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Biofilms And Primary Soft Tissues In Dinosaur Fossils


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#1 Geode

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Posted 14 October 2010 - 11:21 PM

An interesting study involving the recent reports of preserved soft tissues in fossil dinosaur bones. Some sceptics have challenged these findings and suggested that the organic material described is actually from subsequently forming biofilms.

This study sets out to find an understanding of potential mechanisms that could permit preservation of soft-tissues in vertebrate fossils within the framework of geologic time.

biofilms

The results of this study indicate that exquisite preservation of pliable soft-tissues may be related to a microbial masonry process whereby the formation of microbial biofilms wall off internal surfaces of bones during early taphonomic stages. These biofilms metabolize organic materials and mineralize, forming resistant structures or microbial masonry wall surfaces across internal pores openings in bones. These results have potential to allow for more detailed taphonomic reconstructions and contribute to a more nuanced understanding of fossil preservation in the form of soft-tissues structures and biomolecules.

The claim of the presence of primary soft-tissues in fossil vertebrates has been supported by the identification by mass spectroscopy of biomolecules in the form of collagen and proteins, However, these studies have failed to produce a potential mechanism for the preservation of soft tissues throughout geological time. The results presented here suggest an important role of microorganisms in taphonomic processes, notably for the preservation of primary soft-tissues within bone, through a microbial masonry process. Although biomolecular studies on soft-tissue extracts from fossil vertebrates have shown that the proposed alternative interpretation of primary soft-tissue as microbial biofilms is unlikely, biofilms may play a critical role in the preservation process.



#2 ikester7579

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Posted 15 October 2010 - 01:33 AM

There is an excuse for everything. But here is the funny part: No one else but an evolutionist is allowed to conduct the test. I wonder how bias that makes the results?

#3 Geode

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Posted 15 October 2010 - 02:01 AM

There is an excuse for everything. But here is the funny part: No one else but an evolutionist is allowed to conduct the test. I wonder how bias that makes the results?

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I must have missed where there is a prohibition on who can and who cannot do research on biofilms. I think anybody who wishes to do so can proceed. When can we expect such research from the Institute for Creation Research? They have seemed very interested in the subject in the past and kept up on the subject by posting reports. Will they post this one in a discussion on their site?

Here are some past conclusions from the ICR:

“The most parsimonious explanation, thus far unfalsified, is that original molecules persist in some Cretaceous dinosaur fossils,”1 meaning in short that Schweitzer and her team have taken great care to make it painfully clear that these soft tissues really exist and they’re from the dinosaurs in question. Scientists worldwide now need to reconcile their belief in vast eons with these cold, hard facts. The simplest explanation for the presence of blood vessels and their proteins in these bones is that the dinosaurs were recently and rapidly inundated and preserved, just as one would expect to observe in a world that began thousands rather than millions of years ago.


Soft Tissue

But even though this is not research conducted by the ICR I do not see them say that they cannot do their own studies. They should attempt to see if the results reported here are repeatable. If not they are doing "armchair" attempts at science and really don't have much of a basis to reach objective opinions. After all they are a research institution are they not, so shouldn't their prime reason for existence be to conduct research?

I look forward to comments on the actual science involved in the paper. Where was their methodology wrong or where are their conclusions biased? I think it commendable that instead of sitting on the sidelines and simply giving opinions on whether or not the tissues indicated in the fossils were primary or the result of biofilms (something others have done) that they actually conducted experiments to shed light on the subject coming up with interesting results and providing a basis for further research. I think I have seen threads where criticism has been leveled that an idea or concept posed by scientists lacked empirical evidence coming from research. Well, here we have some.

#4 Cassiterides

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Posted 15 October 2010 - 05:15 AM

''The results of this study indicate that exquisite preservation of pliable soft-tissues may be related to a microbial masonry process whereby the formation of microbial biofilms wall off internal surfaces of bones during early taphonomic stages. These biofilms metabolize organic materials and mineralize, forming resistant structures or microbial masonry wall surfaces across internal pores openings in bones. These results have potential to allow for more detailed taphonomic reconstructions and contribute to a more nuanced understanding of fossil preservation in the form of soft-tissues structures and biomolecules.

The claim of the presence of primary soft-tissues in fossil vertebrates has been supported by the identification by mass spectroscopy of biomolecules in the form of collagen and proteins, However, these studies have failed to produce a potential mechanism for the preservation of soft tissues throughout geological time. The results presented here suggest an important role of microorganisms in taphonomic processes, notably for the preservation of primary soft-tissues within bone, through a microbial masonry process. Although biomolecular studies on soft-tissue extracts from fossil vertebrates have shown that the proposed alternative interpretation of primary soft-tissue as microbial biofilms is unlikely, biofilms may play a critical role in the preservation process.''

Just more ''mays'' ''suggests'' ''reconstructions'' etc from the evolutionists, no actual factual evidence.

#5 MamaElephant

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Posted 15 October 2010 - 07:42 AM

What I would like to know is why ICR should conduct their own experiments when it has already been done?

Schweitzer confronted her boss, famous paleontologist ‘Dinosaur’ Jack Horner, with her doubts about how these could really be blood cells. Horner suggested she try to prove they were not red blood cells, and she says, ‘So far, we haven’t been able to.’

As far as I know these researchers did not set out looking for soft tissue in dinosaur fossils, but were shocked to find it and then very thoroughly tested it. Why now is it wrong for anyone to publish articles about these findings?

I feel that someone's bias is being revealed when they state that they are waiting for "real science".

#6 Geode

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Posted 15 October 2010 - 08:34 AM

''The results of this study indicate that exquisite preservation of pliable soft-tissues may be related to a microbial masonry process whereby the formation of microbial biofilms wall off internal surfaces of bones during early taphonomic stages. These biofilms metabolize organic materials and mineralize, forming resistant structures or microbial masonry wall surfaces across internal pores openings in bones. These results have potential to allow for more detailed taphonomic reconstructions and contribute to a more nuanced understanding of fossil preservation in the form of soft-tissues structures and biomolecules.

The claim of the presence of primary soft-tissues in fossil vertebrates has been supported by the identification by mass spectroscopy of biomolecules in the form of collagen and proteins, However, these studies have failed to produce a potential mechanism for the preservation of soft tissues throughout geological time. The results presented here suggest an important role of microorganisms in taphonomic processes, notably for the preservation of primary soft-tissues within bone, through a microbial masonry process. Although biomolecular studies on soft-tissue extracts from fossil vertebrates have shown that the proposed alternative interpretation of primary soft-tissue as microbial biofilms is unlikely, biofilms may play a critical role in the preservation process.''

Just more ''mays'' ''suggests'' ''reconstructions'' etc from the evolutionists, no actual factual evidence.

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That is the beauty of scientific studies that are done according to good scientific principles, they do not make claims that are not proven. You see that in the wording here. Other workers can now test what was done here and through time the hypotheses suggested here should develop further. This is a line of investigation that is quite new to paleontology. But I guess you didn't read the paper, for it gave quite a bit of evidence. the conclusions were stated as they should be at this point. But the bottom-line is that they did some actual research, and have not just boldly made claims like the ICR comments. Future studies might lead to a rejection of what was suggested as possible explanations here.

#7 Geode

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Posted 15 October 2010 - 08:45 AM

What I would like to know is why ICR should conduct their own experiments when it has already been done?  As far as I know these researchers did not set out looking for soft tissue in dinosaur fossils, but were shocked to find it and then very thoroughly tested it. Why now is it wrong for anyone to publish articles about these findings?

I feel that someone's bias is being revealed when they state that they are waiting for "real science".

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The ICR seems to more interested in the topic of soft-tissue preservation than most people or institutions since they feel it proves rapid burial of the fossils involved in the flood. Do you think that the ICR will accept the results of this paper, which suggests that such preservation might be possible in fossils many millions of years old? If they do, their basic premise of a young earth is threatened. If they reject the results without providing alternative evidence showing this to be impossible or unlikely, will their claims in this direction hold any weight since all they will be doing is presenting an opinion with no evidence to offer? As such it would have little value in the debate.

Actually this research is a follow-up to what you noted. There is nothing wrong in writing about the findings. But if in doing so a different opinion is tendered in conflict with the study, with no data or research to back it up, it remains just an opinion in conflict without offering a scientific alternative. I think we all should be waiting for "real science" to come forth, and seek this vs. science that is done only from a position of bias towards one possibility. The real McCoy does entail doing the actual work of science in experimentation and research, not just stating opinions. I expect that some non-creationist scientists will disagree or be critical of the findings here, and also not do research of their own. Their opinions will also be of little or no value, except in causing others to take up the cause of further research.

I feel that someone's bias is being revealed when they state that they are waiting for "real science".


Yes, depending upon context. Personally I am biased towards scientific studies that are done objectively. I don't know who you are quoting, but I would agree with that person if he or she made such a statement to contrast a real and honestly objective scientific experiment as contrasted with claims made without following the scientific process using good methods. I have seen papers published in rather well-read peer-reviewed journals (which you would term secular) that were not good science and used faulty methods in their research leaving their conclusions, based upon nothing very meaningful, in doubt. But that is what the peer-review process is all about. Opinions critical of the methods and conclusions were forthcoming, and later research led to different conclusions.

#8 scott

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Posted 15 October 2010 - 10:17 AM

Soft unfossilized tissue is most likely quite common. It's very common in petrified trees, so I don't see why it wouldn't be a problem for bones.

Ever see a soft spot in a petrified tree? Well, once you see one, you won't deny that even bone can have parts that remain unfossilized. So yes, there is soft tissue in the Dinosaur bones as well.

#9 MamaElephant

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Posted 15 October 2010 - 06:52 PM

Young Earth Creationist Ministries are not the only ones giving this discovery a spin of support for a recent demise of dinosaurs. "When this shy paleontologist found soft, fresh-looking tissue inside a T. rex femur, she erased a line between past and present. Then all hell broke loose."-- Yeoman, B., Schweitzer’s Dangerous Discovery, Discover 27(4):37–41, 77, April 2006


sets out to find an understanding of potential mechanisms that could permit preservation of soft-tissues in vertebrate fossils within the framework of geologic time.

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This study is simply trying to come up with a mechanism to preserve proteins over millions of years because current science says that it is not possible (see bolded part of the quote below).

Why do we go to such extents to deny the obvious?

There has been more confirmation that "the materials were original proteins from the dinosaur" with an even "older" fossil.

http://www.physorg.c...s160320581.html



In seeking an answer, evolutionists of course maintain the millions-of-years framework as their ‘base assumption’. Mary Schweitzer demonstrates this regarding her 68 million-year-old T. rex finds:

    ‘The presence of original molecular components is not predicted for fossils older than a million years [refs.1–7] and the discovery of collagen in this well-preserved dinosaur supports the use of actualistic conditions to formulate molecular degradation rates and models, rather than relying on theoretical or experimental extrapolations derived from conditions that do not occur in nature.’9

But Schweitzer then claims that this prediction should be questioned because we found exactly that (collagen originally formed in the T. rex bone) in a dinosaur bone. Schweitzer said elsewhere of her first finds of blood cells in T. rex bones: ‘I just got goose bumps, because everyone knows these things don’t last for 65 million years’ [emphasis added].10 This assumes that dinosaurs are ‘obviously’ (according to evolutionists) at least 65 million years old, which is exactly what they’re trying to prove! However, their assumption (that dinosaurs are more than 65 million years old) is completely at odds with the experimental data.

This is why Schweitzer says we should rely on ‘actualistic conditions’ rather than ‘theoretical or experimental extrapolations’ to tell how long collagen can last. We have to rethink our entire understanding of how complex biomolecules degrade—why? Because dinosaurs are ‘obviously’ millions of years old. The ‘millions of years’ belief trumps experimental science!

What about the accusation that the experimental and theoretical predictions made are not based on conditions that occur in nature? The very point of such projections is that they serve not as an average degradation time but as an upper limit.
7 The experiments and theory therefore assume the best possible conditions for preservation. While such conditions are extremely unlikely to occur in nature, this is a hindrance to Schweitzer’s reasoning because the lab conditions are designed to be better than the preservation conditions normally found in nature, not worse. She requires the exact opposite to be true for her reasoning to be valid.


Quoted from this link. Schweitzer quoted from Discover magazine.

#10 Geode

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Posted 16 October 2010 - 07:21 AM

Young Earth Creationist Ministries are not the only ones giving this discovery a spin of support for a recent demise of dinosaurs. "When this shy paleontologist found soft, fresh-looking tissue inside a T. rex femur, she erased a line between past and present. Then all hell broke loose."-- Yeoman, B., Schweitzer’s Dangerous Discovery, Discover  27(4):37–41, 77, April 2006

This study is simply trying to come up with a mechanism to preserve proteins over millions of years because current science says that it is not possible (see bolded part of the quote below).

Why do we go to such extents to deny the obvious?

There has been more confirmation that "the materials were original proteins from the dinosaur" with an even "older" fossil.

http://www.physorg.c...s160320581.html

This is why Schweitzer says we should rely on ‘actualistic conditions’ rather than ‘theoretical or experimental extrapolations’ to tell how long collagen can last. We have to rethink our entire understanding of how complex biomolecules degrade—why? Because dinosaurs are ‘obviously’ millions of years old. The ‘millions of years’ belief trumps experimental science!

What about the accusation that the experimental and theoretical predictions made are not based on conditions that occur in nature? The very point of such projections is that they serve not as an average degradation time but as an upper limit.7 The experiments and theory therefore assume the best possible conditions for preservation. While such conditions are extremely unlikely to occur in nature, this is a hindrance to Schweitzer’s reasoning because the lab conditions are designed to be better than the preservation conditions normally found in nature, not worse.
She requires the exact opposite to be true for her reasoning to be valid.


Quoted from this link.  Schweitzer quoted from Discover magazine.

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First of all you are reaching conclusions that were not from the original study. Schweitzer's claim was to have found original protein material in the bones, and the study I linked in the OP supports her conclusion. That was the main thrust of the work, to see whether or not her claim was correct or that of her critics who claimed that what she had seen were biofilms. You seem to have missed this. The intent was not as you claim. If the motivation had been to "deep six" a young earth conclusion this could have been done far easier in simply siding with the biofilms as being the "original material" she had claimed. One thing you will have to keep in mind. There really is not a conspiracy in science as you hint at here and others boldy claim. The vast majority of the scientific community are unaware that there are people who attempt to use scientific evidence to show that the earth is young. I doubt a young vs. old debate even came to mind in the research. There really is no debate in most geologic work since there are so many lines of evidence consistently supporting an old age for the planet that it is considered a proven fact. There are independent lines of evidence showing the great antiquity of the dinosaur bones.

Mineralized and permineralized bone is the most common form of fossilization in the vertebrate record. Preservation of gross soft tissues is extremely rare, but recent studies have suggested that primary soft tissues and biomolecules are more commonly preserved within preserved bones than had been presumed. Some of these claims have been challenged, with presentation of evidence suggesting that some of the structures are microbial artifacts, not primary soft tissues. The identification of biomolecules in fossil vertebrate extracts from a specimen of Brachylophosaurus canadensis has shown the interpretation of preserved organic remains as microbial biofilm to be highly unlikely. These discussions also propose a variety of potential mechanisms that would permit the preservation of soft-tissues in vertebrate fossils over geologic time.


It appears to me that the last part, about preservation simply came from what the acquired data showed.

When the original study came out I posted on a different board that all should remain objective and see where future research led, that softer material had been been preserved in very rare instances in fossils. Some immediately jumped to the conclusion that this discovery proved the dinosaurs were young. Others just as dogmatically claimed that it had to be biofilm contamination. This recent paper shows a possible inter-relationship and does not jump to conclusions, but bases the discussion upon the data that was acquired. It will be interesting to see what further work reveals.

All in all this shows scientific inquiry as it should be done.

#11 MamaElephant

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Posted 16 October 2010 - 08:20 AM

I look forward to comments on the actual science involved in the paper. Where was their methodology wrong or where are their conclusions biased? I think it commendable that instead of sitting on the sidelines and simply giving opinions on whether or not the tissues indicated in the fossils were primary or the result of biofilms (something others have done) that they actually conducted experiments to shed light on the subject coming up with interesting results and providing a basis for further research. I think I have seen threads where criticism has been leveled that an idea or concept posed by scientists lacked empirical evidence coming from research. Well, here we have some.

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I see what you are saying now. B)

#12 Geode

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Posted 22 October 2010 - 11:20 PM

I see what you are saying now. :lol:

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This is an interesting development in vertebrate paleontology. Now that materials not expected to be found in fossils have been identified in multiple experiments there should no longer be a dogmatic refusal to accept the possibility of such preservation.

#13 MamaElephant

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Posted 23 October 2010 - 03:44 AM

This is an interesting development in vertebrate paleontology. Now that materials not expected to be found in fossils have been identified in multiple experiments there should no longer be a dogmatic refusal to accept the possibility of such preservation.

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That is great. I would like more open-mindedness as to the reason for these materials to be present.

These discussions also propose a variety of potential mechanisms that would permit the preservation of soft-tissues in vertebrate fossils over geologic time.


It appears to me that the last part, about preservation simply came from what the acquired data showed.


Okay, you lost me with those statements. What now?

#14 Geode

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Posted 23 October 2010 - 05:12 AM

"These discussions also propose a variety of potential mechanisms that would permit the preservation of soft-tissues in vertebrate fossils over geologic time."

"It appears to me that the last part, about preservation simply came from what the acquired data showed."

Okay, you lost me with those statements. What now?

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The paper stated:

Mineralized and permineralized bone is the most common form of fossilization in the vertebrate record. Preservation of gross soft tissues is extremely rare, but recent studies have suggested that primary soft tissues and biomolecules are more commonly preserved within preserved bones than had been presumed. Some of these claims have been challenged, with presentation of evidence suggesting that some of the structures are microbial artifacts, not primary soft tissues. The identification of biomolecules in fossil vertebrate extracts from a specimen of Brachylophosaurus canadensis has shown the interpretation of preserved organic remains as microbial biofilm to be highly unlikely. These discussions also propose a variety of potential mechanisms that would permit the preservation of soft-tissues in vertebrate fossils over geologic time.


The main thrust of the conclusions of the paper was that primary tissues were apparently preserved and the material was not from subsequent biofilm formation. But they went on the say that the creation of biofilms might add the preservation of the original softer protein material in the bones. Although that was the one mechanism that came out of their study, there could be others.

The second statement was made as a comment to their results. I was simply saying that their results and conclusions were reached through an evaluation of the data they collected.

#15 AFJ

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Posted 26 October 2010 - 08:36 PM

I must have missed where there is a prohibition on who can and who cannot do research on biofilms. I think anybody who wishes to do so can proceed. When can we expect such research from the Institute for Creation Research? They have seemed very interested in the subject in the past and kept up on the subject by posting reports. Will they post this one in a discussion on their site?

Here are some past conclusions from the ICR:
Soft Tissue

But even though this is not research conducted by the ICR I do not see them say that they cannot do their own studies. They should attempt to see if the results reported here are repeatable. If not they are doing "armchair" attempts at science and really don't have much of a basis to reach objective opinions. After all they are a research institution are they not, so shouldn't their prime reason for existence be to conduct research?

I look forward to comments on the actual science involved in the paper. Where was their methodology wrong or where are their conclusions biased? I think it commendable that instead of sitting on the sidelines and simply giving opinions on whether or not the tissues indicated in the fossils were primary or the result of biofilms (something others have done) that they actually conducted experiments to shed light on the subject coming up with interesting results and providing a basis for further research. I think I have seen threads where criticism has been leveled that an idea or concept posed by scientists lacked empirical evidence coming from research. Well, here we have some.

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Geode,
I think you would know that research costs money. That's why alot of research is done within the confines of grad student labs, in state funded universities.

And how would one get heme molecules from microbial biofilms, or am I misunderstanding something? Or how would microbial biofilms preserve, as they are proteins, and polysaccharides-- organic molecules? Or how would microbes have the necessary resources for millions of years from a bone? Would they not decay the bone, instead of preserving it? All organic material would be consumed.

Most of the fossils have crystallized because their atomic substance has been substituted. This is a totally different atomic arrangement than what is found in organic molecules. The crystallized mineral arrangement can endure time, but organic molecules are subject to enzymatic and/or bacterial breakdown after death. The truth is that the dinosaur bones are rather fresh.

#16 MamaElephant

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Posted 27 October 2010 - 06:33 AM

I must have missed where there is a prohibition on who can and who cannot do research on biofilms. I think anybody who wishes to do so can proceed. When can we expect such research from the Institute for Creation Research? They have seemed very interested in the subject in the past and kept up on the subject by posting reports. Will they post this one in a discussion on their site?


If they did their own work on this question most would not accept the outcome anyway, so what would be the point?

#17 Geode

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Posted 27 October 2010 - 09:27 PM

Geode,
I think you would know that research costs money.  That's why alot of research is done within the confines of grad student labs, in state funded universities.

And how would one get heme molecules from microbial biofilms, or am I misunderstanding something?  Or how would microbial biofilms preserve, as they are proteins, and polysaccharides-- organic molecules?  Or how would microbes have the necessary resources for millions of years from a bone?  Would they not decay the bone, instead of preserving it?  All organic material would be consumed.

Most of the fossils have crystallized because their atomic substance has been substituted.  This is a totally different atomic arrangement than what is found in organic molecules.  The crystallized mineral arrangement can endure time, but  organic molecules are subject to enzymatic and/or bacterial breakdown after death.  The truth is that the dinosaur bones are rather fresh.

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What is the purpose of a research institute if it never intends to do research? The ICR has funding they could use in prime reseacrh instead of some of their usual picking at articles published by others. They have grad students and I think they claim to have lab facilities.

I think the paper explained all of your questions better than my version would do. They offered their impressions and I certainly do not have the background to say that they are right or wrong.

Many fossils have original material preserved, that is the whole point of such studies. What is presented here is not about the endurance of non-organic compounds. It is implicit in the discussion that the study was not concerned with re-crystallized fossil materials. The dinosaur bone samples were taken through a process of demineralization before analysis.

Your conclusion about the bones being fresh is not supported by the data presented, but in my opinion a conclusion drawn outside of this study which found some evidence that soft tissue preservation may be more common than thought in very old fossils, as dated by independent studyies, and there might be processes not really studied before that might add and abet this process. Soft tissue preservation in fossils, although rare, has been known for many years. Assuming freshness is in my opinion dogmatically following a paradigm that many assume, that there is a limit to how long some organic substances can remain without destruction. I often see creationists claim that mainstream science is biased by a worldview and that scientists lack having an open-mind as a result. Some of this was shown in the disbelief that dinosaur proteins could possibly still be within the bones. Creationists latched onto this to claim and said that it showed dinosaurs must have lived in the past few thousand years. But now, if evidence can show a mechanism that could preserve such material in bones that could be millions of years old, will creationists accept where the data leads? Will mainstream workers? This is what scientific research should be about, to find answers through objective research methods.

#18 Geode

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Posted 27 October 2010 - 09:28 PM

If they did their own work on this question most would not accept the outcome anyway, so what would be the point?

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Then what is the point in their existing?

#19 MamaElephant

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Posted 27 October 2010 - 11:04 PM

Assuming freshness is in my opinion dogmatically following a paradigm that many assume, that there is a limit to how long some organic substances can remain without destruction.

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Again: current science says that preserving proteins over millions of years is not possible.

We have to rethink our entire understanding of how complex biomolecules degrade—why? Because dinosaurs are ‘obviously’ millions of years old.

experimental and theoretical predictions ... serve not as an average degradation time but as an upper limit. The experiments and theory therefore assume the best possible conditions for preservation.



#20 Geode

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Posted 30 October 2010 - 10:54 PM

Again: current science says that preserving proteins over millions of years is not possible.

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The entire point of the article I posted is that some current scientists do believe that preserving proteins for millions of years is possible. Saying that "current science says that preserving proteins over millions of years is not possible" is not a correct statement, but instead a sweeping generality. Some hold this to be true, others do not. But it is a statement that creationists seem to be hanging onto so as to descredit the accepted ages of the dinosaur bones in the studies. So on which side of the debate are we seeing the most dogmatic attitude and reluctance to accept evidence as it is acquired?




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