that enable this skill from algae that they've eaten. With their contraband genes, the slugs can carry out photosynthesis &mdash; the process plants use to convert sunlight into energy.</htmltext>
<tokenext>http : //www.msnbc.msn.com/id/34824610/ns/technology \ _and \ _science-science/ ? GT1 = 43001 [ msn.com ] The sneaky slugs seem to have stolen the genes that enable this skill from algae that they 've eaten .
With their contraband genes , the slugs can carry out photosynthesis    the process plants use to convert sunlight into energy .</tokentext>
<sentencetext>http://www.msnbc.msn.com/id/34824610/ns/technology\_and\_science-science/?GT1=43001 [msn.com] 

The sneaky slugs seem to have stolen the genes that enable this skill from algae that they've eaten.
With their contraband genes, the slugs can carry out photosynthesis — the process plants use to convert sunlight into energy.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912748</id>
	<title>Re:It's still natural selection</title>
	<author>kungfugleek</author>
	<datestamp>1264517520000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>I've always thought altruism is when one person sacrifices oneself; not when a society chooses which ones get sacrificed.</htmltext>
<tokenext>I 've always thought altruism is when one person sacrifices oneself ; not when a society chooses which ones get sacrificed .</tokentext>
<sentencetext>I've always thought altruism is when one person sacrifices oneself; not when a society chooses which ones get sacrificed.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911836</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914074</id>
	<title>Old Hat</title>
	<author>Sam Garedner</author>
	<datestamp>1264532520000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>In my classes genetics I learned this some 30 years ago, so why an article now?</htmltext>
<tokenext>In my classes genetics I learned this some 30 years ago , so why an article now ?</tokentext>
<sentencetext>In my classes genetics I learned this some 30 years ago, so why an article now?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912134</id>
	<title>Re:Well duh?</title>
	<author>wealthychef</author>
	<datestamp>1264512600000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>3</modscore>
	<htmltext><p> <i>Just why is it that ultra-conservative rants about God or racial superiority or anti-socialism are instantly modded off-topic, troll, and/or flamebait until they sink beneath the thresh hold</i> </p><p>
You're seriously asking this question?
</p><p> <i> and yet completely off-topic attacks on Creationism in every story even vaguely connected with biology or evolution get modded +5 insightful?</i> </p><p>
I think you are exaggerating.</p></htmltext>
<tokenext>Just why is it that ultra-conservative rants about God or racial superiority or anti-socialism are instantly modded off-topic , troll , and/or flamebait until they sink beneath the thresh hold You 're seriously asking this question ?
and yet completely off-topic attacks on Creationism in every story even vaguely connected with biology or evolution get modded + 5 insightful ?
I think you are exaggerating .</tokentext>
<sentencetext> Just why is it that ultra-conservative rants about God or racial superiority or anti-socialism are instantly modded off-topic, troll, and/or flamebait until they sink beneath the thresh hold 
You're seriously asking this question?
and yet completely off-topic attacks on Creationism in every story even vaguely connected with biology or evolution get modded +5 insightful?
I think you are exaggerating.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912010</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914018</id>
	<title>This is significant</title>
	<author>Chicken\_Kickers</author>
	<datestamp>1264531860000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>Someone above ranted about the overuse of the word "paradigm-shift" and I couldn't agree more. However, in this case, I think the use is warranted. Woese himself caused a paradigm-shift when he discovered that the 16S and 18S ribosomal gene is highly conserved in all known organism, meaning that organisms that have similar 16S or 18S sequences are more closely related to each other and vice versa. The previous paradigm, and if you were old enough to remember learning in school was based largely on the morphological and to a certain extent, biochemical properties of the organisms. The current model used in life-sciences are tree-like where "more evolved" species branch off from "less evolved" species and if you trace back this tree, you get to the root of life, where the hypothetical Last Universal Common Ancestor (LUCA)is. This new paradigm proposed by Woese drastically change this neat picture into a cloud-like diagram, with organisms having multiple links with other organisms. No longer can you say organism x2 has a direct lineage to organism x1 since horizontal gene transfers have clouded the relationships with a big impact on the study of evolution. This also has a big impact on computational biology and I am sure, this is more in line with the speciality of the Slashdot crowd. More complex algorithms and computational power have to be utilised to visualize this 3D relationship. As an aside, to those who are virulently defending Darwin, please stop and reconsider what you are doing. I'm not saying that you shouldn't but amidst calls to boycott the New Scientist by Dawkins himself, don't fall into the same behaviour that you tarred the intelligent design crowd.</htmltext>
<tokenext>Someone above ranted about the overuse of the word " paradigm-shift " and I could n't agree more .
However , in this case , I think the use is warranted .
Woese himself caused a paradigm-shift when he discovered that the 16S and 18S ribosomal gene is highly conserved in all known organism , meaning that organisms that have similar 16S or 18S sequences are more closely related to each other and vice versa .
The previous paradigm , and if you were old enough to remember learning in school was based largely on the morphological and to a certain extent , biochemical properties of the organisms .
The current model used in life-sciences are tree-like where " more evolved " species branch off from " less evolved " species and if you trace back this tree , you get to the root of life , where the hypothetical Last Universal Common Ancestor ( LUCA ) is .
This new paradigm proposed by Woese drastically change this neat picture into a cloud-like diagram , with organisms having multiple links with other organisms .
No longer can you say organism x2 has a direct lineage to organism x1 since horizontal gene transfers have clouded the relationships with a big impact on the study of evolution .
This also has a big impact on computational biology and I am sure , this is more in line with the speciality of the Slashdot crowd .
More complex algorithms and computational power have to be utilised to visualize this 3D relationship .
As an aside , to those who are virulently defending Darwin , please stop and reconsider what you are doing .
I 'm not saying that you should n't but amidst calls to boycott the New Scientist by Dawkins himself , do n't fall into the same behaviour that you tarred the intelligent design crowd .</tokentext>
<sentencetext>Someone above ranted about the overuse of the word "paradigm-shift" and I couldn't agree more.
However, in this case, I think the use is warranted.
Woese himself caused a paradigm-shift when he discovered that the 16S and 18S ribosomal gene is highly conserved in all known organism, meaning that organisms that have similar 16S or 18S sequences are more closely related to each other and vice versa.
The previous paradigm, and if you were old enough to remember learning in school was based largely on the morphological and to a certain extent, biochemical properties of the organisms.
The current model used in life-sciences are tree-like where "more evolved" species branch off from "less evolved" species and if you trace back this tree, you get to the root of life, where the hypothetical Last Universal Common Ancestor (LUCA)is.
This new paradigm proposed by Woese drastically change this neat picture into a cloud-like diagram, with organisms having multiple links with other organisms.
No longer can you say organism x2 has a direct lineage to organism x1 since horizontal gene transfers have clouded the relationships with a big impact on the study of evolution.
This also has a big impact on computational biology and I am sure, this is more in line with the speciality of the Slashdot crowd.
More complex algorithms and computational power have to be utilised to visualize this 3D relationship.
As an aside, to those who are virulently defending Darwin, please stop and reconsider what you are doing.
I'm not saying that you shouldn't but amidst calls to boycott the New Scientist by Dawkins himself, don't fall into the same behaviour that you tarred the intelligent design crowd.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913918</id>
	<title>Re:It's still natural selection</title>
	<author>Anonymous</author>
	<datestamp>1264530720000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>2</modscore>
	<htmltext><blockquote><div><p>If the survival of each individual's genes were paramount, there would be no homosexuality and no parents killing their own children, 'cause those are pretty much dead-end paths from the standpoint of survival of the individual.</p></div></blockquote><p>
You just missed the flaw in your reasoning - you confuse an individual's GENES with the INDIVIDUAL.  Consider that a parent only has 50\% of their genes in a child; if it turns out that killing the child would allow for the opportunity to invest more in other children, and increase their probability of having offspring (i.e. getting more copies of your genes in circulation), it might be very RATIONAL to kill your own child from the standpoint of increasing the frequency of your genes in the population.  This behavior is observed frequently in animal species besides man.  Consider how violently men react to adulterous women and thier offspring - the possibility that they might have been investing resources in a child with 0\% of their genes means they have nothing to lose, genetically, by offing them.  The math of kin selection has been worked out quite precisely, in many different species with different mating habits, and the numbers work out; we (as in man and virtually every other species) tend to behave in such a way as to maximize the spread of our genes, regardless of whether the copies come from us or from our kin.<br>
<br>
 You mention ants - ants behave the way they do because of the highly unusual way they pass genes on - or should I say, the way most ants DON'T.  In a given colony, all the future ants (and future genes) come from the queen, who has sex briefly (for a day or two) with between 1 and 10 males, and stores their sperm to produce eggs for the rest of her life.  The reason so many ants work themselves to death, engage in combat to the death to protect the queen, and in general seem to not care for themselves as individuals, is they are, as individual reproducers, done.  The only chance they have for enhancing the odds of their GENES being spread is by doing everything possible to protect and nuture the only possible reproducer of those genes - the queen.  And guess what - the genes that influence aunt behavior in that way are the ones that have been the most successful.<br>
<br>
Group level selection has very little evidence going for it, although in highly advanced creatures (like us), it may play a greater role than in general.  You should read The Selfish Gene, and The Extended Phenotype, by Dawkins, to see the arguments about group vs. individual vs. genetic selection really hashed out in detail.</p></div>
	</htmltext>
<tokenext>If the survival of each individual 's genes were paramount , there would be no homosexuality and no parents killing their own children , 'cause those are pretty much dead-end paths from the standpoint of survival of the individual .
You just missed the flaw in your reasoning - you confuse an individual 's GENES with the INDIVIDUAL .
Consider that a parent only has 50 \ % of their genes in a child ; if it turns out that killing the child would allow for the opportunity to invest more in other children , and increase their probability of having offspring ( i.e .
getting more copies of your genes in circulation ) , it might be very RATIONAL to kill your own child from the standpoint of increasing the frequency of your genes in the population .
This behavior is observed frequently in animal species besides man .
Consider how violently men react to adulterous women and thier offspring - the possibility that they might have been investing resources in a child with 0 \ % of their genes means they have nothing to lose , genetically , by offing them .
The math of kin selection has been worked out quite precisely , in many different species with different mating habits , and the numbers work out ; we ( as in man and virtually every other species ) tend to behave in such a way as to maximize the spread of our genes , regardless of whether the copies come from us or from our kin .
You mention ants - ants behave the way they do because of the highly unusual way they pass genes on - or should I say , the way most ants DO N'T .
In a given colony , all the future ants ( and future genes ) come from the queen , who has sex briefly ( for a day or two ) with between 1 and 10 males , and stores their sperm to produce eggs for the rest of her life .
The reason so many ants work themselves to death , engage in combat to the death to protect the queen , and in general seem to not care for themselves as individuals , is they are , as individual reproducers , done .
The only chance they have for enhancing the odds of their GENES being spread is by doing everything possible to protect and nuture the only possible reproducer of those genes - the queen .
And guess what - the genes that influence aunt behavior in that way are the ones that have been the most successful .
Group level selection has very little evidence going for it , although in highly advanced creatures ( like us ) , it may play a greater role than in general .
You should read The Selfish Gene , and The Extended Phenotype , by Dawkins , to see the arguments about group vs. individual vs. genetic selection really hashed out in detail .</tokentext>
<sentencetext>If the survival of each individual's genes were paramount, there would be no homosexuality and no parents killing their own children, 'cause those are pretty much dead-end paths from the standpoint of survival of the individual.
You just missed the flaw in your reasoning - you confuse an individual's GENES with the INDIVIDUAL.
Consider that a parent only has 50\% of their genes in a child; if it turns out that killing the child would allow for the opportunity to invest more in other children, and increase their probability of having offspring (i.e.
getting more copies of your genes in circulation), it might be very RATIONAL to kill your own child from the standpoint of increasing the frequency of your genes in the population.
This behavior is observed frequently in animal species besides man.
Consider how violently men react to adulterous women and thier offspring - the possibility that they might have been investing resources in a child with 0\% of their genes means they have nothing to lose, genetically, by offing them.
The math of kin selection has been worked out quite precisely, in many different species with different mating habits, and the numbers work out; we (as in man and virtually every other species) tend to behave in such a way as to maximize the spread of our genes, regardless of whether the copies come from us or from our kin.
You mention ants - ants behave the way they do because of the highly unusual way they pass genes on - or should I say, the way most ants DON'T.
In a given colony, all the future ants (and future genes) come from the queen, who has sex briefly (for a day or two) with between 1 and 10 males, and stores their sperm to produce eggs for the rest of her life.
The reason so many ants work themselves to death, engage in combat to the death to protect the queen, and in general seem to not care for themselves as individuals, is they are, as individual reproducers, done.
The only chance they have for enhancing the odds of their GENES being spread is by doing everything possible to protect and nuture the only possible reproducer of those genes - the queen.
And guess what - the genes that influence aunt behavior in that way are the ones that have been the most successful.
Group level selection has very little evidence going for it, although in highly advanced creatures (like us), it may play a greater role than in general.
You should read The Selfish Gene, and The Extended Phenotype, by Dawkins, to see the arguments about group vs. individual vs. genetic selection really hashed out in detail.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911836</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911712</id>
	<title>I dunno...</title>
	<author>Anonymous</author>
	<datestamp>1264509600000</datestamp>
	<modclass>Funny</modclass>
	<modscore>5</modscore>
	<htmltext>I pass on my genes horizontally</htmltext>
<tokenext>I pass on my genes horizontally</tokentext>
<sentencetext>I pass on my genes horizontally</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911632</id>
	<title>Neo-Lamarkian Evolution</title>
	<author>Anonymous</author>
	<datestamp>1264509120000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>This would be epigenetic, neo-Lamarkian evolution, with the inheritance of acquired traits.</p><p>Not: Larkian evolution is NOT Lysenkoian evolution.</p></htmltext>
<tokenext>This would be epigenetic , neo-Lamarkian evolution , with the inheritance of acquired traits.Not : Larkian evolution is NOT Lysenkoian evolution .</tokentext>
<sentencetext>This would be epigenetic, neo-Lamarkian evolution, with the inheritance of acquired traits.Not: Larkian evolution is NOT Lysenkoian evolution.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912844</id>
	<title>Re:Once again</title>
	<author>Cassius Corodes</author>
	<datestamp>1264518780000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>4</modscore>
	<htmltext>The basic problem is that you don't have infinite time, and as such you have to 'outsource' your knowledge gathering to other people. The problem then becomes one of who do you trust? If you use a heuristic of who has got good results in the past and that leads you to 'blindly' believe in the brand of science - well I can't really find any fault with that. As a researcher, while I know lots about my area, I don't know jack about others so I blindly trust what my doctor, mathematician, physicist tell me. If its an issue of importance I get a second opinion from another doctor etc, but at the end of the day I am blindly trusting them. I don't think there is anything wrong with that.</htmltext>
<tokenext>The basic problem is that you do n't have infinite time , and as such you have to 'outsource ' your knowledge gathering to other people .
The problem then becomes one of who do you trust ?
If you use a heuristic of who has got good results in the past and that leads you to 'blindly ' believe in the brand of science - well I ca n't really find any fault with that .
As a researcher , while I know lots about my area , I do n't know jack about others so I blindly trust what my doctor , mathematician , physicist tell me .
If its an issue of importance I get a second opinion from another doctor etc , but at the end of the day I am blindly trusting them .
I do n't think there is anything wrong with that .</tokentext>
<sentencetext>The basic problem is that you don't have infinite time, and as such you have to 'outsource' your knowledge gathering to other people.
The problem then becomes one of who do you trust?
If you use a heuristic of who has got good results in the past and that leads you to 'blindly' believe in the brand of science - well I can't really find any fault with that.
As a researcher, while I know lots about my area, I don't know jack about others so I blindly trust what my doctor, mathematician, physicist tell me.
If its an issue of importance I get a second opinion from another doctor etc, but at the end of the day I am blindly trusting them.
I don't think there is anything wrong with that.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912246</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30915070</id>
	<title>Re:Viruses</title>
	<author>cyberfringe</author>
	<datestamp>1264591980000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>... and <b>prions</b> (infectious agents composed primarily of protein; responsible for a number of diseases in animals), what are also distributed laterally.
<p>
Prions can confer evolutionary advantages through protein-based inheritance.
<a href="http://www.ncbi.nlm.nih.gov/pubmed/11260797" title="nih.gov" rel="nofollow">http://www.ncbi.nlm.nih.gov/pubmed/11260797</a> [nih.gov]
</p><p>
and are themselves subject to mutation and natural selection.
<a href="http://www.ncbi.nlm.nih.gov/pubmed/20044542" title="nih.gov" rel="nofollow">http://www.ncbi.nlm.nih.gov/pubmed/20044542</a> [nih.gov]
</p><p><nobr> <wbr></nobr>...and <b>parasites</b>.   Plant parasitism is a medium for horizontal gene transfer between different species  Genes can be transmitted in both directions in this case.
<a href="http://newsinfo.iu.edu/news/page/normal/1716.html" title="iu.edu" rel="nofollow">http://newsinfo.iu.edu/news/page/normal/1716.html</a> [iu.edu]</p></htmltext>
<tokenext>... and prions ( infectious agents composed primarily of protein ; responsible for a number of diseases in animals ) , what are also distributed laterally .
Prions can confer evolutionary advantages through protein-based inheritance .
http : //www.ncbi.nlm.nih.gov/pubmed/11260797 [ nih.gov ] and are themselves subject to mutation and natural selection .
http : //www.ncbi.nlm.nih.gov/pubmed/20044542 [ nih.gov ] ...and parasites .
Plant parasitism is a medium for horizontal gene transfer between different species Genes can be transmitted in both directions in this case .
http : //newsinfo.iu.edu/news/page/normal/1716.html [ iu.edu ]</tokentext>
<sentencetext>... and prions (infectious agents composed primarily of protein; responsible for a number of diseases in animals), what are also distributed laterally.
Prions can confer evolutionary advantages through protein-based inheritance.
http://www.ncbi.nlm.nih.gov/pubmed/11260797 [nih.gov]

and are themselves subject to mutation and natural selection.
http://www.ncbi.nlm.nih.gov/pubmed/20044542 [nih.gov]
 ...and parasites.
Plant parasitism is a medium for horizontal gene transfer between different species  Genes can be transmitted in both directions in this case.
http://newsinfo.iu.edu/news/page/normal/1716.html [iu.edu]</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911980</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912142</id>
	<title>pathogens</title>
	<author>Taibhsear</author>
	<datestamp>1264512720000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Horizontal gene passing is what make several organisms have strains that go from harmless to pathogenic.<br>Some useful info for the curious masses:<br><a href="http://en.wikipedia.org/wiki/Pilus" title="wikipedia.org">http://en.wikipedia.org/wiki/Pilus</a> [wikipedia.org]<br><a href="http://en.wikipedia.org/wiki/Horizontal\_gene\_transfer" title="wikipedia.org">http://en.wikipedia.org/wiki/Horizontal\_gene\_transfer</a> [wikipedia.org]</p></htmltext>
<tokenext>Horizontal gene passing is what make several organisms have strains that go from harmless to pathogenic.Some useful info for the curious masses : http : //en.wikipedia.org/wiki/Pilus [ wikipedia.org ] http : //en.wikipedia.org/wiki/Horizontal \ _gene \ _transfer [ wikipedia.org ]</tokentext>
<sentencetext>Horizontal gene passing is what make several organisms have strains that go from harmless to pathogenic.Some useful info for the curious masses:http://en.wikipedia.org/wiki/Pilus [wikipedia.org]http://en.wikipedia.org/wiki/Horizontal\_gene\_transfer [wikipedia.org]</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30947964</id>
	<title>Huh? Something's wrong here.</title>
	<author>Hurricane78</author>
	<datestamp>1264771380000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><div class="quote"><p>Carl Woese, one of whose earlier discoveries was the third branch of life on Earth, the Archaea.</p></div><p>Uum, H.P. Lovecraft already mentioned Archaea in his &ldquo;Mountains of Madness&rdquo; story. So unless Carl Woese is doing science since 1931, I have to doubt this statement...</p></div>
	</htmltext>
<tokenext>Carl Woese , one of whose earlier discoveries was the third branch of life on Earth , the Archaea.Uum , H.P .
Lovecraft already mentioned Archaea in his    Mountains of Madness    story .
So unless Carl Woese is doing science since 1931 , I have to doubt this statement.. .</tokentext>
<sentencetext>Carl Woese, one of whose earlier discoveries was the third branch of life on Earth, the Archaea.Uum, H.P.
Lovecraft already mentioned Archaea in his “Mountains of Madness” story.
So unless Carl Woese is doing science since 1931, I have to doubt this statement...
	</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30914110</id>
	<title>Re:I realize scientists need a breakthrough</title>
	<author>Anonymous</author>
	<datestamp>1264532880000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext>It's more exciting to the common knucklehead if it looks like there is going to be a winner or loser.
<br> <br>
Also, there's no such thing as evolution.  4000 years is not nearly long enough for us to have evolved from lizard men.</htmltext>
<tokenext>It 's more exciting to the common knucklehead if it looks like there is going to be a winner or loser .
Also , there 's no such thing as evolution .
4000 years is not nearly long enough for us to have evolved from lizard men .</tokentext>
<sentencetext>It's more exciting to the common knucklehead if it looks like there is going to be a winner or loser.
Also, there's no such thing as evolution.
4000 years is not nearly long enough for us to have evolved from lizard men.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911600</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912614</id>
	<title>Isn't horizontal gene transfer just ...</title>
	<author>newhoggy</author>
	<datestamp>1264516200000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>
an example of Darwinian Evolution, but just at a different level?
</p><p>
For example, if you think of the unit of evolution as a gene instead of an organism and a bacteria as a habitat instead of an organism, then the gene evolves vertically, by replication and duplication.  The transfer between two bacteria are just the gene migrating from one habitat to another.</p></htmltext>
<tokenext>an example of Darwinian Evolution , but just at a different level ?
For example , if you think of the unit of evolution as a gene instead of an organism and a bacteria as a habitat instead of an organism , then the gene evolves vertically , by replication and duplication .
The transfer between two bacteria are just the gene migrating from one habitat to another .</tokentext>
<sentencetext>
an example of Darwinian Evolution, but just at a different level?
For example, if you think of the unit of evolution as a gene instead of an organism and a bacteria as a habitat instead of an organism, then the gene evolves vertically, by replication and duplication.
The transfer between two bacteria are just the gene migrating from one habitat to another.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30916242</id>
	<title>Re:I realize scientists need a breakthrough</title>
	<author>mhelander</author>
	<datestamp>1264602840000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>I wonder why this would not be called Darwinian evolution by natural selection? The modern synthesis considers self replicating entities, they don't have to replicate "vertically" - "horizontally" works just as well. This seems like yet a misinformed attack on Darwinism, such that someone investigates a particular feature of Darwinian evolution, and because it doesn't look exactly like what they were taught Darwinism to be, they think it is something else. But it isn't.</p></htmltext>
<tokenext>I wonder why this would not be called Darwinian evolution by natural selection ?
The modern synthesis considers self replicating entities , they do n't have to replicate " vertically " - " horizontally " works just as well .
This seems like yet a misinformed attack on Darwinism , such that someone investigates a particular feature of Darwinian evolution , and because it does n't look exactly like what they were taught Darwinism to be , they think it is something else .
But it is n't .</tokentext>
<sentencetext>I wonder why this would not be called Darwinian evolution by natural selection?
The modern synthesis considers self replicating entities, they don't have to replicate "vertically" - "horizontally" works just as well.
This seems like yet a misinformed attack on Darwinism, such that someone investigates a particular feature of Darwinian evolution, and because it doesn't look exactly like what they were taught Darwinism to be, they think it is something else.
But it isn't.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911600</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30913062</id>
	<title>Re:Gene Synthesis</title>
	<author>Anonymous</author>
	<datestamp>1264521120000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>There is a big gap between the so called primordial world or RNA world and the first forms of unicellular organisms, the ones holding a specialized set of genes, the genome. For such a gap there is little known. So it is very hard to know from where all these genes came in the first place. However, geneticists from the early 50's started to describe many different mechanisms by which a gene can duplicate, get transferred or gain a new function. In some cases such a function allowed the organism to live in an otherwise killer environment. Later in 60's along with the development of DNA/RNA sequencing techniques, many other genes and their phenotypes were characterized giving a light to a bunch of more sophisticated mechanism of function gain. For example and related to article in discussion, horizontal gene transfer, gene duplication, gene regulation, de-regulation, partial gene transfer, etc. Now we are in the genomic era, where an entire genome can be sequenced with a bunch of bucks. So there is a sea of data showing impressive things on how genomes can earn players. For example and answering your question, yes an enzyme can gain a function by changing very little of the total protein (less than 5\%). Or membrane proteins, they can share up to 98\% identity on their structure but yet bind different targets. And yes, there are enzymes that are specialized for one substrate but also very related ones can take more substrates. A lot has been done in this field as well, where by single aminoacid substitutions a different substrate was selected. So it is not an all or nothing thing. Specially if considering that genes code for proteins, but that this proteins are composed of domains. For example, the insertion of a domain into a protein would change its subcellular target, and therefore maybe its function.</p><p>So there are enough mechanisms to explain how unicellular organisms of about 2.8K genes got 30K more genes to become humans. However, what is remarkable is that an insignificant microbe has only 10 times less genes that us....</p></htmltext>
<tokenext>There is a big gap between the so called primordial world or RNA world and the first forms of unicellular organisms , the ones holding a specialized set of genes , the genome .
For such a gap there is little known .
So it is very hard to know from where all these genes came in the first place .
However , geneticists from the early 50 's started to describe many different mechanisms by which a gene can duplicate , get transferred or gain a new function .
In some cases such a function allowed the organism to live in an otherwise killer environment .
Later in 60 's along with the development of DNA/RNA sequencing techniques , many other genes and their phenotypes were characterized giving a light to a bunch of more sophisticated mechanism of function gain .
For example and related to article in discussion , horizontal gene transfer , gene duplication , gene regulation , de-regulation , partial gene transfer , etc .
Now we are in the genomic era , where an entire genome can be sequenced with a bunch of bucks .
So there is a sea of data showing impressive things on how genomes can earn players .
For example and answering your question , yes an enzyme can gain a function by changing very little of the total protein ( less than 5 \ % ) .
Or membrane proteins , they can share up to 98 \ % identity on their structure but yet bind different targets .
And yes , there are enzymes that are specialized for one substrate but also very related ones can take more substrates .
A lot has been done in this field as well , where by single aminoacid substitutions a different substrate was selected .
So it is not an all or nothing thing .
Specially if considering that genes code for proteins , but that this proteins are composed of domains .
For example , the insertion of a domain into a protein would change its subcellular target , and therefore maybe its function.So there are enough mechanisms to explain how unicellular organisms of about 2.8K genes got 30K more genes to become humans .
However , what is remarkable is that an insignificant microbe has only 10 times less genes that us... .</tokentext>
<sentencetext>There is a big gap between the so called primordial world or RNA world and the first forms of unicellular organisms, the ones holding a specialized set of genes, the genome.
For such a gap there is little known.
So it is very hard to know from where all these genes came in the first place.
However, geneticists from the early 50's started to describe many different mechanisms by which a gene can duplicate, get transferred or gain a new function.
In some cases such a function allowed the organism to live in an otherwise killer environment.
Later in 60's along with the development of DNA/RNA sequencing techniques, many other genes and their phenotypes were characterized giving a light to a bunch of more sophisticated mechanism of function gain.
For example and related to article in discussion, horizontal gene transfer, gene duplication, gene regulation, de-regulation, partial gene transfer, etc.
Now we are in the genomic era, where an entire genome can be sequenced with a bunch of bucks.
So there is a sea of data showing impressive things on how genomes can earn players.
For example and answering your question, yes an enzyme can gain a function by changing very little of the total protein (less than 5\%).
Or membrane proteins, they can share up to 98\% identity on their structure but yet bind different targets.
And yes, there are enzymes that are specialized for one substrate but also very related ones can take more substrates.
A lot has been done in this field as well, where by single aminoacid substitutions a different substrate was selected.
So it is not an all or nothing thing.
Specially if considering that genes code for proteins, but that this proteins are composed of domains.
For example, the insertion of a domain into a protein would change its subcellular target, and therefore maybe its function.So there are enough mechanisms to explain how unicellular organisms of about 2.8K genes got 30K more genes to become humans.
However, what is remarkable is that an insignificant microbe has only 10 times less genes that us....</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912130</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911836</id>
	<title>Re:It's still natural selection</title>
	<author>Anonymous</author>
	<datestamp>1264510440000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>3</modscore>
	<htmltext>In social animals, it is the survival of the group that is driving evolution, not the survival of individual or their genes. If the survival of each individual's genes were paramount, there would be no homosexuality and no parents killing their own children, 'cause those are pretty much dead-end paths from the standpoint of survival of the individual. Another way of thinking of this is that altruism really does have survival value; just like with army ants, being willing to sacrifice individuals for the good of the group is a good evolutionary strategy.</htmltext>
<tokenext>In social animals , it is the survival of the group that is driving evolution , not the survival of individual or their genes .
If the survival of each individual 's genes were paramount , there would be no homosexuality and no parents killing their own children , 'cause those are pretty much dead-end paths from the standpoint of survival of the individual .
Another way of thinking of this is that altruism really does have survival value ; just like with army ants , being willing to sacrifice individuals for the good of the group is a good evolutionary strategy .</tokentext>
<sentencetext>In social animals, it is the survival of the group that is driving evolution, not the survival of individual or their genes.
If the survival of each individual's genes were paramount, there would be no homosexuality and no parents killing their own children, 'cause those are pretty much dead-end paths from the standpoint of survival of the individual.
Another way of thinking of this is that altruism really does have survival value; just like with army ants, being willing to sacrifice individuals for the good of the group is a good evolutionary strategy.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911724</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30912070</id>
	<title>GM Foods anyone?</title>
	<author>Beerdood</author>
	<datestamp>1264512240000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext>"horizontal gene transfer - in which organisms acquire genetic material "horizontally" from other organisms around them, rather than vertically from their parents or ancestors."
<br> <br>
Genetically modified foods are like the "artificial selection" equivalent of nature / natural selection - if the transfer of genes can happen from one set of species to another, then GM crops are kinds of an accelerated / selective version of this.  If I were Monsanto or another big GM food company, I'd be looking to twist this into "Genetic material gets transferred to other species in nature, what's wrong with us doing it?"</htmltext>
<tokenext>" horizontal gene transfer - in which organisms acquire genetic material " horizontally " from other organisms around them , rather than vertically from their parents or ancestors .
" Genetically modified foods are like the " artificial selection " equivalent of nature / natural selection - if the transfer of genes can happen from one set of species to another , then GM crops are kinds of an accelerated / selective version of this .
If I were Monsanto or another big GM food company , I 'd be looking to twist this into " Genetic material gets transferred to other species in nature , what 's wrong with us doing it ?
"</tokentext>
<sentencetext>"horizontal gene transfer - in which organisms acquire genetic material "horizontally" from other organisms around them, rather than vertically from their parents or ancestors.
"
 
Genetically modified foods are like the "artificial selection" equivalent of nature / natural selection - if the transfer of genes can happen from one set of species to another, then GM crops are kinds of an accelerated / selective version of this.
If I were Monsanto or another big GM food company, I'd be looking to twist this into "Genetic material gets transferred to other species in nature, what's wrong with us doing it?
"</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_01_26_2143251.30911928</id>
	<title>Original paper on arXiv</title>
	<author>PaulBu</author>
	<datestamp>1264511040000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>5</modscore>
	<htmltext><p>For those who do not care to register for that New Scientist, we still have arXiv...<nobr> <wbr></nobr>:)</p><p><a href="http://arxiv.org/abs/q-bio/0702015" title="arxiv.org">http://arxiv.org/abs/q-bio/0702015</a> [arxiv.org]</p><p>Paul B.</p></htmltext>
<tokenext>For those who do not care to register for that New Scientist , we still have arXiv... : ) http : //arxiv.org/abs/q-bio/0702015 [ arxiv.org ] Paul B .</tokentext>
<sentencetext>For those who do not care to register for that New Scientist, we still have arXiv... :)http://arxiv.org/abs/q-bio/0702015 [arxiv.org]Paul B.</sentencetext>
</comment>
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