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Author Topic:   Ancient bacteria with modern DNA, problem for evolution?
Quetzal
Member (Idle past 4291 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 responded

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

Percy
Member
Posts: 19435
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 32 of 77 (340277)
08-15-2006 12:25 PM
Reply to: Message 29 by randman
08-15-2006 11:01 AM


Re: OK
randman writes:

If you want to discuss the topic, please explain why the data should be ignored, crash, and if you cannot discuss the topic, then please don't foul up the thread with more off-topic posts.

Ah, there's nothing like the fervor of the recently converted! :D

--Percy


This message is a reply to:
 Message 29 by randman, posted 08-15-2006 11:01 AM randman has responded

Replies to this message:
 Message 33 by randman, posted 08-15-2006 1:12 PM Percy has responded

randman 
Suspended Member (Idle past 3318 days)
Posts: 6367
Joined: 05-26-2005


Message 33 of 77 (340295)
08-15-2006 1:12 PM
Reply to: Message 32 by Percy
08-15-2006 12:25 PM


Re: OK
So if I respond to evo's off-topic demands, I can be banned, but ridiculed by an evo admin in non-admin mode if I don't, eh?

This message is a reply to:
 Message 32 by Percy, posted 08-15-2006 12:25 PM Percy has responded

Replies to this message:
 Message 35 by Percy, posted 08-15-2006 1:23 PM randman has not yet responded

randman 
Suspended Member (Idle past 3318 days)
Posts: 6367
Joined: 05-26-2005


Message 34 of 77 (340300)
08-15-2006 1:15 PM
Reply to: Message 31 by Quetzal
08-15-2006 11:31 AM


Re: selective acceptance of data
On the other hand, there have been an equal or greater number of studies that have not backed Vreeland up

Really? What arguments have not been refuted?

Funny how when a fossil of, say, Pakicetus is found, it's front-page news even if just one fossil, but when an extraordinary find of ancient bacteria is found, all the sudden you apply a double-standard and insist more samples be found. Seems a tad hypocritical to me.

Edited by Admin, : Fix quote.


This message is a reply to:
 Message 31 by Quetzal, posted 08-15-2006 11:31 AM Quetzal has responded

Replies to this message:
 Message 36 by Admin, posted 08-15-2006 1:31 PM randman has not yet responded
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Percy
Member
Posts: 19435
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 35 of 77 (340305)
08-15-2006 1:23 PM
Reply to: Message 33 by randman
08-15-2006 1:12 PM


Re: OK
You make so much extra work for me and my merry band, please don't begrudge us a little fun at your expense now and then. :)

--Percy

Edited by Percy, : Tweak.

Edited by Percy, : Can't type.


This message is a reply to:
 Message 33 by randman, posted 08-15-2006 1:12 PM randman has not yet responded

Admin
Director
Posts: 12657
From: EvC Forum
Joined: 06-14-2002


Message 36 of 77 (340308)
08-15-2006 1:31 PM
Reply to: Message 34 by randman
08-15-2006 1:15 PM


Re: selective acceptance of data
randman writes:

Funny how when a fossil of, say, Pakicetus is found, it's front-page news even if just one fossil, but when an extraordinary find of ancient bacteria is found, all the sudden you apply a double-standard and insist more samples be found. Seems a tad hypocritical to me.

Let's see, where to start. You're introducing one of your old favorite topics, Pakicetus. And you're questioning the integrity of your fellow members with implications of double-standards and hypocrisy.

See you in 24 hours.


--Percy
EvC Forum Director

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

Quetzal
Member (Idle past 4291 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 yet responded

randman 
Suspended Member (Idle past 3318 days)
Posts: 6367
Joined: 05-26-2005


Message 38 of 77 (340544)
08-16-2006 3:19 PM
Reply to: Message 31 by Quetzal
08-15-2006 11:31 AM


Re: selective acceptance of data
On the other hand, there have been an equal or greater number of studies that have not backed Vreeland up.

Huh? I just showed you the follow-up studies that discounted the earlier criticisms. Have you read any of them?

In addition, Vreeland himself has yet to replicate the original study - not an unusual circumstance when dealing with ancient DNA.

What do you mean by "replicated"? Be specific. Studies have been conducted to confirm every aspect of the find that can be completed. Do you propose that the exact same bacteria strain must be found again?

They found 2 samples originally, right? There have been other finds of ancient bacteria.

The primary argument now against the find is that molecular dating techniques place the bacteria as a modern bacteria....in other words, the data is rejected based on the theory rather than the theory being adjusted to the data.

Edited by randman, : No reason given.


This message is a reply to:
 Message 31 by Quetzal, posted 08-15-2006 11:31 AM Quetzal has responded

Replies to this message:
 Message 39 by Quetzal, posted 08-16-2006 4:01 PM randman has responded

Quetzal
Member (Idle past 4291 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 responded

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

randman 
Suspended Member (Idle past 3318 days)
Posts: 6367
Joined: 05-26-2005


Message 40 of 77 (340566)
08-16-2006 5:10 PM
Reply to: Message 39 by Quetzal
08-16-2006 4:01 PM


Re: selective acceptance of data
No, you didn't, in fact. You showed a single article where Vreeland and supporters claimed they had met all objections.

Really? Looks like more than one to me. Plus, the articles reference other studies as well.

http://www.americanscientist.org/template/AssetDetail/assetid/47368
http://dsc.discovery.com/news/briefs/20050411/oldestlife.html
http://news.bbc.co.uk/2/hi/science/nature/1375505.stm

What's your beef?

The key item missing is that the Bacillus 2-9-3 strain that Vreeland discovered has yet to be duplicated by any other lab.

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? Extremely rare finds should not be expected to be just laying around unless you can show that the ancient find is not so rare. For example, if you found a lot of a particular type of ancient bacteria, you could suggest that this is such a common occurrence that the researchers should find some bacteria with the same traits to validate their ideas.

Furthermore, are you arguing that ancient bacteria have not been found in general?

Your argument appears to consist of discounting any rare find, period, if it disagrees with your ideas on molecular dating. The simple fact is finding ancient bacteria is duplicating earlier finds of ancient bacteria. Demanding the same strain be found when very rare conditions must be met to find any bacteria is simply moving the goalposts, imo.

Why do YOU consider this to be something weird or damaging to evolution?

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. If the data is valid, it poses a problem. Here is the relevant section.

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?

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.

Edit to add. Would you also take the time to read the links posted above? This is the 2nd time posting them, and you erroneously claimed only one article was posted. If we are to have a fruitful discussion, you need to actually address the science within the discussion, namely the studies references in the articles, and how the critics have been answered, contrary to your earlier claims, and then talk about the remaining issues, and whether it is reasonable to demand that all evidence conform to existing theory relative to molecular dating or not.

Edited by randman, : No reason given.

Edited by randman, : No reason given.


This message is a reply to:
 Message 39 by Quetzal, posted 08-16-2006 4:01 PM Quetzal has responded

Replies to this message:
 Message 41 by Quetzal, posted 08-16-2006 6:43 PM randman has responded

Quetzal
Member (Idle past 4291 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 responded

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

randman 
Suspended Member (Idle past 3318 days)
Posts: 6367
Joined: 05-26-2005


Message 42 of 77 (340609)
08-16-2006 6:59 PM
Reply to: Message 41 by Quetzal
08-16-2006 6:43 PM


Re: selective acceptance of data
As yet, there is nothing more than the scientific equivalent of Vreeland's say-so.

If you are not going to acknowledge the published science articles as more than someone's say-so, and refuse to engage the facts, we have nothing to discuss.

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.

If you wish to engage the topic, please do so. Address the facts, acknowledge the issues raised in the studies and the arguments involved and state how you think they are flawed or whatever. Merely claiming published articles in peer-reviewed literature is merely someone's say-so means nothing and imo, is a total dodge of the thread topic.

Edited by randman, : No reason given.

Edited by randman, : No reason given.

Edited by randman, : No reason given.

Edited by randman, : No reason given.


This message is a reply to:
 Message 41 by Quetzal, posted 08-16-2006 6:43 PM Quetzal has responded

Replies to this message:
 Message 43 by Percy, posted 08-16-2006 9:39 PM randman has responded
 Message 45 by Quetzal, posted 08-16-2006 10:49 PM randman has responded

Percy
Member
Posts: 19435
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 43 of 77 (340662)
08-16-2006 9:39 PM
Reply to: Message 42 by randman
08-16-2006 6:59 PM


Re: selective acceptance of data
Hi Randman,

You seem to be in a big hurry to rush to judgment, and I think it is causing you to misunderstand what Quetzal is saying. I'll try to explain.

randman writes:

As yet, there is nothing more than the scientific equivalent of Vreeland's say-so.

If you are not going to acknowledge the published science articles as more than someone's say-so, and refuse to engage the facts, we have nothing to discuss.

Your excerpt from Quetzal's message was part of a longer passage. Quetzal was only explaining that in science accepting unreplicated results would be like taking someone's word on just their say-so. It was not intended as a disparaging comment about Vreeland's research techniques. Hence, when you proceed in this manner:

Address the facts, acknowledge the issues raised in the studies and the arguments involved and state how you think they are flawed or whatever. Merely claiming published articles in peer-reviewed literature is merely someone's say-so means nothing and imo, is a total dodge of the thread topic.

It indicates that you've completely missed the point. Aside from mentioning that contamination by modern or more common strains is a constant and difficult problem for all researchers of rare or ancient bacteria, Quetzal hasn't issued any charges that Vreeland's approach and techniques are incorrect or wrong or flawed. His primary point is that such unexpected results should await replication before exploring the issues surrounding their incorporation into evolutionary theory. The implications you're anticipating may one day have to be faced, but until these results are replicated that day is not today.

Modern science *does* have a process that it follows, and replication is a longstanding part of that process. So it makes it all the more bizarre when your reaction to a typically conservative scientific attitude is to go off half-cocked complaining that problems are being ignored and facts are not being addressed and the topic is being dodged. My suggestion is to display some patience and await replication.

--Percy


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

Replies to this message:
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randman 
Suspended Member (Idle past 3318 days)
Posts: 6367
Joined: 05-26-2005


Message 44 of 77 (340664)
08-16-2006 10:08 PM
Reply to: Message 43 by Percy
08-16-2006 9:39 PM


Re: selective acceptance of data
This was my earlier post.

What do you mean by "replicated"? Be specific. Studies have been conducted to confirm every aspect of the find that can be completed. Do you propose that the exact same bacteria strain must be found again?

They found 2 samples originally, right? There have been other finds of ancient bacteria.

The primary argument now against the find is that molecular dating techniques place the bacteria as a modern bacteria....in other words, the data is rejected based on the theory rather than the theory being adjusted to the 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.

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?

I think you know they would not. These are the points, imo, being consistently ignored.

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.

Keep in mind the argument here has been that the find is probably suspect, which is way too strong a description. If you want to caution that until we find more ancient bacteria, we may need to be cautious, that's one thing, but dismissing the find outright when the pattern so often is to embrace initial finds that support ToE indicates to me a bias.

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.

So when someone posts these studies represent nothing more than someone's say-so, I have to wonder if a creationist took that approach, what the reaction would be? The peer-reviewed papers are not merely someone's say-so.

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.

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.

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.

This has to work both ways, right? He mentions cold fusion (which is far more off-topic than my mentioning fossils) but fails to realize the negative conclusions towards cold fusion were the result of failed replication efforts.

Well, where are the failed replication efforts to justify evo skepticism on this?

Edited by randman, : No reason given.

Edited by randman, : No reason given.

Edited by randman, : No reason given.


This message is a reply to:
 Message 43 by Percy, posted 08-16-2006 9:39 PM Percy has not yet responded

Replies to this message:
 Message 48 by Quetzal, posted 08-16-2006 11:19 PM randman has responded
 Message 61 by Admin, posted 08-17-2006 1:21 PM randman has responded

Quetzal
Member (Idle past 4291 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 responded

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