Ancient bacteria with modern DNA, problem for evolution?

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.

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?

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.

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

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."

http://www.americanscientist.org/template/AssetDetail/assetid/47368

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.

http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637

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.

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.

http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637

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.

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.

http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637

Edited by randman, : No reason given.

Okay, so its a scientific controversy. If it is a controversy, then it is being looked at, and people are devising experiments to settle the disagreement.

So there isn't any evo conspiracy here. It's just a controversy over data. Such controversies come up from time to time. I'm not seeing any cause for concern.

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.

I have no idea whether both sides are reasonable. I'm not a biologist, so I leave it to those in the area to settle the question.

There has always been controversy in science. And there always will be. If controversy ceases, then science will have ceased.

... and no creationist conspiracy exists too?

Creationists can think what they like. It is no concern of mine. It only becomes a problem when then try to force their religion into the science class.

It isn't a scientific controversy, because only one side is doing the looking and experimental testing that NWR described. The only controversy over EvC is over whether ID and creation science should be given a bye for all the normal tests required of scientific theories and be plunked straight into the middle of teaching curricula as if by divine fiat.

TTFN,

WK

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.

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.

randman writes: It's getting absurd to hear you continually deny the obvious and try to avoid the OP altogether.

There's been a lot like this from you recently. I'd like to suggest that you might get better results, and be able to be here more consistently, if you think of this more as a team effort working constructively toward a common understanding.

---

--	Percy
	EvC Forum Director

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.