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Author | Topic: Ancient bacteria with modern DNA, problem for evolution? | |||||||||||||||||||||||
randman  Suspended Member (Idle past 4929 days) Posts: 6367 Joined: |
Because, as I've explained, in my opinion it doesn't pose any sort of problem at all. Fine. That's your opinion. If you want to say that's your opinion, fine, but stating that it is other people's opinions when they have not stated that is what I am getting at. You claimed, for example, modulous had stated that, and that was the consensus of the people on the thread and that was incorrect. The consensus until I posted was no follow-up studies had been done. That was false, and I provided studies or articles about those studies to prove my point. Based on that, the consensus by the evos was it could be false since there were no follow-up studies (an erroneous impression), not that if it were true, it was not significant as you suggested.
YOU, my dear rand, appear to be the only one in this thread that still DOES consider that it's a problem. Until a moderator intervenes and points out that you have been answered several times, I guess I will keep pointing out the OP. Here is part of the OP once again.
So, the central paradox opens up plenty of questions for the biologists here and I'll paraphrase it. We have geological data which interprets these bacteria as being ancient. We have an equal amount of molecular evidence which says they are modern. This incongruence is precisely the kind of falsification test that evolutionists have been harping on about for Lord only knows how long. So, surely this classes as strong falsification for at least one of the methods used in dating the bacteria? Has this data be reconciled, or is it still one of the thorns that remains fixed in the side of evolutionary dogma? Edited by randman, : No reason given. Edited by randman, : No reason given.
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randman  Suspended Member (Idle past 4929 days) Posts: 6367 Joined: |
Quetzal, this thread is about dating techniques as it is in the section, Dates and Dating. You seem to agree that molecular dating techniques are flawed. Good for you. Do you agree that the principal objection to this find is that it contradicts molecular dating?
Yes or no. If you disagree, do you think if the find agreed with molecular dating, that there would be such a controversy? I think if we can come to an agreement on the questions above, we can consider, perhaps on a different thread devoted to that or maybe on this thread, the significance for ToE as a whole if evo assumptions about mutational rates are wrong. For example, how would this affect molecular phylogenies? But to just insist the conversation ignore the OP is not going to work. So are you saying that molecular dating techniques are wrong anyway, and for you at least, that your only objection to this find is that it isn't yet confirmed with more finds?
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randman  Suspended Member (Idle past 4929 days) Posts: 6367 Joined: |
What data, rand? I take it you didn't even read the abstract I took the trouble to post for you from Vreeland himself which showed that the bug was in fact different from its modern counterparts. Oh, so Vreeland's an expert now, eh? Vreeland has sought to find some ways the find could still be compatible with molecular dating.....Hmmm, why would he do that? Could it be that, just maybe, the fact the find disagrees with molecular dating is the real beef with the find? Couldn't be that, could it? My references to data being rejected because they disagree with the theory are clearly and unequivocally referring to the find itself, which has been rejected by some because it conflicts with theory. Got that?
Since NONE of the papers referenced so far on this thread, from Vreeland's team or anyone else, calls into question the concept of molecular dating techniques - except as I pointed out in reference to my criticism of the molecular clock - I don't see why you continue to harp on this subject. Amazing you could have read the thread and the articles about the controversy and not grasped this basic fact. Did you read this?
The third criticism, based on DNA similarities, has been harder to dismiss. Despite a protocol of sterilization and controls that even critics describe as "heroic," contamination remained a potential source of the 2-9-3 bacterium based on its molecular resemblance to current strains. Understandably, Vreeland defends the work against charges of contamination. He even views the genetic objections as the least valid, stating that of all the challenges (geologic, chemical and genetic), "this is by far the weakest of the critiques." | American Scientist How about this?
But, according to the authors of the latest report, Professor Dan Graur and Dr Tal Pupko of Tel Aviv University, Israel, the claims of 250 million-year-old bacteria are false: the bacteria are modern, they say. The scientist behind the original claim, Russell Vreeland from West Chester University, Pennsylvania, is not happy with the new publication. "I have read it," he told BBC News Online. "They asked me to review it for publication but refused to consider any of my comments or consider printing my response alongside the article." To reach their conclusion, Professor Graur and Dr Pupko downloaded the genetic information about strain 2-9-3, sometimes called B. permians, from the GenBank directory on the internet. They then compared 2-9-3's genes with those of modern bacteria to see how different they were. According to the molecular clock model, the more they differed, the greater the time difference between the two strains of bacteria. That is, the longer that 2-9-3 has existed, the greater would be the number of mutations it would have accumulated when compared with a bacteria alive today. If strain 2-9-3 was very similar to modern bacteria it could not be all that old, the Israeli scientists believed. They found that 2-9-3 was genetically almost identical to a "modern" species of common bacteria, S. marismortui. http://news.bbc.co.uk/2/hi/science/nature/1375505.stm How about this?
The isolation of microorganisms from ancient materials and the verification that they are as old as the materials from which they were isolated continue to be areas of controversy. Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels. This fact has historically been used by critics to argue that these isolates are not ancient but are modern contaminants introduced either naturally after formation of the surrounding material (for further details, see Hazen and Roeder 2001 and the reply by Powers, Vreeland, and Rosenzweig 2001 ) or because of flaws in the methodology of sample isolation (reviewed recently in Vreeland and Rosenzweig 2002 ). Such criticism has been addressed experimentally by the development of highly rigorous protocols for sample selection, surface sterilization, and contamination detection and control procedures. Paradox of the Ancient Bacterium Which Contains Modern Protein-Coding Genes | Molecular Biology and Evolution | Oxford Academic This last reference which is cited on this thread in the OP, is titled "The Paradox of the "Ancient" Bacterium Which Contains "Modern" Protein-Coding Genes." That's the topic of the OP. If no one really discounts the find based on molecular studies as you claim, then what's the fuss about? Why is the paper titled "The Paradox....", and why have subsequent studies tried to dismiss the find claiming the bacteria are too similar to modern strains to be ancient? It seems like you are just denying the basic facts of what the debate is here.
My criticism of Vreeland's discovery rests on the lack of replication by anyone else. Period. That may be. If so, then I assume you have no problem in theory with the idea that ancient bacteria resemble modern strains or are nearly identical? I assume your answer is yes, and with that, can we now discuss the OP, such as the paper linked in the OP?
Crap. Until Vreeland, the oldest viable bacteria were approx. 50 my old. Also found in halide crystals. However, this fact alone doesn't help Vreeland on this particular sample. Well, let's look at the first paragraph in Vreeland's paper again.
Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels. This fact has historically been used by critics to argue that these isolates are not ancient but are modern contaminants introduced either naturally after formation of the surrounding material (for further details, see Hazen and Roeder 2001 and the reply by Powers, Vreeland, and Rosenzweig 2001 ) or because of flaws in the methodology of sample isolation (reviewed recently in Vreeland and Rosenzweig 2002 ). Such criticism has been addressed experimentally by the development of highly rigorous protocols for sample selection, surface sterilization, and contamination detection and control procedures. Using the most scrupulous and well-documented sampling procedures and contamination-protection techniques reported to date, Vreeland, Rosenzweig, and Powers (2000) reported the isolation of a sporeforming bacterium, Bacillus strain 2-9-3, from a brine inclusion within a halite crystal recovered from the 250-Myr-old Permian Salado Formation in Carlsbad, NM So what happens is ancient bacteria are found, you admit that, but they always resemble modern bacteria, right? And the criticism is that the bacteria have to be contaminants since they should be different and are not. Just how many times does ancient bacteria have to be found that disagree with molecular assumptions before you guys say the finds have been replicated?
Unless another team comes up with some of the same results, all we have is one data point. So you believe all the other teams that found ancient bacteria that resembled modern bacteria are somehow the same team? Or do they all have to find the exact same strains in the exact same places? Seems like you are just moving the goalposts here. How often do scientists have to find ancient bacteria before you guys will say finding ancient bacteria has been replicated?
I'm waiting for someone besides the original team to provide corroboration. Corroboration on what point? That the crystals really were that old? They have corroborated that. That ancient bacteria have been found that resemble modern bacteria. Other teams have corroborated that.
Cold fusion???? Cold fusion was considered something extraordinary. You, on the other hand, insist that ancient bacteria looking like modern bacteria is no big deal. So the finds in your book are relatively uncontroversial, correct? And where are the studies that have failed to replicate these findings? If we are to take criticism seriously, the critics need to provide instances where they tried to duplicate these efforts and failed, right? You agree that asserting that just because the bacteria look like modern bacteria is not a valid criticism, I assume, right?
And the more spectacular the find What's skeptical about the find? You have stated that it's not the fact the ancient bacteria look like modern bacteria, right? Isn't the case though that the real opposition to these finds is that ancient bacteria look like modern bacteria and thus confound molecular assumptions? Edited by randman, : No reason given.
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randman  Suspended Member (Idle past 4929 days) Posts: 6367 Joined: |
The principle objection to the find is that Vreeland was claiming to have discovered a 250 my viable bacterial spore that was indistinguishable from a modern strain. Did it go right over your head why this was objectionable? If so, the paper cited in the OP might help, if you would read it. It is titled, "The Paradox of the "Ancient" Bacterium Which Contains "Modern" Protein-Coding Genes." The paradox is summed up nicely.
We have a large set of rigorous geological and microbiological data which can be interpreted in favor of the antiquity of these organisms, and an equally large set of rigorously obtained molecular data which can be interpreted in favor of their modernity. Paradox of the Ancient Bacterium Which Contains Modern Protein-Coding Genes | Molecular Biology and Evolution | Oxford Academic The OP also requests the participants address this question.
So, the central paradox opens up plenty of questions for the biologists here and I'll paraphrase it. We have geological data which interprets these bacteria as being ancient. We have an equal amount of molecular evidence which says they are modern. This incongruence is precisely the kind of falsification test that evolutionists have been harping on about for Lord only knows how long. So, surely this classes as strong falsification for at least one of the methods used in dating the bacteria? Has this data be reconciled, or is it still one of the thorns that remains fixed in the side of evolutionary dogma? You appear to consistently deny such a paradox exists in this debate. Why?
Now that he's shown that substitution has occurred, as predicted, I expect that part at least of the controversy will die down. You appear here to realize the controversy is about how the find affects molecular assumptions, but it's hard to know since you denied that above.
The phylogenies based on genetics would likely be unaffected. If the differences are so great, that even with more time, revisions to the molecular clock indicate that mutations cannot be responsible for evolving from one common ancestor to the others, then ToE is greatly affected because the mechanism of natural selection acting upon random mutatons will have been shown to be insufficient a mechanism for organic macro-evolution.
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randman  Suspended Member (Idle past 4929 days) Posts: 6367 Joined: |
Just to remind everyone what the thread is about and the basic controversy in scientific circles, this is it in a nutshell.
We have a large set of rigorous geological and microbiological data which can be interpreted in favor of the antiquity of these organisms, and an equally large set of rigorously obtained molecular data which can be interpreted in favor of their modernity. Paradox of the Ancient Bacterium Which Contains Modern Protein-Coding Genes | Molecular Biology and Evolution | Oxford Academic Edited by randman, : No reason given.
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randman  Suspended Member (Idle past 4929 days) Posts: 6367 Joined: |
nwr, does that mean within the EvC controversy, since it is a controversy, that you think all sides are reasonable and no creationist conspiracy exists too? So there is no cause for concern for the ID and creationist movements and their ideas to be taught in schools, etc,....?
Edited by randman, : No reason given. Edited by randman, : No reason given.
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randman  Suspended Member (Idle past 4929 days) Posts: 6367 Joined: |
Quetzal, do I have to repost all of this for you to finally acknowledge that opposition to the find is based on the fact molecular studies indicate it must be of recent origin? It's getting absurd to hear you continually deny the obvious and try to avoid the OP altogether.
You also seeem to have forgotten that I pointed out already Vreeland was trying to find a way to make the ancient bacteria "fit" due to being more different to modern bacteria than other finds. However, your ludicrous assumption this nullifies the paradox is unfounded. First, the opposition to the find is still basing their opposition on molecular studies. Second, this is not the only find. As Vreeland points out, nearly all finds of ancient bacteria confound molecular dating. So the paradox remains. Vreeland does offer soms ways that perhaps molecular dating can be fooled but be a valid concept. One you mention, but another is that ancient bacteria could be rereleased to the wild, but exploring these options does not mean the opposition to the finds based on their stark incongruence with molecular dating has ended. Moreover, the fact he is able to put a little more distance between the ancient bacteria and the modern strain still doesn't solve the problem as you claim.
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randman  Suspended Member (Idle past 4929 days) Posts: 6367 Joined: |
If you're already firm in this conclusion and are only interested from this point on in repeating this charge, then please stop participating in this thread. With all due respect and hear me out on this please, there is some confusion as to what I am saying here. I am not attacking or demeaning motives here as you surmise when saying there is a paradox or conflict between molecular dating and the find, but pointing out what public, scientific criticism of the find actually is. It's not me coming up with this analysis, but what critics of the find have come up. If you are saying we cannot acknowledge the molecular criticism of the find, then how are we suppossed to discuss the OP since that is the topic of this thread?
To reach their conclusion, Professor Graur and Dr Pupko downloaded the genetic information about strain 2-9-3, sometimes called B. permians, from the GenBank directory on the internet. They then compared 2-9-3's genes with those of modern bacteria to see how different they were. According to the molecular clock model, the more they differed, the greater the time difference between the two strains of bacteria. That is, the longer that 2-9-3 has existed, the greater would be the number of mutations it would have accumulated when compared with a bacteria alive today. If strain 2-9-3 was very similar to modern bacteria it could not be all that old, the Israeli scientists believed. They found that 2-9-3 was genetically almost identical to a "modern" species of common bacteria, S. marismortui. http://news.bbc.co.uk/2/hi/science/nature/1375505.stm This isn't belligerency on my part. The criticism of the find, such as in the study above, largely consists of it's disagreement with molecular dating techniques. That's what the OP was about, and that's what I have tried to stick to discussing. My frustration has been that things like the quotes above are being treated as if this is just my slur or my opinion on the matter, and it's hard to have a discussion about the meaning of a scientific debate if there isn't even an acknowledgement of what that debate is, and this isn't my opinion. The terms "paradox" are from the scientists themselves. As a sidenote:
In a paper published online August 30, 2005 in the journal Extremophiles, Vreeland presented evidence that four strains of Permian microbes (2-9-3 and three others that were found later) are different enough from modern relatives in a number of categories that they could not arise from contamination.
Vreeland does then offer a study to show that the microbes could not be from contamination. He is not saying the paradox is solved, however. Honestly percy, if you read the OP, it lays out this paradox as the topic of this thread, and so discussing the topic of the thread would seem to be on-topic, but if you want me to abandon the thread, I will. If you note, however, in bringing this back up, I have been the one providing links and studies to more recent studies and nerws on this, and I would think that is commendable, and what one is suppossed to do here. I realize things have been cantankerous, but that works both ways. If you had provided links, quotes, and studies showing that molecular dating was indeed the remaining primary criticism, I think you would be frustrated if someone said, without providing any substantiation, that you were just misreading the debate. it's hard to discuss facts when one side doesn't acknowledge their existence, and the facts here are the basis of scientific criticism in published peer-reviewed journals concerning the find. Edited by randman, : No reason given. Edited by randman, : No reason given.
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randman  Suspended Member (Idle past 4929 days) Posts: 6367 Joined: |
Since you asked what I think, I will respond. I am not asking to be showcased (you enjoy creating new verbs) though have asked to be able to start a thread there, and was rejected.
But in all fairness, you are misreading my request. I am not asking you to decide who is right. The thread is suppossed to be about the contradiction of this find with molecular dating. So threatening me saying to stay off the thread if I want to discuss that point was bizarre. I mean what the heck, percy. We are suppossed to be talking about molecular criticism of the find. That's the doggone thread topic! This is the topic of this thread from the OP.
So, the central paradox opens up plenty of questions for the biologists here and I'll paraphrase it. We have geological data which interprets these bacteria as being ancient. We have an equal amount of molecular evidence which says they are modern. This incongruence is precisely the kind of falsification test that evolutionists have been harping on about for Lord only knows how long. So, surely this classes as strong falsification for at least one of the methods used in dating the bacteria? Has this data be reconciled, or is it still one of the thorns that remains fixed in the side of evolutionary dogma? ? Edited by randman, : No reason given. Edited by randman, : No reason given.
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