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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 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."
| American Scientist
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/.../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
 Message 15 by RickJB, posted 08-15-2006 1:11 AM randman has replied
 Message 19 by Quetzal, posted 08-15-2006 9:34 AM randman has replied

randman 
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Posts: 6367
Joined: 05-26-2005


Message 16 of 77 (340179)
08-15-2006 9:10 AM
Reply to: Message 14 by Dr Adequate
08-15-2006 12:56 AM


people are people
People are people and have been creating myths for thousands of years. You just don't recognize the process when it comes to evolutionism.

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 Message 14 by Dr Adequate, posted 08-15-2006 12:56 AM Dr Adequate has not replied

randman 
Suspended Member (Idle past 4919 days)
Posts: 6367
Joined: 05-26-2005


Message 17 of 77 (340180)
08-15-2006 9:11 AM
Reply to: Message 15 by RickJB
08-15-2006 1:11 AM


unsubstantiated garbage
Find one post where I use the Bible to argue against the Theory of Evolution, please, and if you cannot substantiate your argument, please retract it.
You won't find any because it's not my approach. Heck, there are even some parts of the Bible that sound like evolution: "let the waters bring forth...", but the issue with evolutionism is selective acceptance of data and logic, as we see here on this topic.
Edited by randman, : No reason given.

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randman 
Suspended Member (Idle past 4919 days)
Posts: 6367
Joined: 05-26-2005


Message 20 of 77 (340194)
08-15-2006 9:41 AM
Reply to: Message 18 by Jazzns
08-15-2006 9:29 AM


Re: Why do you debate?
I have stated throughout my time here that I think the reasoning process of mainstream evolutionism is severely flawed and ignores data and reasoning, and is a believe first, understand later process that makes correcting errors and assessing data objectively very difficult. I could go on, but let's don't get off-topic.
Suffice to say, I have echoed the same refrain since I've been here, and have often pointed out that my reasons for rejecting ToE are not because of the Bible, etc,....but that I think mainstream evo theories are not fact-based.
Edited by randman, : No reason given.

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randman 
Suspended Member (Idle past 4919 days)
Posts: 6367
Joined: 05-26-2005


Message 21 of 77 (340195)
08-15-2006 9:46 AM
Reply to: Message 19 by Quetzal
08-15-2006 9:34 AM


Re: selective acceptance of data
Modulous lays out the details in the OP. The lack of change suggests that the molecular clock concept, often used in evo models, is incorrect. I will add that the immense amount of time for the bacteria to survive is a problem unless the time periods are off.
The discovery definitely poses a problem for some aspects of mainstream evo models.
As far as falsifying ToE, since the ToE is an inherently non-falsifiable theory, it probably is not possible to come up with any data that can do that, but that just shows the inherent flaw within ToE as a scientific theory, imo. It's considered true by definition, and so the data doesn't form the theory, but the theory the data.

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randman 
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Posts: 6367
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Message 25 of 77 (340227)
08-15-2006 10:33 AM


OK
OK, here is the reason given that the discovery must be due to contanimation. There is nothing I can see about the procedures that suggests they were flawed. What the criticism is based on is that molecular studies indicate the bacteria must be young. Since the molecular clock angle is considered to be a fact, then any fact such as this that challenges that is considered to be erroneous, and so a circular reasoning is in effect.
Find something that demonstrates ancient bacteria were not so different than a current strain today, and this is dismissed because everyone knows ancient bacteria MUST BE different because ToE says so.
The other criticisms have been duly answered with published studies, but you cannot answer the last one as effectively because by it's very nature, it is a circular argument. The conclusion is taken as fact, the molecular clock angle, and so any data that disagrees with that conclusion must be contanimation even if the best measures were taken to prevent it.

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randman 
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Posts: 6367
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Message 26 of 77 (340228)
08-15-2006 10:38 AM
Reply to: Message 24 by Quetzal
08-15-2006 10:30 AM


Re: selective acceptance of data
In the first place, nothing cited thus far in this thread indicates that Vreeland's original hypothesis concerning the critter being that old has been substantiated.
Did you read the links? There certainly has been published studies backing Vreeland up.
On the issue of the molecular clock, it may well be there are plenty that call that into question but that doesn't stop the chief and only remaining basis for criticism of Vreeland's find being molecular studies based on the molecular clock.

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randman 
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Posts: 6367
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Message 28 of 77 (340240)
08-15-2006 10:57 AM


btw, "problem for evolution"
The phrase "problem for evolution" is in Modulous' OP. So quetzal and others, I suggest you reread the OP and think about it.

Replies to this message:
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randman 
Suspended Member (Idle past 4919 days)
Posts: 6367
Joined: 05-26-2005


Message 29 of 77 (340243)
08-15-2006 11:01 AM
Reply to: Message 27 by crashfrog
08-15-2006 10:57 AM


Re: OK
That is because there is a million times as much confirming evidence for the molecular clock models as there is disconfirming evidence.
No, there is not, and merely saying there is evidence does not mean there is evidence.
qs By all means, I invite you to establish a similar weight of evidence for creationism.[/qs]
Your post is off-topic, and I won't be baited to getting banned. So don't expect me to do anything but ignore your posts, crash.
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.

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randman 
Suspended Member (Idle past 4919 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?

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randman 
Suspended Member (Idle past 4919 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.

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randman 
Suspended Member (Idle past 4919 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.

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randman 
Suspended Member (Idle past 4919 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.
| American Scientist
Whoops! Page Not Found | Discovery
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.

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randman 
Suspended Member (Idle past 4919 days)
Posts: 6367
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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.

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 Message 45 by Quetzal, posted 08-16-2006 10:49 PM randman has replied

randman 
Suspended Member (Idle past 4919 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.

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