RE: Documented evolution of new functions and behaviors in bacteria

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Jhud -> RE: Documented evolution of new functions and behaviors in bacteria (5/23/2008 10:55:52 AM)
quote: Every time you sequence a genome you are testing the results of evolution. Every time a new fossil species is found the theory is being tested. Well, no, one imposes on such things ones idea about evolution; genomes and fossils are just what they are, what they mean in the larger picture of things comes from us.

gluadys -> RE: Documented evolution of new functions and behaviors in bacteria (5/23/2008 11:09:57 AM)
quote: ORIGINAL: Zuniceratops quote: Why? We don't expect history to repeat itself in other fields? Why should we expect the unique events of evolutionary history to be repeated. Remember, modern bacteria are descendants of those bacteria which were never involved in the development of eukaryotes in the first place. What makes it likely that they would be now? quote: Why would we see bacteria go against 3.5 billion years of evolution? Because they apparently did it in the past. It’s said that a major indication of whether something is scientific is that it’s repeatable. You can do it again, or cause something like it to happen again. Evolution is a vital component of biological science, so it is claimed, so it must be repeatable in some form. Repeatable "in some form" is the key. Scientists do experiment with the process of evolution and get the results expected repeatedly. But that is not the same as repeating history. The idea that you have to replicate specific histories to be scientifically valid is nonsense. If that were the case, you would have to require a murderer to do it again in front of the jury to get a conviction. The bacteria and archea that apparently co-operated to form eukaryotes in the past are long since gone. So are the environments in which eukaryotes originated. There is no reason why different bacteria and archea in different environments today should repeat the process. The contingencies of history don't allow for it. quote: And if they don’t need it today, why did they need it back then? Well, they didn't "need" it then, either. Plenty of bacteria and archea survived through those environments without becoming eukaryotes. quote: And if bacteria absolutely cannot be expected to be able to form any eukaryote characteristics today, how do we know they could do it in the past? Because we have the remnants of bacterial symbionts functioning in modern eukaryote cells.

Jhud -> RE: Documented evolution of new functions and behaviors in bacteria (5/23/2008 11:24:55 AM)
quote: Because we have the remnants of bacterial symbionts functioning in modern eukaryote cells. Actually, that is not neccesarily an indicator of ancestry... Genomics and the Irreducible Nature of Eukaryote Cells Abstract: Large-scale comparative genomics in harness with proteomics has substantiated fundamental features of eukaryote cellular evolution. The evolutionary trajectory of modern eukaryotes is distinct from that of prokaryotes. Data from many sources give no direct evidence that eukaryotes evolved by genome fusion between archaea and bacteria. Comparative genomics shows that, under certain ecological settings, sequence loss and cellular simplification are common modes of evolution. Subcellular architecture of eukaryote cells is in part a physical-chemical consequence of molecular crowding; subcellular compartmentation with specialized proteomes is required for the efficient functioning of proteins. Comparative genomics and proteomics have strengthened the view that modern eukaryote and prokaryote cells have long followed separate evolutionary trajectories. Because their cells appear simpler, prokaryotes have traditionally been considered ancestors of eukaryotes (14). Nevertheless, comparative genomics has confirmed a lesson from paleontology: Evolution does not proceed monotonically from the simpler to the more complex (59). Here, we review recent data from proteomics and genome sequences suggesting that eukaryotes are a unique primordial lineage.

swan42 -> RE: Documented evolution of new functions and behaviors in bacteria (5/23/2008 12:31:24 PM)
quote: ORIGINAL: Jhud quote: Because we have the remnants of bacterial symbionts functioning in modern eukaryote cells. Actually, that is not neccesarily an indicator of ancestry... Genomics and the Irreducible Nature of Eukaryote Cells Abstract: Large-scale comparative genomics in harness with proteomics has substantiated fundamental features of eukaryote cellular ... This is the thick of the latest discussion; I'm enjoying this level of detail, but there was a "strong voiced" rebuttal to Kurland's paper. http://www.arn.org/blogs/index.php/literature/2007/04/27/disturbing_thoughts_about_the_irreducibl The critics declared that this paper "delivered only biased opinions" and that the authors "arbitrarily pick and choose among available observations relating to sequence similarity". http://www.sciencemag.org/cgi/content/citation/316/5824/542c I may have to see about reading the response.

gluadys -> RE: Documented evolution of new functions and behaviors in bacteria (5/23/2008 1:19:20 PM)
quote: ORIGINAL: Jhud quote: Because we have the remnants of bacterial symbionts functioning in modern eukaryote cells. Actually, that is not neccesarily an indicator of ancestry... Genomics and the Irreducible Nature of Eukaryote Cells Abstract: Large-scale comparative genomics in harness with proteomics has substantiated fundamental features of eukaryote cellular evolution. The evolutionary trajectory of modern eukaryotes is distinct from that of prokaryotes. Data from many sources give no direct evidence that eukaryotes evolved by genome fusion between archaea and bacteria. Comparative genomics shows that, under certain ecological settings, sequence loss and cellular simplification are common modes of evolution. Subcellular architecture of eukaryote cells is in part a physical-chemical consequence of molecular crowding; subcellular compartmentation with specialized proteomes is required for the efficient functioning of proteins. Comparative genomics and proteomics have strengthened the view that modern eukaryote and prokaryote cells have long followed separate evolutionary trajectories. Because their cells appear simpler, prokaryotes have traditionally been considered ancestors of eukaryotes (14). Nevertheless, comparative genomics has confirmed a lesson from paleontology: Evolution does not proceed monotonically from the simpler to the more complex (59). Here, we review recent data from proteomics and genome sequences suggesting that eukaryotes are a unique primordial lineage. It is fascinating to read about these debates, but I will let the scientists duke it out among themselves. I do note that they are still speaking of archaebacterial and eubacterial origins of the genes in eukaryotes and that spells ancestry to me. Though I love this observation on the distribution of the bacterial genes in the eukaryote genome: quote: But strangely, archaebacterial operational and eubacterial informational genes are almost completely absent from eukaryotes, even though the first eukaryote contained two sets of informational and operational genes." The author, James Lake, uses the analogy of the Roman god Janus. "Like the two faces of the Roman god Janus, thought to represent the Moon and the Sun, the phylogenetic origins of informational and operational genes in eukaryotes are as different as night and day. Finding a gene distribution such as this is the statistical equivalent of finding that a coin tossed at night (Janus's archaebacterial face) always comes up heads (informational genes), and tossed during the day (Janus's eubacterial face) always comes up tails (operational genes)."

swan42 -> RE: Documented evolution of new functions and behaviors in bacteria (5/23/2008 1:29:59 PM)
quote: It is fascinating to read about these debates, but I will let the scientists duke it out among themselves. Oh I suppose.... I'd like see debate on this forum rise to the level of sophistication found in journal letters. I'm itching to resubscribe to Nature.

Method -> RE: Documented evolution of new functions and behaviors in bacteria (5/23/2008 3:39:51 PM)
quote: ORIGINAL: Jhud Actually, that is not neccesarily an indicator of ancestry... I agree, endosymbiosis does not indicate ancestry. The root of the prokaryote and eukaryote trees are completely mangled into an undecipherable root ball. This is largely due to horizontal gene transfer. I often get lazy and speak of a last common ancestor, but it is much more accurate to refer to a last common ancestral gene pool which probably spanned several "species".

gluadys -> RE: Documented evolution of new functions and behaviors in bacteria (5/23/2008 5:22:23 PM)
quote: ORIGINAL: swan42 quote: It is fascinating to read about these debates, but I will let the scientists duke it out among themselves. Oh I suppose.... I'd like see debate on this forum rise to the level of sophistication found in journal letters. I'm itching to resubscribe to Nature. Well, I think you need people with much more background in the relevant science than I have for that. I am quite happy to sit on the sidelines and watch the fun.

gluadys -> RE: Documented evolution of new functions and behaviors in bacteria (5/23/2008 5:29:26 PM)
quote: ORIGINAL: Method quote: ORIGINAL: Jhud Actually, that is not neccesarily an indicator of ancestry... I agree, endosymbiosis does not indicate ancestry. The root of the prokaryote and eukaryote trees are completely mangled into an undecipherable root ball. This is largely due to horizontal gene transfer. I often get lazy and speak of a last common ancestor, but it is much more accurate to refer to a last common ancestral gene pool which probably spanned several "species". That makes sense. What I was trying to get to was that genes are heritable material and the most likely source of them is from some previous possessor of the genes. But with things like horizontal transfer and endosymbiosis in play the genes possessed by the existing cell need not have come from its biological predecessor. Still they did not pop out of thin air either. If we are finding bacterial genes in eukaryotes, the probability is that they came from bacteria one way or another. A question for you. Is horizontal gene transfer as prevalent among unicellular eukaryotes (protista?) as among bacteria?

Method -> RE: Documented evolution of new functions and behaviors in bacteria (5/23/2008 5:52:19 PM)
quote: ORIGINAL: gluadys A question for you. Is horizontal gene transfer as prevalent among unicellular eukaryotes (protista?) as among bacteria? HGT is not very common among eukaryotes compared to prokaryotes. There are certainly examples of HGT in eukaryotes, one of which is transfer of mitochondrial genes into the nuclear genome (numt's). However, there is not enough transfer between eukaryote species to produce a detectable signal, and it has not been observed to my knowledge.

Jhud -> RE: Documented evolution of new functions and behaviors in bacteria (5/25/2008 11:53:28 PM)
quote: It is fascinating to read about these debates, but I will let the scientists duke it out among themselves. I do note that they are still speaking of archaebacterial and eubacterial origins of the genes in eukaryotes and that spells ancestry to me. Perhaps; I was simply demonstrating that the claim that there are, "remnants of bacterial symbionts functioning in modern eukaryote cells" isn't neccesarily true.

gluadys -> RE: Documented evolution of new functions and behaviors in bacteria (5/26/2008 12:38:11 AM)
quote: ORIGINAL: Jhud quote: It is fascinating to read about these debates, but I will let the scientists duke it out among themselves. I do note that they are still speaking of archaebacterial and eubacterial origins of the genes in eukaryotes and that spells ancestry to me. Perhaps; I was simply demonstrating that the claim that there are, "remnants of bacterial symbionts functioning in modern eukaryote cells" isn't neccesarily true. You didn't say it wasn't true. You said it wasn't an indication of ancestry.

Jhud -> RE: Documented evolution of new functions and behaviors in bacteria (5/26/2008 12:39:43 AM)
quote: You didn't say it wasn't true. You said it wasn't an indication of ancestry. No, I said: not neccesarily an indicator of ancestry...

gluadys -> RE: Documented evolution of new functions and behaviors in bacteria (5/26/2008 12:47:08 AM)
quote: ORIGINAL: Jhud quote: You didn't say it wasn't true. You said it wasn't an indication of ancestry. No, I said: not neccesarily an indicator of ancestry... Even better.

Jhud -> RE: Documented evolution of new functions and behaviors in bacteria (5/26/2008 12:49:28 AM)
quote: Even better. Better than what?

gluadys -> RE: Documented evolution of new functions and behaviors in bacteria (5/26/2008 8:41:32 AM)
quote: ORIGINAL: Jhud quote: Even better. Better than what? If it is not necessarily an indication of ancestry, then it may be an indication of ancestry.

Method -> RE: Documented evolution of new functions and behaviors in bacteria (5/27/2008 10:53:34 AM)
quote: ORIGINAL: Jhud Well, no, one imposes on such things ones idea about evolution; genomes and fossils are just what they are, what they mean in the larger picture of things comes from us. So if a non-evolutionist looks at a bird fossil it will have three middle ear bones? If a non-evolutionist looks at ERVs are they no longer found in the same place in different genomes? The theory of evolution predicts the discovery of facts. Is your only defense an attempt at denying the facts?

Jhud -> RE: Documented evolution of new functions and behaviors in bacteria (5/27/2008 1:48:45 PM)
quote: So if a non-evolutionist looks at a bird fossil it will have three middle ear bones? Why would who looks at fossil have anything to do with what it may or may not have? quote: If a non-evolutionist looks at ERVs are they no longer found in the same place in different genomes? ERVs are interesting, but they tell us nothing about the mechanisms that are said to propel evolution. quote: The theory of evolution predicts the discovery of facts. Is your only defense an attempt at denying the facts? I appreciate cherry picking as much as the next guy, but science theories aren’t merely judged on what they purport to explain, but also on what they cannot – and neo-darwinism does a horrible job of explaining a number of things. Among these are the various explosions of body plans and taxa that have occurred throughout history, the phenomenal stasis that appears to occur in various lineages, the very early information and structural complexity we find in life, the occurrence of multiple genetic attributes that anticipate later usage, the mechanisms that actually limit incidental modification of the genome, the occurrence of similar structures multiple times in separate lineages, the conservation of unexpressed genetic information across lineages, the fact that the basic vertebrate genome provides a structure that can be modified through regulation of extant rather than the acquisition of novel information, etc, etc, etc,

gluadys -> RE: Documented evolution of new functions and behaviors in bacteria (5/27/2008 2:56:48 PM)
quote: ORIGINAL: Jhud I appreciate cherry picking as much as the next guy, but science theories aren’t merely judged on what they purport to explain, but also on what they cannot – and neo-darwinism does a horrible job of explaining a number of things. One thing to be cautious of is faulting evolution for not explaining things which it does NOT purport to explain. I don't recall you personally falling into this trap often, but we do see it regularly. It is especially common to cite the "failure" of evolution to explain the origin of life. But this is not a failure of ToE since it does not purport to explain this. quote: Among these are the various explosions of body plans Just how many times, in addition to the Cambrian, has there been an explosion of new body plans? My impression, which may be mistaken, is that virtually all body plans emerged in the Cambrian. Andrew Parker (In the Blink of an Eye) notes that "544 million years ago, there were indeed three animal phyla with their various body plans, but at 538 million years ago there were 38, the same number that exists today." This seems to contradict the implication that body plans emerged in great numbers in more than one "explosion". quote: and taxa that have occurred throughout history, Well, "taxa" is a pretty general term. Every species is a taxon. As well as every genus, family, order and class. Niles Eldredge associates explosions of new taxa with a preceding period of mass extinction. He seems to have no difficulty with an evolutionary scenario. quote: the phenomenal stasis that appears to occur in various lineages, Again, I am not certain why you think evolution does a poor job of explaining this. quote: the very early information and structural complexity we find in life, I expect the chief difficulty here is lack of evidence. There is also the question of how much complexity emerged in the pre-biotic state and was already there with the first true cellular beings. quote: the occurrence of multiple genetic attributes that anticipate later usage, That is an interesting one. Pre-adaptation is, in a sense, a necessity of natural selection, but how much time can separate a mutation and the new use of the gene is an unsolved mystery as yet. Is there a maximum limit? How often does co-optation enter the picture? quote: the mechanisms that actually limit incidental modification of the genome, Again, I don't see what makes evolution a poor explanation of this. quote: the occurrence of similar structures multiple times in separate lineages, or of this. quote: the conservation of unexpressed genetic information across lineages, that's an interesting one. quote: the fact that the basic vertebrate genome provides a structure that can be modified through regulation of extant rather than the acquisition of novel information, etc, etc, etc, I don't see any problem with an evolutionary explanation of this.

Method -> RE: Documented evolution of new functions and behaviors in bacteria (5/27/2008 3:09:51 PM)
quote: ORIGINAL: Jhud Why would who looks at fossil have anything to do with what it may or may not have? You said as much with this statement, "Well, no, one imposes on such things ones idea about evolution; genomes and fossils are just what they are, what they mean in the larger picture of things comes from us." Evolution states that one should not find a bird with three middle ear bones. Does this mean that we are imposing things on fossils when we don't see three middle ear bones in bird fossils? quote: ERVs are interesting, but they tell us nothing about the mechanisms that are said to propel evolution. But they are evidence of common ancestry. You claim that this evidence is being imposed on the evidence, and yet when we ignore the theory the evidence is still there. quote: I appreciate cherry picking as much as the next guy, but science theories aren’t merely judged on what they purport to explain, but also on what they cannot – and neo-darwinism does a horrible job of explaining a number of things. Among these are the various explosions of body plans and taxa that have occurred throughout history, the phenomenal stasis that appears to occur in various lineages, the very early information and structural complexity we find in life, the occurrence of multiple genetic attributes that anticipate later usage, the mechanisms that actually limit incidental modification of the genome, the occurrence of similar structures multiple times in separate lineages, the conservation of unexpressed genetic information across lineages, the fact that the basic vertebrate genome provides a structure that can be modified through regulation of extant rather than the acquisition of novel information, etc, etc, etc, You still don't get it, do you? Every theory has things it can not explain in vivid detail. However, none of these things you have mentioned go against the theory which would be a problem. Why is stasis a problem for evolution? Why is complexity a problem for evolution? How are any of these problems for the theory? Explosion of body plans: Rapid evolution is evidence against evolution? Really? Early information: The oldest DNA I am aware of is around 50,000 years old. Where do you get this stuff from? Genetic pre-adaption: More baloney. The infamous sea cucumber/human comparison showing that sea cucumber genes code for eyes in vertebrates. What you seem to forget is that divergence followed by new function is a hallmark of evolution. Stasis: Why change when no change is needed? How is strong selective pressure for the current morphology a problem for evolution? Is slow change and rapid change both problems for evolution? Limit of change: There is no base in the genome which is protected from an insertion, deletion, or point mutation event. "occurrence of similar structures multiple times in separate lineages": Example? Conservation of unexpressed DNA: You have heard of gene regulation, have you not? "the fact that the basic vertebrate genome provides a structure that can be modified through regulation of extant rather than the acquisition of novel information": Wrong again. The only way to change regulation is to change the sequence.

Jhud -> RE: Documented evolution of new functions and behaviors in bacteria (5/27/2008 3:16:50 PM)
quote: One thing to be cautious of is faulting evolution for not explaining things which it does NOT purport to explain. I don't recall you personally falling into this trap often, but we do see it regularly. It is especially common to cite the "failure" of evolution to explain the origin of life. But this is not a failure of ToE since it does not purport to explain this. Why would you post this response when the argument hadn't been made? quote: Just how many times, in addition to the Cambrian, has there been an explosion of new body plans? My impression, which may be mistaken, is that virtually all body plans emerged in the Cambrian. Andrew Parker (In the Blink of an Eye) notes that "544 million years ago, there were indeed three animal phyla with their various body plans, but at 538 million years ago there were 38, the same number that exists today." This seems to contradict the implication that body plans emerged in great numbers in more than one "explosion". There to appears have been the Avalon explosion as well, and many other subsequent explosions of animal and plants types. Regardless, evolution doesn't particularly explain it. quote: Again, I am not certain why you think evolution does a poor job of explaining this. I detailed it in the thread of the same name. quote: I expect the chief difficulty here is lack of evidence. There is also the question of how much complexity emerged in the pre-biotic state and was already there with the first true cellular beings. There isn't a 'lack of evidence' concerning the incredible complexity of even the most basic cells, and the evidence increasingly indicates that such complexity is ubiquitous thorughout living systems. quote: Again, I don't see what makes evolution a poor explanation of this. It contradicts the notion of incidental modification, a necessity of neo-darwinism. quote: or of this. Well, when evolution apparently creates the mammalian ear more than once, or the basic structres of water transportation system in plant systems, one has to question how it is an incidental process can do this. quote: I don't see any problem with an evolutionary explanation of this. You may not, but it isn't a particularly evolutionary process.

gluadys -> RE: Documented evolution of new functions and behaviors in bacteria (5/27/2008 5:22:59 PM)
quote: ORIGINAL: Jhud quote: One thing to be cautious of is faulting evolution for not explaining things which it does NOT purport to explain. I don't recall you personally falling into this trap often, but we do see it regularly. It is especially common to cite the "failure" of evolution to explain the origin of life. But this is not a failure of ToE since it does not purport to explain this. Why would you post this response when the argument hadn't been made? To make sure it doesn't get made. quote: There to appears have been the Avalon explosion as well, and many other subsequent explosions of animal and plants types. Regardless, evolution doesn't particularly explain it. Interesting. I hadn't seen that before. So we have two "explosions" of body plans very early in the history of animal life. Any since the Cambrian? And how does evolution not explain it? Do we have any evidence of a different process? Or is it only that we lack the specific history that bothers you? quote: quote: Again, I am not certain why you think evolution does a poor job of explaining this. I detailed it in the thread of the same name. Link? quote: quote: I expect the chief difficulty here is lack of evidence. There is also the question of how much complexity emerged in the pre-biotic state and was already there with the first true cellular beings. There isn't a 'lack of evidence' concerning the incredible complexity of even the most basic cells, Of course not. I should have completed the thought. The lack I was referring to was a detailed knowledge of the structure of cells and pre-cellular entities 3 billion+ years ago. We have plenty of evidence of basic cellular structure in the present. quote: quote: Again, I don't see what makes evolution a poor explanation of this. It contradicts the notion of incidental modification, a necessity of neo-darwinism. Well, what is the nature of this limitation? It is not that any information cannot be changed, so what is it that forms a limit? This sounds very like the baseless assertion of creationists that there is something that permits evolution so far, but not beyond a certain barrier. I think you need to describe the alleged barrier. If all you are saying is that descendants are housed in the same taxon as ancestors, that is not a problem for evolution. That is a prediction of evolution. quote: Well, when evolution apparently creates the mammalian ear more than once, or the basic structres of water transportation system in plant systems, one has to question how it is an incidental process can do this. Citations please. quote: quote: I don't see any problem with an evolutionary explanation of this. You may not, but it isn't a particularly evolutionary process. Actually it looks like the essence of evolution to me. Modification of what already is.

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