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Author Topic:   Ancient bacteria with modern DNA, problem for evolution?
randman 
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Posts: 6367
Joined: 05-26-2005


Message 76 of 77 (341164)
08-18-2006 6:13 PM
Reply to: Message 75 by nwr
08-18-2006 5:46 PM


Re: a quote from the original paper in the OP
nwr, you might want to take a look at this.

Two groups have since used phylogenetic analyses of 16S rDNA sequences to argue that isolate 2-9-3 is unlikely to be 250 Myr old. Graur and Pupko (2001) used a relative rate test to compare evolutionary rates of 16S rDNA on the branches leading to isolate 2-9-3 and S. marismortui and found no differences between the evolutionary rates. Considering the possibility that S. marismortui may also be ancient (Arahal et al. 1999 ; Vreeland, Rosenzweig, and Powers 2000 ), they also compared the evolutionary rates of isolate 2-9-3, S. marismortui and Virgibacillus proomi, a close relative of S. marismortui, and again found similar rates of evolution (Graur and Pupko 2001 ). More recently, Nickle et al. (2002) also performed relative rate tests using 16S rDNA with the same result; the branch leading to isolate 2-9-3 is not extraordinarily short, as would be expected of an organism that has not been evolving for millions of years. Nickle et al. (2002) used evolutionary rates derived from enteric bacteria to argue that if isolate 2-9-3 has not been evolving for 250 Myr, then S. marismortui must itself have been evolving 5–10 times more slowly than did aphid endosymbionts on which the rate calculations were based. We note that although the evolutionary rates calculated from enterics and endosymbionts are the best estimates we currently possess, it is entirely likely that rates of sporeformer evolution may indeed be slower by several orders of magnitude. Sporeformers have been shown to remain in the metabolically dormant spore state, thus not replicating their DNA, for conservative estimates of anywhere from 102 to 104 years between times of growth (Kennedy, Reader, and Swierczynski 1994 ; Nicholson et al. 2000 ).

As the analyses discussed above used 16S rDNA genes, the evolution of which may not be representative of the organism as a whole, we wanted to know if the similarities between isolate 2-9-3 and S. marismortui are seen with protein-coding genes as well as with 16S rDNA genes. We therefore analyzed phylogenetic relationships between strain 2-9-3 and S. marismortui, using the spore-forming bacteria as our comparison group. The rationale for this design was that the evolutionary rate among the sporeformers would more closely approximate that of 2-9-3. We used amino acid data from two genes, recA and splB. The recA gene is found throughout all bacteria, and its product is required for homologous recombination and DNA repair. Because of the functional constraints on recA evolution, it can be used to resolve the older evolutionary relationships. The splB gene, on the other hand, has to date only been reported in gram-positive spore-forming bacteria and is important in the repair of spore-specific DNA damage resulting from UV radiation during spore dormancy (Nicholson et al. 2000 ). Because splB is only found in gram-positive spore-forming bacteria, it can be assumed to have a more recent origin than recA has and might be useful in resolving closer evolutionary relationships.

The results of our analyses are consistent with the phylogenetic relationships shown by Graur and Pupko (2001) and Nickle et al. (2002) .

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

Note the phrase above early on "phylogenetic analysis" which is based on molecular studies. Both the dating methods cannot be right. Either the molecular dating is wrong, or the dating based on the geology is wrong. So the significance is that one of these is wrong, and it's a big deal. Read through some papers, such as Woese's paper on that thread, and you can see molecular analysis play a very large role in analyzing data.

Now, you and other raise the issue of contamination, but this is not the first ancient bacteria showing similarities to modern bacteria. Are we to continually assume contamination every time, even with stringent sterilzation measures?

Now, it could be that demanding more evidence is reasonable, but I have noted that when a study or find comes up, such as the molecular study on a gene found in the parathyroid and the precursor to fish gills or some such or the initial find of Pakicetus or really just about every piece of data, real or imagined, that could favor ToE, evos are all over it like white on rice trumpetting the data as solid evidence for ToE.

So there appears to be a double-standard in the standards evos use to accept or reject data, stricter standards for data that is problematic for evos, and looser standards for data that supports ToE, and this bias, imo, is why so many errors and overstatments and in the case of Haeckel's stuff, outright frauds, work their way into the accepted lore of so-called "facts" supporting evolution. Furthermore, as these discoveries are heralded widely in the media and school, the public gets the impression of a mountain of evidence for ToE without every realizing that most of it was subsequently shown to be erroneous.

I realize this gets us to a new topic and plan to start a thread when I have time on selective use and acceptance of data, here in Showcase.


This message is a reply to:
 Message 75 by nwr, posted 08-18-2006 5:46 PM nwr has replied

Replies to this message:
 Message 77 by nwr, posted 08-18-2006 8:09 PM randman has taken no action

nwr
Member
Posts: 5969
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 3.2


Message 77 of 77 (341191)
08-18-2006 8:09 PM
Reply to: Message 76 by randman
08-18-2006 6:13 PM


Re: a quote from the original paper in the OP
Either the molecular dating is wrong, or the dating based on the geology is wrong.

Those are two of the possibilities. There could be errors elsewhere.

Now, you and other raise the issue of contamination, but this is not the first ancient bacteria showing similarities to modern bacteria. Are we to continually assume contamination every time, even with stringent sterilzation measures?

It is known that contamination can be a problem when dealing with micro-organisms. You need to give this controversy time to play out.

Here is the view of it from a report in American Scientist.

So there appears to be a double-standard in the standards evos use to accept or reject data, stricter standards for data that is problematic for evos, ...

This isn't any different from what happens elsewhere in real life. If you were a bank security office, looking for possible forgery in checks, you would be far more concerned about a million dollar check than about a two dollar check. Data that is consistent with other observations actually provides very little new information. It isn't earthshaking, whether the data is properly obtained or not, because it doesn't report anything that isn't already taken for granted. But data that suggest a possible problem is very valuable if it turns out to be valid. Because of its importance, scientists want to be very careful to fully scrutinize it, and to not accept it without skeptical scrutiny. Science depends on such careful analysis.

This isn't a double standard.


This message is a reply to:
 Message 76 by randman, posted 08-18-2006 6:13 PM randman has taken no action

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