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Author Topic:   Ancient bacteria with modern DNA, problem for evolution?
Quetzal
Member (Idle past 5871 days)
Posts: 3228
Joined: 01-09-2002


Message 19 of 77 (340191)
08-15-2006 9:34 AM
Reply to: Message 13 by randman
08-14-2006 9:14 PM


Re: selective acceptance of data
Rand,
This appears to be another instance where you need to explain to me in words of one syllable or less ('cause after all, I'm an ignorant evilutionist) exactly why you think this bacterium poses any problem to the ToE. Ideally, I'd appreciate it if you could (for once) dispense with random insults, allusions to conspiracy, or claims of sheer scientific fraud/dogmatism/etc. Just plainly explain why you think this has any bearing on the ToE.
Thanks.

This message is a reply to:
 Message 13 by randman, posted 08-14-2006 9:14 PM randman has replied

Replies to this message:
 Message 21 by randman, posted 08-15-2006 9:46 AM Quetzal has replied

Quetzal
Member (Idle past 5871 days)
Posts: 3228
Joined: 01-09-2002


Message 24 of 77 (340223)
08-15-2006 10:30 AM
Reply to: Message 21 by randman
08-15-2006 9:46 AM


Re: selective acceptance of data
I dunno, rand. There have been a lot of studies calling into question the assumptions (dating from Kimura's neutral evolution paper and continuing to the present) of the molecular clock either in toto or in part. Many of the more recent studies focus on the wide variance in mutation/substitution rate (remember: Kimura based his idea on a straight Poisson distribution, which doesn't appear to be the case generally, the devil being in the details). See, for example, Thomas JA, Welch JJ, Woolfit M, Bromham L, 2006, There is no universal molecular clock for invertebrates, but rate variation does not scale with body size, PNAS 103:7366-7371. There's an on-going research effort to figure out a way to "predict" and quantify the rate variances to permit the "molecular clock" idea to be useful. IOW, it's recognized that Kimura didn't have all the facts and figures right. Doesn't effect the ToE at all, as far as I can see. Additionally, in some cases Kimura's idea has been substantiated (see, for instance, Fitch WM, Ayala FJ 1995, "The Superoxide Dismutase Molecular Clock Revisited", in Fitch and Ayala, eds, Tempo and Mode in Evolution, National Academy Press, pg 235-250).
On the other hand, I'm still not clear why you think this bacteria poses a problem to evolution. In the first place, nothing cited thus far in this thread indicates that Vreeland's original hypothesis concerning the critter being that old has been substantiated. The article you cited simply asserts that the objections have been met, but without much in the way of evidence. Secondly, even if it were shown that everything Vreeland et al claimed was correct, I don't get why it would be a problem. You STATE that it's a problem, but still haven't explained why.
As far as falsifying ToE, since the ToE is an inherently non-falsifiable theory, it probably is not possible to come up with any data that can do that, but that just shows the inherent flaw within ToE as a scientific theory, imo. It's considered true by definition, and so the data doesn't form the theory, but the theory the data.
Couldn't make a single post without something like this, could you? Ah well, what did I expect?

This message is a reply to:
 Message 21 by randman, posted 08-15-2006 9:46 AM randman has replied

Replies to this message:
 Message 26 by randman, posted 08-15-2006 10:38 AM Quetzal has replied

Quetzal
Member (Idle past 5871 days)
Posts: 3228
Joined: 01-09-2002


Message 30 of 77 (340253)
08-15-2006 11:25 AM
Reply to: Message 28 by randman
08-15-2006 10:57 AM


Re: btw, "problem for evolution"
Actually, Modulus carefully placed a question mark at the end of that phrase. Indeed, he has accepted Mammuthus's discussion of why the Vreeland discovery may not be valid. Irreproducible results in biology aren't uncommon - especially concerning "ancient" DNA studies which are subject to contamination, among many other problems. After that point in this discussion, you appear to be the only one who is still hanging on the "problem" issue - the concensus among the other participants (including me), appears to be that the jury is still out.
Since you're the one still insisting on the bacterium being a "problem" for the ToE, I guess I still need an explanation from you why this would be the case. I'm not even saying you're wrong - I'm saying I don't understand your argument.

This message is a reply to:
 Message 28 by randman, posted 08-15-2006 10:57 AM randman has not replied

Quetzal
Member (Idle past 5871 days)
Posts: 3228
Joined: 01-09-2002


Message 31 of 77 (340256)
08-15-2006 11:31 AM
Reply to: Message 26 by randman
08-15-2006 10:38 AM


Re: selective acceptance of data
Did you read the links? There certainly has been published studies backing Vreeland up.
I noted that. On the other hand, there have been an equal or greater number of studies that have not backed Vreeland up. In addition, Vreeland himself has yet to replicate the original study - not an unusual circumstance when dealing with ancient DNA. Moreover, the 16sDNA sequence he used has been shown to be highly variable (that was one of the conclusions of both papers I cited, especially the first). In other words, the critique is not primarily based on the molecular clock he used, but rather the fact that the study has not been replicated by anyone else. Whether he's right or wrong, however, has no bearing on my question: why do YOU consider it a problem?

This message is a reply to:
 Message 26 by randman, posted 08-15-2006 10:38 AM randman has replied

Replies to this message:
 Message 34 by randman, posted 08-15-2006 1:15 PM Quetzal has replied
 Message 38 by randman, posted 08-16-2006 3:19 PM Quetzal has replied

Quetzal
Member (Idle past 5871 days)
Posts: 3228
Joined: 01-09-2002


Message 37 of 77 (340341)
08-15-2006 4:23 PM
Reply to: Message 34 by randman
08-15-2006 1:15 PM


One Trick Pony Rides Again
Congratulations. I see you managed to get yourself suspended again. Hopefully, we can pick this up when you get back. If not, it's been fun. I'm sure there will be other opportunities.

This message is a reply to:
 Message 34 by randman, posted 08-15-2006 1:15 PM randman has not replied

Quetzal
Member (Idle past 5871 days)
Posts: 3228
Joined: 01-09-2002


Message 39 of 77 (340552)
08-16-2006 4:01 PM
Reply to: Message 38 by randman
08-16-2006 3:19 PM


Re: selective acceptance of data
Huh? I just showed you the follow-up studies that discounted the earlier criticisms. Have you read any of them?
No, you didn't, in fact. You showed a single article where Vreeland and supporters claimed they had met all objections. That does not obviate the fact that there are a number of researchers who are skeptical of the claim even now. The key item missing is that the Bacillus 2-9-3 strain that Vreeland discovered has yet to be duplicated by any other lab. This is almost unheard of. To date no one else has been able to culture the critter from samples of the same deposit - the ONLY way to insure that contamination (or other issues) is not a factor. In other words, replication by an independent observer - one of the hallmarks of science - has yet to occur. None of this indicates that Vreeland is either right or wrong - merely that until the data is replicated by someone else (not, as has been the case so far by Vreeland and his team themselves), we are required by the methodology of science to withhold unqualified acceptance. I personally think it would be absolutely fantastic to find that Vreeland et al was correct. It could have strong implications for the possibility of finding lifeforms not on earth - say viable preserved Martian organisms, etc.
Which brings me to the point you have been completely avoiding throughout this discussion: Why do YOU consider this to be something weird or damaging to evolution? In fact, Vreeland's most recent paper on his bug shows that the organism ISN'T equivalent to its modern counterpart: Vreeland RH, Rosenzweig WD, Lowenstein T, Satterfield C, Ventosa A., 2006, "Fatty acid and DNA analyses of Permian bacteria isolated from ancient salt crystals reveal differences with their modern relatives", Extremophiles 10:71-78
quote:
The isolation of living microorganisms from primary 250-million-year-old (MYA) salt crystals has been questioned by several researchers. The most intense discussion has arisen from questions about the texture and age of the crystals used, the ability of organisms to survive 250 million years when exposed to environmental factors such as radiation and the close similarity between 16S rRNA sequences in the Permian and modern microbes. The data in this manuscript are not meant to provide support for the antiquity of the isolated bacterial strains. Rather, the data presents several comparisons between the Permian microbes and other isolates to which they appear related. The analyses include whole cell fatty acid profiling, DNA-DNA hybridizations, ribotyping, and random amplified polymorphic DNA amplification (RAPD). These data show that the Permian strains, studied here, differ significantly from their more modern relatives. These differences are accumulating in both phenotypic and molecular areas of the cells. At the fatty acid level the differences are approaching but have not reached separate species status. At the molecular level the variation appears to be distributed across the genome and within the gene regions flanking the highly conserved 16S rRNA itself. The data show that these bacteria are not identical and help to rule out questions of contamination by putatively modern strains.
If your argument is that the ToE is invalid because these Permian bacteria haven't changed in 250 million years, think again.

This message is a reply to:
 Message 38 by randman, posted 08-16-2006 3:19 PM randman has replied

Replies to this message:
 Message 40 by randman, posted 08-16-2006 5:10 PM Quetzal has replied

Quetzal
Member (Idle past 5871 days)
Posts: 3228
Joined: 01-09-2002


Message 41 of 77 (340599)
08-16-2006 6:43 PM
Reply to: Message 40 by randman
08-16-2006 5:10 PM


Re: selective acceptance of data
You're right, I miscounted. However, none of those help you much. You've cited three news articles, one of which refers to the original paper (Vreeland RH, Rosenzweig WD, Powers DW, 2000, "Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal", Nature 407:897-900), one of which is commentary on the controversy, and one of which refers to a study - again conducted by Vreeland's team - that corroborates the age of the halite and brine (Satterfield CL, Lowenstein TK, Vreeland RH, Rosenzweig WD, Powers DW, 2004, "New evidence for 250 Ma age of halotolerant bacterium from a Permian salt crystal", Geology e93). This does NOT reflect "multiple" sources nor does it reflect corroboration from an independent observer. As yet, there is nothing more than the scientific equivalent of Vreeland's say-so. If you'd bother to look, his team has written multiple papers addressing one or more aspect of the find - but no one else has. As I noted, I'd love it if he were right, but as a scientist I must perforce withhold acceptance until someone else comes up with some corroborating data. For some reason, you still don't get that. In spite of your insistence, I haven't "discounted" anything.
Labs don't duplicate bacteria. Bacteria must first be found. Ancient finds can be very rare. What is the basis for expecting that such an event is not so rare that it should be duplicated?
BS. Of course the idea is to find another set of bacteria in the same strata and same conditions from the same location. The only difference being it is found by some other team. Happens all the time (although not with ancient bacteria). It's called replication. If a different team using the same protocols in the same location can't locate and isolate the bacteria (or even a different strain), then the original find is suspect. Think cold fusion.
Please post what you think this says, and why molecular dating techniques would not be affected by this, nor phylogenies and the vaunted "nested heirarchies" based on such molecular dating techniques would not be affected, and if not, then what sort of facts can even in theory affect the ToE in this area. You may wish to open a new thread depending on whether your answers are on or off-topic.
I've already addressed the molecular clock issue. There is no real problem posed by this bacterium because the molecular clock concept - except in specific lineages - is already a mess. I posted references in support of that conclusion. I suggest you go back and read them.
I don't want to risk being off-topic so I will point you to the OP, which states, and btw, Modolous's opinion on this does not appear to have changed, contrary to your claims.
Wrong again. Please see message 5.
So now we come down to your opinion - which I've asked you for multiple times. Do YOU, randman, consider this bacterium a problem for evolution and why? Why do YOU think this find - if corroborated - has an effect on the determination of genetic distance (which is basically what the molecular clock is really about)? Why do YOU consider this some kind of falsification of the ToE? If you can avoid mentioning the three verbotten words in your reply, perhaps we can move this discussion along.

This message is a reply to:
 Message 40 by randman, posted 08-16-2006 5:10 PM randman has replied

Replies to this message:
 Message 42 by randman, posted 08-16-2006 6:59 PM Quetzal has replied

Quetzal
Member (Idle past 5871 days)
Posts: 3228
Joined: 01-09-2002


Message 45 of 77 (340672)
08-16-2006 10:49 PM
Reply to: Message 42 by randman
08-16-2006 6:59 PM


Re: selective acceptance of data
I will just add for clarity that modulous' concern the find may not be true does not change the fact that he stated in the OP that if the find were true, this poses a problem. This has been brought to your attention before, and yet you continue to claim that the find poses no problem whatsoever to the basic assumptions and techniques mentioned in the OP. I am not sure why you continue to do that.
Because, as I've explained, in my opinion it doesn't pose any sort of problem at all. Except, as noted, for the substitution rate issue which is at the heart of the molecular clock, and which I've already noted is problematic because of documented rate variations in many major lineages - references to which I have already posted. YOU, my dear rand, appear to be the only one in this thread that still DOES consider that it's a problem. So, for the last time, why?

This message is a reply to:
 Message 42 by randman, posted 08-16-2006 6:59 PM randman has replied

Replies to this message:
 Message 46 by randman, posted 08-16-2006 11:02 PM Quetzal has not replied
 Message 47 by randman, posted 08-16-2006 11:12 PM Quetzal has replied

Quetzal
Member (Idle past 5871 days)
Posts: 3228
Joined: 01-09-2002


Message 48 of 77 (340685)
08-16-2006 11:19 PM
Reply to: Message 44 by randman
08-16-2006 10:08 PM


Re: selective acceptance of data
I don't see the issues being addressed. Stating that peer-review articles are the equivalent of taking Vreeland's word for it is a bogus argument. The studies do address and substantiate the original criticisms, albeit the one criticism which is based on molecular dating techniques whicb quetzal says are considered dubious by others anyway. But arguing the theory is correct and the not the data is not a good argument.
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. He is using this data to show that the claim of modern contamination is incorrect - and lends credence to the age of the beastie. Talk about not addressing the references...
Let me put it this way. If the bacteria confirmed molecular dating technigues, do you think the same people would say it must be a result of contamination?
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. My criticism of Vreeland's discovery rests on the lack of replication by anyone else. Period. And yeah, I'm convinced that any new, startling discovery is going to be questioned by hard-core skeptics. But the basis of the skepticism was the idea that 250 my bacteria could be viable, and could be at first glance so similar to modern species. Remember Alvarez? It took years and finally many other, independent researchers coming to the same conclusion, before the bolide impact hypothesis was accepted by the scientific community. Now, it's old hat. Same deal here. Get off your conspiracy horse for a minute will you?
On the issue of replication, I asked for specifics and specific scientific reasoning to go along with it. The fact is ancient bacteria have been found before. So in a sense there is precedent and replication on that point. The simple fact of the matter is this find is being dismissed because it doesn't fit evo molecular assumptions.
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.
Also, before I got on the thread, the talk suggested no follow-up studies had confirmed the original finding, and that was bogus. There have been follow-up studies, and imo I was the one on this thread bringing the facts to light.
Crap again. The follow-up studies have all been done by the same team, and I'm the only one on this thread who's actually referenced the published articles. Unless another team comes up with some of the same results, all we have is one data point. Try again.
Let me put it this way. If we are to demand replication before conclusions and quetzal and other evos here take that stance, then until someone disproves the find, we cannot take the attitude the find is due to contamination or is likely due to contamination. His stance suggested we basically can't trust anything from Vreeland's team, that their work and papers amount to "the scientific equivalent of Vreeland's say-so" and so insinuates the conclusions are unreliable.
Again, you miss the point. It's not an attempt for someone else to "disprove" it. I'm waiting for someone besides the original team to provide corroboration. Until then, the absolute best thing you can say is that it seems to be a pretty neat idea, and there's nothing to disconfirm it. I thought, for example, that the chemical traces found in the Martian meteorite that led the first team to proclaim them organic was about the most exciting find I could imagine. However, I waited until someone else was able to replicate the results - with the result that further, independent testing showed that the traces were more likely inorganic in origin. I was very disappointed. However, unlike you, I waited to open the champagne until the results were in. Same for Vreeland's discovery.
His reason is that no other team, (ignoring the fact that it's not the same people each time and so is really wrong on that point to a great degree), has done the research to duplicate the research, and so we cannot trust their conclusions.
Crap. All the papers I referenced, including the most recent one from the geologists, included both Vreeland and Rosenzweig in the authors' list. It's the same team. Unless the results can be independently corroborated, it's all still the same people making the claim. That's the way science works, rand. Doesn't matter what the claim is, it has to be confirmed by someone outside the original group. Cold fusion????
And yet WITHOUT ANYONE, not even an initial study much less replicating that study, having confirmed that the bacteria are contaminants, some feel certain this is the case. It's a double-standard here. Shouldn't the correct attitude be that we probably have a genuine find here instead of insisting that without bothering to research the same salt crystals, that no ancient bacteria exists? If you want to discount Vreeland, then you need to go out there and see if replication is possible.
You really have no clue, do you? People are proposing alternative hypotheses (like the contaminant issue) to explain the data. NO ONE in science accepts any new find without corroboration. And the more spectacular the find, the more skeptics are going to come out of the woodwork. That's the way the process works. If you don't like it, too bad. Won't change the way science is done. Get over it.

This message is a reply to:
 Message 44 by randman, posted 08-16-2006 10:08 PM randman has replied

Replies to this message:
 Message 50 by randman, posted 08-16-2006 11:49 PM Quetzal has not replied

Quetzal
Member (Idle past 5871 days)
Posts: 3228
Joined: 01-09-2002


Message 49 of 77 (340691)
08-16-2006 11:34 PM
Reply to: Message 47 by randman
08-16-2006 11:12 PM


Re: maybe this will help
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?
No. 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. This is what led to the contamination claim. Vreeland's latest work shows that the bacteria is in fact different from its modern counterparts. A point, by the way, which is very much in favor of Vreeland's initial contention.
If you disagree, do you think if the find agreed with molecular dating, that there would be such a controversy?
To be honest, probably. The mere idea of a viable 250 my old bacterial spore would require a bunch of corroborating evidence. It was Vreeland's initial evaluation of the bug as being not just similar but nearly identical to a modern bacillus that caused the controversy. Now that he's shown that substitution has occurred, as predicted, I expect that part at least of the controversy will die down.
For example, how would this affect molecular phylogenies?
That might be an interesting speculation. However, there is a difference that needs to be clarified between molecular phylogenies and the dates attributed to the so-called molecular clock. The phylogenies based on genetics would likely be unaffected. The dates, on the other hand, are in many lineages having to be changed even now based on newer, more "realistic" assumptions.
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?
Yes and no. Not all dates based on molecular substition rates are wrong - just that there are way more exceptions and variable rates than Kimura originally believed. As for Vreeland's bug, yes, my only objection to it is the lack of replication.
Edited by Quetzal, : fix screwy UBB code thingy

This message is a reply to:
 Message 47 by randman, posted 08-16-2006 11:12 PM randman has replied

Replies to this message:
 Message 51 by randman, posted 08-17-2006 12:00 AM Quetzal has replied

Quetzal
Member (Idle past 5871 days)
Posts: 3228
Joined: 01-09-2002


Message 57 of 77 (340785)
08-17-2006 10:51 AM
Reply to: Message 51 by randman
08-17-2006 12:00 AM


Re: maybe this will help
I have read the original paper - you apparently have not, relying instead on news articles discussing the paper. In any event, you clearly did NOT read the most recent article by Vreeland's team that obviates your most recent citation. In that paper - the abstract of which I provided - Vreeland states that there is sufficient difference between his bug and the modern counterpart to classify them as different species. IOW, in spite of what was in the initial paper, the bug HAS changed, and IS different from S. marismortui. This isn't someone denying the data, this is the original researcher modifying his initial assessment. Of course, you personally will undoubtedly attribute this reassessment to pressure from the Vast Evilutionist Conspiracy, but the reality is that Vreeland is doing science. Too bad.
You appear to consistently deny such a paradox exists in this debate.
Why? Because it doesn't exist. It initially looked like it might, but further examination shows that it doesn't. Quite obviously, the bug has a very low substitution rate. This kind of anomaly has been noted in other organisms (see the invertebrate paper I referenced earlier). There may be numerous reasons for this, but since I'm not a molecular biologist I'm not qualified to address it. If Taz or Mammuthus were here, undoubtedly your question would be answered in full. Perhaps WK might be willing to provide a response.
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.
Because one (of several) skeptical objections was that there was no way that an ancient organism could be identical to a modern one. Since it in fact isn't, there's no problem. Right? You get that part?
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.
You've overstepped. There is no correlation between the molecular clock being off and the concept of common ancestry. Nor is there anything in any of this that would implicate natural selection, random mutation, or anything else dealing with the ToE as a whole.

This message is a reply to:
 Message 51 by randman, posted 08-17-2006 12:00 AM randman has replied

Replies to this message:
 Message 58 by randman, posted 08-17-2006 12:34 PM Quetzal has replied

Quetzal
Member (Idle past 5871 days)
Posts: 3228
Joined: 01-09-2002


Message 60 of 77 (340830)
08-17-2006 1:06 PM
Reply to: Message 58 by randman
08-17-2006 12:34 PM


Forget it rand
Rand, as far as I can tell I have addressed each of your rather ambiguous arguments as well as I can. I have addressed the molecular clock issue. I have addressed the replication issue. I have addressed the OP, the original paper and subsequent papers up to the most recent by Vreeland himself. Your continual attempts to create a tempest in a teacup are pointless. THERE IS NO PARADOX. At the absolute best, the only thing you can make out of all this is that - as I have repeatedly stated - there are anomalies, exceptions and variances in neutral substitution rates that currently call into question the universal applicability of "molecular clock" dating methods. It has sod all to do with common ancestry, natural selection, etc, or the ToE as a whole as you attempted to assert in your previous post.
Insult and accuse all you wish, it doesn't change the facts. I have answered or at least addressed every single one of your accusations, questions and comments. That you are incapable of seeing that is not my problem. Once again, we will have to leave the final judgement up to the readers.

This message is a reply to:
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