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Author Topic:   Ancient DNA indicates bacteria have not undergone millions of years of generations
Tranquility Base
Inactive Member


Message 1 of 8 (20366)
10-21-2002 3:06 AM


Bacteria revived from ancient materials, including halite crystals, consistently show almost no divergence of sequences by comparison with their modern counterparts!

This is leading mainstream researchers to briefly propose that the modern counterparts have also been dormant for the same time. This is immediatley rejected becasue this would require all bacterial taxa which have been compared with ancient sources to have had the same dormancy.

The "most scrupulous and well-documented" procedures designed to rule out any chance of contaminaiton with modern sources has shown 250 My old bacteria sample "2-9-3", for example, to be almost identical to modern day Salibacillus marismortui at RNA and protein coding genes. These should have been significantly changed sequences after 250 My and yet show 99% identity at the DNA nucleotide level.

quote:

Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels. H. Maughan et al Mol Biol Evol 19: 1637-1639 (2002)

So much for the molecular clock. Either almost all bacteria have hybernated for the last 250 My, despite proliferating today, or maybe these ancient strata are not separated from us by millions of years. The molecular clock may simply measure taxonomic differnce and not time as this data cries out! It of course would measure time if that time had transpired. We do not doubt the principle of the clock but we doubt the reality of the time period.

[This message has been edited by Tranquility Base, 10-21-2002]


Replies to this message:
 Message 2 by Mammuthus, posted 10-21-2002 4:33 AM Tranquility Base has responded
 Message 3 by Mammuthus, posted 10-21-2002 4:44 AM Tranquility Base has responded

  
Mammuthus
Member (Idle past 4585 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 2 of 8 (20368)
10-21-2002 4:33 AM
Reply to: Message 1 by Tranquility Base
10-21-2002 3:06 AM


{Quotation of entire previous message deleted - Adminnemooseus}
----------

As one who has worked with ancient DNA for quite some time I found the halite bacterial study extremely suspect for several reasons 1) it was never reproduced in a second laboratory ( a criteria for publishing aDNA) 2) the sequences from amber have all been shown to be artifacts and they were substantially younger 3) it is fully inconsistent with the chemistry of DNA that preservation would last for over 100,000 years much less 250 million. Another problem is that when one amplifies ancient bacterial sequences with Taq DNA polymerase one ALWAYS picks up bacterial DNA sequences from the Taq prep itself.

While the result would have been interesting in principle I know of nobody (especially in the aDNA community) that took the result seriously.

Cheers,
M

[This message has been edited by Adminnemooseus, 10-22-2002]


This message is a reply to:
 Message 1 by Tranquility Base, posted 10-21-2002 3:06 AM Tranquility Base has responded

Replies to this message:
 Message 4 by Tranquility Base, posted 10-21-2002 6:42 PM Mammuthus has responded

  
Mammuthus
Member (Idle past 4585 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 3 of 8 (20370)
10-21-2002 4:44 AM
Reply to: Message 1 by Tranquility Base
10-21-2002 3:06 AM


Further evidence that this is pure contamination is that modern bacteria observed for 10,000 generations show tremendous divergence from one another....

Proc Natl Acad Sci U S A 1999 Mar 30;96(7):3807-12 Related Articles, Links

Genomic evolution during a 10,000-generation experiment with bacteria.

Papadopoulos D, Schneider D, Meier-Eiss J, Arber W, Lenski RE, Blot M.

Abteilung Mikrobiologie, Biozentrum, CH-4056 Basel, Switzerland.

Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species. However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms. To overcome this limitation, we sampled genomes from populations of Escherichia coli evolving in the laboratory for 10,000 generations. We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach reflect rearrangements (including transpositions) rather than point mutations. The evolving genomes became increasingly different from their ancestor over time. Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint after 10,000 generations. As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population. Certain pivotal mutations were shared by all descendants in a population, and these are candidates for beneficial mutations, which are rare and difficult to find. More generally, these data show that the genome is highly dynamic even over a time scale that is, from an evolutionary perspective, very brief.

: Science 1996 Jun 21;272(5269):1802-4 Related Articles, Links

If they find a way to get non contaminant DNA from millions of years old fossils I will be the first to sign on since I have some extinct relatives of elephants I would love to sequence....but contamination I can already get now anytime I want Usually it does not get published in Nature however


This message is a reply to:
 Message 1 by Tranquility Base, posted 10-21-2002 3:06 AM Tranquility Base has responded

Replies to this message:
 Message 5 by Tranquility Base, posted 10-21-2002 7:09 PM Mammuthus has not yet responded

  
Tranquility Base
Inactive Member


Message 4 of 8 (20419)
10-21-2002 6:42 PM
Reply to: Message 2 by Mammuthus
10-21-2002 4:33 AM


Mammuthus

I appreciate your skepticism. However, if creationists are right then it all makes complete sense. The controls used in recent ancient DNA work are very carefully done. And this journal of high reputaiton as well as Maughan him/herself et al treat it seriously.

For the laymen here let me outline the sorts of controls. You do the work with and without the halite crystal. You only get that bacteria when you use that crystal. OK so it could be something growing in the container that you kept the crystal in. So you keep a similar container for he same time without the crystal in it. And then when you get the sequence it is still unique even though it closely matches a modern strain. You can check up that it does not match any known strain exactly.

I do not doubt the plasticity of the genome. I doubt how long it has been plastic.

I think these studies have progressed to the next level Mammuthus.

[This message has been edited by Tranquility Base, 10-21-2002]


This message is a reply to:
 Message 2 by Mammuthus, posted 10-21-2002 4:33 AM Mammuthus has responded

Replies to this message:
 Message 6 by Mammuthus, posted 10-22-2002 4:37 AM Tranquility Base has responded

  
Tranquility Base
Inactive Member


Message 5 of 8 (20421)
10-21-2002 7:09 PM
Reply to: Message 3 by Mammuthus
10-21-2002 4:44 AM


Mammuthus

The ancient DNA regions of this bacteria studied are coding regons (functional RNA and proteins) so we expect some degree of conservation. But not 99% if it were 250 My old. Much of the non-coding regions would have scrambled no doubt since it can happen in only 10,000 generations as you rightly point out.


This message is a reply to:
 Message 3 by Mammuthus, posted 10-21-2002 4:44 AM Mammuthus has not yet responded

  
Mammuthus
Member (Idle past 4585 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 6 of 8 (20452)
10-22-2002 4:37 AM
Reply to: Message 4 by Tranquility Base
10-21-2002 6:42 PM


TB:
I appreciate your skepticism. However, if creationists are right then it all makes complete sense. The controls used in recent ancient DNA work are very carefully done. And this journal of high reputaiton as well as Maughan him/herself et al treat it seriously.

M: The controls in the amber studies were more carefully done, the controls in the famous dinosaur DNA debacle were even more rigorous than presented in the halite paper. In addition, halite forms cracks and fissures where modern bacteria can grow..(this is what killed amber studies to by the way). None of the people involved in the study is known to anyone in the ancient DNA community. And ultimatley, they did not independently reproduce the result which makes it highly surprising that the paper got into Nature. Read the neanderthal DNA papers sometime if you want to see how ancient DNA studies are supposed to be done.

On another issue, how is lack of DNA variation consistent with creationism as creationism makes no testable predictions. TB, be honest, if the bacteria were totally different in sequence you would also claim it is consistent with creationism.

TB:
For the laymen here let me outline the sorts of controls. You do the work with and without the halite crystal. You only get that bacteria when you use that crystal. OK so it could be something growing in the container that you kept the crystal in. So you keep a similar container for he same time without the crystal in it. And then when you get the sequence it is still unique even though it closely matches a modern strain. You can check up that it does not match any known strain exactly.

M: Your entire paragraph demonstrates that you are a layman regarding this subject. Doing the work with or without the halite crystal is hardly a control for contamination as the crystal itself would bear the contamination..all it says is their lab reagents are clean. odern strain of bacteria is a criteria? They are most likely sequencing E. coli DNA from the Taq prep as I saw happen to colleagues of mine working on sloths. But in any case, the killer for aDNA from bacteria is matching to known strains. 99% of bacteria are genetically unknown. I could get never before seen bacterial sequences by taking a plug of dirt from the ground outside of my window.

TB:

I do not doubt the plasticity of the genome. I doubt how long it has been plastic.

M: Doubt away...the Lenski studies demonstrate for bacteria that the results are consistent with a contamination but not with what is observed in modern populations of bacteria which after a mere 10,000 generations differentiate more than what was seen by these researchers with their purported aDNA.

TB:
I think these studies have progressed to the next level Mammuthus.

M: I know that they have not. You forget that a criteria of science is that it is reproducible and the paper you are quoting has not been. As Paabo and colleagues say..Do it right or don't do it at all.


This message is a reply to:
 Message 4 by Tranquility Base, posted 10-21-2002 6:42 PM Tranquility Base has responded

Replies to this message:
 Message 7 by Tranquility Base, posted 10-22-2002 9:43 PM Mammuthus has responded

  
Tranquility Base
Inactive Member


Message 7 of 8 (20527)
10-22-2002 9:43 PM
Reply to: Message 6 by Mammuthus
10-22-2002 4:37 AM


Mammuthus

Getting into Nature isn't easy. They would have had to do pretty much state of the art controls. If you disagree I respect that but I still equally respect the Nature referees.

YECism certainly does make the prediction that ancient bacteria would not deonstrate millions of years worth of mutations. I'll list a whole bunch of predicitons of YECism in a new thread when I've got time.

I simply listed the obvious controls that would have been done and you listed some even better ones. Yes I am a layman on ancient DNA but not a garden variety one. I would be very surprised if their controls didn't eliminate every possibility other than the bugs having got into the crystal in situ (ie whilst in the stratum).

Anyway, it's a pleasure to have 'met' a genuine ancient DNAer.


This message is a reply to:
 Message 6 by Mammuthus, posted 10-22-2002 4:37 AM Mammuthus has responded

Replies to this message:
 Message 8 by Mammuthus, posted 10-23-2002 5:16 AM Tranquility Base has not yet responded

  
Mammuthus
Member (Idle past 4585 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 8 of 8 (20547)
10-23-2002 5:16 AM
Reply to: Message 7 by Tranquility Base
10-22-2002 9:43 PM


TB or should I say Adminiquility
[QUOTE]Originally posted by Tranquility Base:
Mammuthus

Getting into Nature isn't easy. They would have had to do pretty much state of the art controls. If you disagree I respect that but I still equally respect the Nature referees.

M: Niether is getting into Science and your trust in the referees would have been misplaced here...

Henikoff S. Related Articles, Links

Detecting dinosaur DNA.
Science. 1995 May 26;268(5214):1192; discussion 1194. No abstract available.
PMID: 7761841 [PubMed - indexed for MEDLINE]

10: Allard MW, Young D, Huyen Y. Related Articles, Links

Detecting dinosaur DNA.
Science. 1995 May 26;268(5214):1192; discussion 1194. No abstract available.
PMID: 7761840 [PubMed - indexed for MEDLINE]

11: Hedges SB, Schweitzer MH. Related Articles, Links

Detecting dinosaur DNA.
Science. 1995 May 26;268(5214):1191-2; discussion 1194. No abstract available.
PMID: 7761839 [PubMed - indexed for MEDLINE]

12: Zischler H, Hoss M, Handt O, von Haeseler A, van der Kuyl AC, Goudsmit J. Related Articles, Links

Detecting dinosaur DNA.
Science. 1995 May 26;268(5214):1192-3; discussion 1194.

Amber DNA suffered a similar fate if you would like a reference to those papers as well..

TB:
YECism certainly does make the prediction that ancient bacteria would not deonstrate millions of years worth of mutations. I'll list a whole bunch of predicitons of YECism in a new thread when I've got time.

M: Please do and I will challenge you to provide evidence for your prediction in that thread

TB:
I simply listed the obvious controls that would have been done and you listed some even better ones. Yes I am a layman on ancient DNA but not a garden variety one. I would be very surprised if their controls didn't eliminate every possibility other than the bugs having got into the crystal in situ (ie whilst in the stratum).

M: That is what the dinosaur, dinosaur egg, and amber researchers thought as well. Unless these guys get another lab to independently reproduce the data I consider it unsubstantiated.

TB:
Anyway, it's a pleasure to have 'met' a genuine ancient DNAer.

M: Actually, my DNA is only about 34 years old...but my mammoths, muskoxen, and giant ground sloths DNA vary from 2000 to 50000 years old


This message is a reply to:
 Message 7 by Tranquility Base, posted 10-22-2002 9:43 PM Tranquility Base has not yet responded

  
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