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Author Topic:   Ancient bacteria with modern DNA, problem for evolution?
Mammuthus
Member (Idle past 6505 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 3 of 67 (295833)
03-16-2006 6:31 AM
Reply to: Message 1 by Modulous
03-16-2006 3:28 AM


quote:
or is it still one of the thorns that remains fixed in the side of evolutionary dogma?
It remains unreplicated and extremely dubious.
Here is a listing of some of the criticsim of this and relateds studies
Attention Required! | Cloudflare
keep in mind, when working with ancient DNA, there are some fairly basic precautions to avoid artifacts. The simplest is to send the sample to another lab and see if they get the same results. None of the studies of this nature ever have done this. Why after 6 years they have not bothered to do this is odd. Another problem with bacteria is that you could go out into your back yard and culture bacteria that nobody has ever seen before not to mention bacteria can live in virtually any environment...so getting bacteria to grow from strange substances is trivial. And sterilizing is bs...they have to show that the crystals have no fractures through which bacteria could enter (amber for example has microfracturing that allows modern bacteria in). If they sterilized the inside of the sample then there would be no DNA of any kind.
Also keep in mind that every claim of preservation of DNA in the million year old range from amber has either been shown to be artifact or non-reproducible...so in a better preservation system that is truly isolated from the environment and conducive to DNA preservation, no DNA has been recovered, yet they claim living bacteria and intact DNA are found in a non-closed system?
DNA is particularly unstable and even when frozen it does not stay intact..even for bacteria...from the website
quote:
a recent study of bacterial DNA in permafrost”an environment considered the most promising for long-term DNA survival”has shown that DNA from endospore-forming bacteria >600 bp in size cannot be obtained from samples older than 0.5 Ma, and not even 120-bp DNA fragments can be reproducibly obtained from samples 2 Ma (Willerslev et al., 2004a).
Another point is that all DNA analysis requires amplification with Taq DNA polymerase..guess where Taq comes from? Bacteria! Often cloned into E.coli to express it and then boiled and purified leaving Taq left over. You could easily amplify left over DNA from the Taq enyzme prep..which I have personally seen happen. Of note, this is a problem for mammalian work as well because to get rid of co-extracted inhibitors, you often use bovine serum albumin..and in some cases end up amplfiying cow sequences as a result.
The relative rate test is also a problem for this work..why does the bacteria then not cluster with the outgroup? Why do ancient sequences that have been verified by replication, amino acid racemization tests, independent verification match expections but all the studies of extremely old DNA don't, are never replicated, never followed up and then just disappear? This is just cold fusion for ancient DNA...sort of like the report of dinosaur DNA that turned out to be a human cytochrome b sequence....and they sterlized the sample to.

This message is a reply to:
 Message 1 by Modulous, posted 03-16-2006 3:28 AM Modulous has replied

Replies to this message:
 Message 5 by Modulous, posted 03-16-2006 7:56 AM Mammuthus has replied

Mammuthus
Member (Idle past 6505 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 6 of 67 (295862)
03-16-2006 8:17 AM
Reply to: Message 5 by Modulous
03-16-2006 7:56 AM


Re: bizarre science
I would not be so harsh but this study along with several by Raul Cano (look up Cano RJ in medline) have lead to a string of never reproduced studies. Everyone tells them to replicate their results independently yet Cano continues to publish new unreplicated studies...it also does not help that one of his amber DNA studies turned out to be demonstrably false (if not worse)as seen here
Gutierrez G, Marin A.
The most ancient DNA recovered from an amber-preserved specimen may not be as ancient as it seems.
Mol Biol Evol. 1998 Jul;15(7):926-9. No abstract available.
Here was a systematic study to try to replicate amber results..it ultimately killed off the field
Austin JJ, Ross AJ, Smith AB, Fortey RA, Thomas RH. Problems of reproducibility--does geologically ancient DNA survive in amber-preserved insects?
Proc Biol Sci. 1997 Apr 22;264(1381):467-74.
Then Vreeland does the same thing..he has had since 2000 to reproduce the results...Cano has had since 1995. There is even one study claiming to retrieve an RNA virus from really old materials and RNA is many fold less stable than DNA.
Ironically, they get away with it because of the lack of info on bacterial biodiversity. As I said, you probably have never before seen bacteria in your armpit and yard. So if you get a new or strange sequence from a sample it is really pretty ridiculous to claim it is ancient. Also, the culturing conditions they use would favor lab contaminants...just because they sterilized their sample does not mean they don't have bacteria in the lab...after all, they are not using antibiotic selection in culturing these things..there is crap floating in the air that will grow if you have a non-selective media.
When you get to the much narrower group of independently reproduced studies of ancient DNA, it shows a limit of about 100,000 years for DNA retrieval...and that tends to be from permafrost samples like woolly mammoths etc.
Anything much over that is cold fusion.

This message is a reply to:
 Message 5 by Modulous, posted 03-16-2006 7:56 AM Modulous has replied

Replies to this message:
 Message 8 by Modulous, posted 03-16-2006 8:43 AM Mammuthus has not replied

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