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Author Topic:   Ancient bacteria with modern DNA, problem for evolution?
Modulous
Member (Idle past 1340 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 1 of 77 (295821)
03-16-2006 3:28 AM


I'm surprised randman hasn't done this one, its right up his alley...

Source 1 (techie science stuff)

Source 2 (BBC article, a way for the layperson to get the gist)

A good few years ago, bacteria was discovered in crystals buried in New Mexico. It was dated at about 250 million years old. The astonishing thing was that the bacteria entombed in the crystal was still alive! Naturally bioinformaticians clamoured over the bacteria and DNA testing was carried in short time.

The discovery was most unusual. Despite the bacteria predating mammals, its DNA was very modern looking. This bacteria was given the name 2-9-3:

As had been noted in earlier studies, a striking observation by Vreeland, Rosenzweig, and Powers (2000) was that the 16S rDNA of isolate 2-9-3 is 99% identical to that of Salibacillus marismortui, a bacterium isolated from the Dead Sea in 1936 (Arahal et al. 1999 ). In fact, Arahal et al. (1999) identified as S. marismortui three strains with 16S rDNA sequences differing by 0.01%, suggesting that isolate 2-9-3 might also be classified as S. marismortui.

Several ideas were put forward, perhaps Salibacillus marismortui is ancient? That seems to have been countered, maybe evolution rates are slower? Unfortunately if the rates were that slow then that means life was on earth 15Billion years ago....

Because the substitutions between 2-9-3 and S. marismortui are all synonymous, they can be used to reflect the mutation rate. If three synonymous substitutions out of the 1,023 total nucleotides examined (1/619 from recA and 2/404 from splB), thus 0.2% divergence, are representative of the mutation rate since the divergence of 2-9-3 and S. marismortui 250 MYA, then the 121 synonymous substitutions (12% divergence) between B. subtilis and B. cereus would place their last common ancestor at 15 BYA, much longer than the age of the earth.

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?

After some consideration I think Dates and Dating might be best.


Replies to this message:
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 Message 13 by randman, posted 08-14-2006 9:14 PM Modulous has taken no action

Adminnemooseus
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Message 2 of 77 (295825)
03-16-2006 5:35 AM


Thread moved here from the Proposed New Topics forum.

Mammuthus
Member (Idle past 5712 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 3 of 77 (295834)
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

http://www.gsajournals.org/i0091-7613-31-6-e93.html

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

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ikabod
Member (Idle past 3729 days)
Posts: 365
From: UK
Joined: 03-13-2006


Message 4 of 77 (295835)
03-16-2006 6:41 AM
Reply to: Message 1 by Modulous
03-16-2006 3:28 AM


Having read your sorces i think the last section of the BBC artical is the most relavent ...none of this has been confirmed by peer tests or second source evidence ... the question of contamination is the most relavent .... so in the best traditions of science this is not accepted data , it need ivestigation and the results need to be reproduced , as the BBC artical ends many similar claims have be shown to be wrong .

Science does not work on headlines , it works on confirmation , querring , testing and retesting .

to try to use this data to argue for or verses any other scientific idea is NOT scientific ..


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Modulous
Member (Idle past 1340 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 5 of 77 (295852)
03-16-2006 7:56 AM
Reply to: Message 3 by Mammuthus
03-16-2006 6:31 AM


bizarre science
From the article I linked to it seems implied that the tests were independently verified (eg when they talk about all the sterilization controls), but close reading does not support it. I am quite content to reject their results assuming that the critique is accurate. I'll check to see if there has been any response to criticisms.

The other information, such as the stability of DNA and the failure of previous attempts, lends to my incredulity about this work. Why was the conclusion that perhaps the sterilization techniques in use failed at some time or that the crystal was contaminated at some earlier time not put forward even as a possibility?

Your characterization of this as cold fusion for biology would seem to be well founded.


This message is a reply to:
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Mammuthus
Member (Idle past 5712 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 6 of 77 (295861)
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.


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Modulous
Member (Idle past 1340 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 7 of 77 (295867)
03-16-2006 8:38 AM
Reply to: Message 4 by ikabod
03-16-2006 6:41 AM


No data is bad data?
Science does not work on headlines , it works on confirmation , querring , testing and retesting .

In all fairness, I wasn't using the BBC article as the prime source for the information, but instead the paper published in 'Molecular Biology and Evolution' in 2002.

to try to use this data to argue for or verses any other scientific idea is NOT scientific

It depends :)

It is quite useful to use this data to show flaws in the methods of the hunt for ancient DNA. It could be used as verification of molecular dating methods - it could be said to have succesfully predicted that the bacteria is not ancient. A bit of a stretch I suppose, but I don't think it's in the spirit of science to regard rejected data as totally useless :)

Oh - and by the way - welcome to EvC!


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Modulous
Member (Idle past 1340 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 8 of 77 (295871)
03-16-2006 8:43 AM
Reply to: Message 6 by Mammuthus
03-16-2006 8:17 AM


Re: bizarre science
I would not be so harsh...

A quick correction to my earlier post, I said:

quote:
Why was the conclusion that perhaps the sterilization techniques in use failed at some time or that the crystal was contaminated at some earlier time not put forward even as a possibility?

The conclusion was paid lip service as a 'historical criticism', implying that the criticism had been overturned. A little bold perhaps.


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gadsen76
Inactive Member


Message 9 of 77 (306384)
04-25-2006 1:38 AM
Reply to: Message 1 by Modulous
03-16-2006 3:28 AM


It says it was alive. If it was alive it was not ancient, the rock it was found in was ancient. Sounds to me like the pretty good proof for evolution. Something found in an ancient rock that managed to evolve through the ages and was still alive some 250 million years later. Evolution is a powerful thing. Just a thought

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Modulous
Member (Idle past 1340 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 10 of 77 (306411)
04-25-2006 5:07 AM
Reply to: Message 9 by gadsen76
04-25-2006 1:38 AM


Something found in an ancient rock that managed to evolve through the ages and was still alive some 250 million years later. Evolution is a powerful thing. Just a thought

I think the idea was that the bacteria was dormant, and not reproducing for 250million years, springing back to life in the right conditions. It also seems that might be a load of crap. Welcome to EvC!


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complexPHILOSOPHY
Inactive Member


Message 11 of 77 (307552)
04-28-2006 7:14 PM
Reply to: Message 10 by Modulous
04-25-2006 5:07 AM


I think the idea was that the bacteria was dormant, and not reproducing for 250million years, springing back to life in the right conditions. It also seems that might be a load of crap. Welcome to EvC!

As the others have said, until it's replicated and verified by their peers, it remains to be seen.

That is, it remains to be validated. Ofcourse, articles are printed hastly and defamation is carried out at will against science but such is the nature of discovery in a world where religion is easier to swallow than exploration.


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Modulous
Member (Idle past 1340 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 12 of 77 (307673)
04-29-2006 5:24 AM
Reply to: Message 11 by complexPHILOSOPHY
04-28-2006 7:14 PM


As the others have said, until it's replicated and verified by their peers, it remains to be seen.

Indeed, hence my comment that, 'It also seems that might be a load of crap'.


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randman 
Suspended Member (Idle past 4135 days)
Posts: 6367
Joined: 05-26-2005


Message 13 of 77 (340095)
08-14-2006 9:14 PM
Reply to: Message 1 by Modulous
03-16-2006 3:28 AM


selective acceptance of data
Modulous, you are correct to see the discovery of ancient bacteria DNA as problematic for mainstream evo assumptions, but the evo solution is basically just to deny the evidence, and that's frankly why I have a real problem with evolutionism. Evos start with ToE as the primary fact and then use that to argue whether data is correct or not, and then claim because all the data they accept agrees with ToE, that the theory is substantiated. It's circular reasoning.

Let's look at the research on this finding since.

The report elicited strong skepticism from many quarters. Biological chemists doubted that nucleic acids could remain pristine over such time periods. Even had the bacterium hibernated as a hardy spore, its DNA surely would have broken down over 250,000 millennia, if not from the barrage of ultraviolet light during its long-ago residence on the surface, then from naturally occurring terrestrial radiation over the Earth's evolution.

Geologists questioned the age of the fluid inclusions, arguing that certain features of the Salado Formation (the source of the halite crystal) suggested that flaws in the rock had permitted the intrusion of more recent fluid (which, by inference, had carried more recent bacteria into the ancient rock).

Geneticists pointed out that one of the bellwether genes that the group had sequenced—one that encodes the so-called 16S ribosomal subunit—was far too similar to its counterpart in another strain of bacteria. According to this critique, either the "ancient" bacterium was actually a contaminant, or its descendants had inexplicably failed to change in the past 250 million years.

Yet Vreeland and an expanding circle of collaborators have followed up the original report with publications that seek to counter each of these criticisms. In 2002, he and two West Chester University colleagues reported in the International Journal of Radiation Biology their calculation that the degree of genetic damage caused by normal traces of radioactive potassium-40 in the surrounding rock was not great enough to rule out a quarter-billion years of bacterial survival. Scratch objection number 1.

In April of 2005, the three authors from the Nature paper teamed with Tim K. Lowenstein, a geologist at Binghamton University in New York, and his student, Cindy L. Satterfield, in publishing a detailed report in the journal Geology. To test the idea put forth by critics that inclusions in the salt crystals were newer than the surrounding rock, they measured the temperature of original crystallization for samples from the same part of the Salado Formation that yielded Virgibacillus sp. 2-9-3. The team reasoned that if microbe-carrying fluid had recently reached the deeply buried salt deposit and recrystallized, the temperatures of those crystallizations would be similar. Instead, they found the opposite: The results ranged from 17 to 37 degrees Celsius, or about 63 to 99 degrees Fahrenheit, a distribution that suggests seasonal climatic variation. In other words, the crystals that formed around pockets of fluid (and presumably bacteria) were created on or near the surface instead of far underground.

A second, more definitive, line of investigation examined the concentrations of various ions in the fluid inclusions. The balance of ions in seawater changes over geological time, so measuring them can provide an approximate date at which the saltwater crystallized. The ion concentrations in the halite inclusions matched those of oceans in the Permian period—a profile that is distinct from the seawater of today and also from larger pockets of trapped brine elsewhere in the Salado. As a final test, the team plans to use an ultrasensitive mass spectrometer to date tiny, individual inclusions by the rubidium-strontium method (87Rb decays into 87Sr with a half-life of 49 billion years). Scratch objection number 2.

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

All of the criticisms have been met with the sole exception that this cannot be ancient DNA because it's so similar to younger bacteria DNA that this doesn't fit with evo theories on the molecular clock, but is this an acceptable argument?

No. It's like saying, hey, we know theory A is true, and so any fact that disagrees with theory A must be false, and so this piece of data is false. It's not real science, imo. Heck, even the critics of Vreeland state the tactics used to prevent contanimation are "herioc",but that doesn't really matter. They will argue any fact that disagrees with them must be the result of contanimation or some other issue, unless perhaps Vreeland can find a way to say the data really doesn't conflict, and then all the evos will say, hey, this is a good find or some such.

Some more evidence:

April 11, 2005 — A new study has confirmed that the brine and salt crystals in which scientists found a controversial 250-million-year-old bacteria truly form a quarter-billion-year time capsule.

http://dsc.discovery.com/news/briefs/20050411/oldestlife.html

http://news.bbc.co.uk/2/hi/science/nature/1375505.stm

Edited by randman, : No reason given.


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Replies to this message:
 Message 14 by Dr Adequate, posted 08-15-2006 12:56 AM randman has replied
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Dr Adequate
Member (Idle past 288 days)
Posts: 16112
Joined: 07-20-2006


Message 14 of 77 (340139)
08-15-2006 12:56 AM
Reply to: Message 13 by randman
08-14-2006 9:14 PM


Re: selective acceptance of data
Heck, even the critics of Vreeland state the tactics used to prevent contanimation are "herioc",but that doesn't really matter. They will argue any fact that disagrees with them must be the result of contanimation or some other issue.

Yes, quite. "Even the critics" will describe the certain measures Vreeland took as "heroic", and that proves him RIGHT RIGHT RIGHT.

But when they suggest that he's done something wrong, then they will "argue any fact" because they're BIASED BIASED BIASED. But not too biased to use the word "heroic". Because of course the huge evil conspiracy of scientists everywhere isn't quite that mean.

Sheesh.

What drives me up the wall is that not only won't creationists take the time to learn about science; they also also refuse to learn anything about the six billion human beings amongst whom they live.

They are cut off not just from science but from people. They can't imagine that people are people, when this statement is a truism.


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RickJB
Member (Idle past 4227 days)
Posts: 917
From: London, UK
Joined: 04-14-2006


Message 15 of 77 (340142)
08-15-2006 1:11 AM
Reply to: Message 13 by randman
08-14-2006 9:14 PM


Re: selective acceptance of data
randman writes:

Evos start with ToE as the primary fact and then use that to argue whether data is correct or not, and then claim because all the data they accept agrees with ToE, that the theory is substantiated. It's circular reasoning.

The line about pots and kettles springs to mind...

"[Creationists] start with [the Bible] as the primary fact and then use that to argue whether data is correct or not, and then claim because all the data they accept agrees with [the Bible], that the theory is substantiated. It's circular reasoning."

Even if your assertions were true (which they aren't) they would still be a mirror-image of your own reasoning!

Edited by RickJB, : No reason given.

Edited by RickJB, : No reason given.


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