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Dinosaur Soft Tissue
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he_who_is_nobodyBloggerUser avatarPosts: 3245Joined: Tue Feb 24, 2009 1:36 amLocation: Albuquerque, New Mexico Gender: Male

Post Re: Dinosaur Soft Tissue

SpecialFrog wrote:
Elshamah wrote:Recently a new paper has been published in regard of soft tissue in dinos.

http://pubs.acs.org/doi/10.1021/acs.jproteome.5b00675

You mean the one Isotelus linked two posts above?


Dustnite wrote:
Elshamah wrote:Recently a new paper has been published in regard of soft tissue in dinos.

http://pubs.acs.org/doi/10.1021/acs.jproteome.5b00675


You couldn't be bothered to read a couple posts up to see this already linked? I guess I should be surprised that you didn't just copy paste the article as your own work.


:lol:

I love it when intelligent design creationists do this! I love it when they make an argument that has already been debunked just a few posts before they make theirs. It is the absolute gold standard confirmation that they are the worse researchers on the planet.
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Post Re: Dinosaur Soft Tissue

So it looks like creationists are trying everything they can to milk the soft tissue thing. You know, since their efforts to debunk absolute dating methods have all failed miserably.

Online I found a thread where the iron, and they commented on the iron mechanism, quoting some creationist "paper":

Creationist Paper wrote:Apparently satisfied that she had an- swered the question of how collagen could have lasted for millions of years, Schweitzer next tackled the question of preserving whole tissues such as blood vessels. Her coauthored paper reported that when placed in homogenized and concentrated blood, bird blood vessels in bone did not appreciably decay even after being held at room temperature for two years (Schweitzer et al., 2013b). On this basis, the authors speculated that blood-derived iron adhered to the inner and outer surfaces of dinosaur blood vessels to preserve them for millions of years. While certainly informative, the bird tissue results fall short of explaining the original tissue fossil data for three reasons


First off we have a strawman. They grossly simplify the mechanism. As I understand it, the way Mary's mechanism actually works is iron atoms are released, and react chemically to form hydroxl radicals. These radicals themselves crosslink protiens and cell membranes, making them much more durable. Then the iron itself precipitates into nanoparticles, which can cover the tissues and further stabalized them.

So already theyre misrepresenting Mary's work. Hardly suprising.

First, without an actual decay rate of vascular tissue in blood concentrate, we cannot reliably extrapolate an age ex- pectation. Two years is too short a time, even at room temperature, from which to draw these authors’ conclusion.


Once more, they miss the point of the experiment. It wasnt to give an age limit. It wasn't to represent the Hell Creek conditons. They just wanted to see it iron may be responsible for the observed crosslinking. Again, a misrepresentation.

Second, not only did the dinosaur soft tissue in bone include collagen protein and blood vessels, but also whole osteocytes with several vertebrate-specific proteins still intact inside them. Osteocytes do not behave like collagen, so apatite sequestration should not be invoked to explain their preservation.


Why not? How do they behave differently? Do the creationists even understand that being associated with the mineral phase of the bone has also been observed to have preserving effects, further stabilizing cellular structures and preventing degrative enzymes from reaching them? I doubt it. They're likely misrepresenting what the scientists are actually invoking, especially given their claims about iron reaching the osteocytes were just that. See below.a

But the tiny points of access to osteocytes in bone like canaliculi have too small a diameter to permit the imaginary blood concentrate access. They are much smaller than capillary tubes. So, even if blood-derived iron can preserve, it does no good if it cannot reach the cells in question.


The tiny pipes leading from the bone to osteocytes is known as the lanculocannalicular network (spelling may be off). It's how osteocytes get nutrients and get rid of wastes. No one is claming blood concentrate must flow through these. Rather, escaped iron atoms may pass through via passive diffusion after escaping red blood cells.

However, let's assume this is not possible. That still does not mean iron would not access the osteocytes. As Mary has pointed out, osteocytes contain the iron binding molecule ferretin. During life, they get iron from the blood along with other nutrients. After death, this iron is released from its cage and is free to react with the cell membranes.

Iron was shown by her to be on the cells. It logically must be able to access it somehow.

Last, many original biomaterial fossils occur in virtually bloodless settings. For ex- ample, no evidence for ancient blood baths presents itself in most of the fossils described above, such as dinosaur skin or Sabellidae worm casings. By far the most straightforward explanation of original tissue fossil preservation involves reas- signing their ages from millions down to thousands of years.


The sabelites were discussed above and are no help to young earthers. Likewise, the dinosaur skin was mineralized, so it's not soft tissue like Mary's find and actually requires being dried out before burrial. How'd that happen in a worldwide flood?

The fossil ages are in no need of reassessment. As Mary herself explained, that's only viable if you have no outside data. But we DO have plenty of outside data indicating the vast ages of the Earth's rocks, and the creationist excuses, like accelerated decay, have been shown many times to just not work. We know the rocks must be ancient, and so must the fossils.

One final thing. I couldn't care less about YEC cries of "Mary's idea is IMPOSSIBLE", and for a simple reason. In 2014, a study by Boatman et al,. showed that both fenton chemistry and glycation induce a crosslinking pattern extremely similar to the crosslinking observed in dinosaur proteins. So, iron may not neccesitate fenton chemistry, but also glycation. Likewise, glycation may be triggered by iron, but as far as I know does not require it, so lack of iron also does not rule out glycation. So YECS can insist over and over again that iron didn't do it. The fact that iron, by at least two mechanisms, creates an extremely similar pattern in modern collagen to that shown in dino collagen is proof positive it's responsible in some way here.

Also, in the thread they brought up Mark Armitage, who's only real talent in this whole issue seems to be to scream "Put up or shut up, SCIENCE is a LIE" in youtube comments.

Needless to say it's hard for me to take any of this seriously.

And I'd REALLY like a creationist to explain why the dinosaur protiens put them basal to birds, exactly as evolution predicts. But none have. They're so good at leaving out such inconvienient information.
Last edited by itsdemtitans on Mon Jul 25, 2016 1:45 am, edited 7 times in total.
Tue Dec 08, 2015 9:35 pm
IsotelusBloggerUser avatarPosts: 317Joined: Tue Nov 02, 2010 12:59 am Gender: Tree

Post Re: Dinosaur Soft Tissue

itsdemtitans wrote:Stuff about Mark Armitage


I agree with everything you posted above. Some of my colleagues (one of which works in dinosaur bone histology) and myself read this paper together:
Armitage, M.A. Anderson, K.A. 2013. Soft sheets of fibrillar bone from a fossil of the supraorbital horn of the dinosaur Triceratops horridus. Acta Histochemica: 115 (6) 603–608.

We agreed that it's not good. The biggest issue in terms of the validity of his results shot off the page when they described the horn core was found both cracked and exposed to the air, with roots growing in it. Like, really? Other things we noticed were things like misuse of histological terms, and the possibly dubious identification of microstructures in the bone. One image shows things that look suspiciously like clay or sand minerals too me; I know because I've taken SEM images of not-yet cleaned dinosaur bone.

I have the pdf of this paper if anyone wants to read it themselves; just send me a pm.

I also found this from an Archaeologist who made some of the same observations: http://www.antievolution.org/cgi-bin/ik ... ntry236761

I think it's safe to say that anything this guy says absolutely needs to be taken with a grain of salt.

And I'd REALLY like a creationist to explain why the dinosaur protiens put them basal to birds, exactly as evolution predicts. But none have. Theyre so good at leaving out such inconvienient information.


There's a paper by Phil Senter that used a creationist-approved baraminology program and showed that birds are related to theropod dinosaurs. I personally haven't seen any proper address to this issue either.



EDIT: Itsdemtitans, did you delete your reply? I was just making a response. I misread my notes; the issue was more with the bone itself than osteocytes per se. That beings said, there was the issue on if they can show unequivocally that they are Ceratopsian osteocytes; that is, is this actually a Ceratopsian horn. As I just read, that Archaeologist I linked to had the same thought.
The weird thing with the bone was that the paper keeps on bringing up fibrillar bone; fibrillar collagen is a thing, but not fibrillar bone, unless it's some not often mentioned type of bone that just happens to not appear in paleohistological literature. I wonder if they were using lamellar and fibrillar synonymously. Either way, it's sketchy.
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Post Re: Dinosaur Soft Tissue

Isotelus wrote:
itsdemtitans wrote:Stuff about Mark Armitage


I agree with everything you posted above. Some of my colleagues (one of which works in dinosaur bone histology) and myself read this paper together:
Armitage, M.A. Anderson, K.A. 2013. Soft sheets of fibrillar bone from a fossil of the supraorbital horn of the dinosaur Triceratops horridus. Acta Histochemica: 115 (6) 603–608.

We agreed that it's not good. The biggest issue in terms of the validity of his results shot off the page when they described the horn core was found both cracked and exposed to the air, with roots growing in it. Like, really? Other things we noticed were things like misuse of histological terms, and the possibly dubious identification of microstructures in the bone. One image shows things that look suspiciously like clay or sand minerals too me; I know because I've taken SEM images of not-yet cleaned dinosaur bone.

I have the pdf of this paper if anyone wants to read it themselves; just send me a pm.

I also found this from an Archaeologist who made some of the same observations: http://www.antievolution.org/cgi-bin/ik ... ntry236761

I think it's safe to say that anything this guy says absolutely needs to be taken with a grain of salt.

And I'd REALLY like a creationist to explain why the dinosaur protiens put them basal to birds, exactly as evolution predicts. But none have. Theyre so good at leaving out such inconvienient information.


There's a paper by Phil Senter that used a creationist-approved baraminology program and showed that birds are related to theropod dinosaurs. I personally haven't seen any proper address to this issue either.


I've read Armitage's paper and have my own copy. Would you mind expanding on why his osteocyte remains are dubious? It might be worth leaving out there.
Wed Dec 09, 2015 1:41 am
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Post Re: Dinosaur Soft Tissue

Isotelus wrote: EDIT: Itsdemtitans, did you delete your reply? I was just making a response. I misread my notes; the issue was more with the bone itself than osteocytes per se. That beings said, there was the issue on if they can show unequivocally that they are Ceratopsian osteocytes; that is, is this actually a Ceratopsian horn. As I just read, that Archaeologist I linked to had the same thought.
The weird thing with the bone was that the paper keeps on bringing up fibrillar bone; fibrillar collagen is a thing, but not fibrillar bone, unless it's some not often mentioned type of bone that just happens to not appear in paleohistological literature. I wonder if they were using lamellar and fibrillar synonymously. Either way, it's sketchy.


Yeah, I can't remember why I did. I've reposted it above best I remember it.
Wed Dec 09, 2015 1:44 am
he_who_is_nobodyBloggerUser avatarPosts: 3245Joined: Tue Feb 24, 2009 1:36 amLocation: Albuquerque, New Mexico Gender: Male

Post Re: Dinosaur Soft Tissue

Isotelus wrote:I also found this from an Archaeologist who made some of the same observations: http://www.antievolution.org/cgi-bin/ik ... ntry236761


Dr. Gary Hurd, one of my heroes. I wish he would start blogging again.

Isotelus wrote:That beings said, there was the issue on if they can show unequivocally that they are Ceratopsian osteocytes; that is, is this actually a Ceratopsian horn. As I just read, that Archaeologist I linked to had the same thought


Is this the best picture of the fossil or is there a better one in the paper? To me, it looks bovid, but that is from looking at it stuck in the ground and not cleaned off (and Hurd’s opinion tainting mine).
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Post Re: Dinosaur Soft Tissue

Another word on Mary's mechanism.

A study by Boatman et al 2014., showed both fenton chemistry and glycation induce hypercrosslinking of tested tissues. Not rudimentary cross-linking, hypercrosslinking. This is the same hypercrosslinking observed in dinosaur fossils (possibly a little weaker than what we see in the fossils). The hypercrosslinking is so stable that chemicals meant to destroy weak covalent bonds (rudimentary bonds?) have no effect on the tissues. Far from rudimentary, its been shown to be quite stable, and possibly irreversible with chemical treatments.

Creationists often criticize Mary's 2013 paper by saying it was her claiming "Aha see this proves iron preserved it for millions of years, no other research is needed." Those that do have clearly missed the point of the experiment. It was not intended to replicate the environment of the Hell Creek formation. Rather, it was to test their hypothesis that iron had any sort of preserving effect at all. Lo and behold, it does. The paper by Schweitzer et al., 2013 allows further research to go into this mechanism and see if it's enough to account for this instance or if other factors are at play, if it can be used in all cases or only some, etc. But it was only meant to test their hypothesis and provide a base to work off of. Which is what it did.

And have they continued work on the iron mechanism? Well, I got a tantalizing answer from Mary via email:

Mary Schweitzer wrote:We continue to test the idea in other fossils. We have some very very cool results, but haven't written anything up on it yet. But we are understanding the mechanisms better all the time.


THAT has me excited. Whatever their results, I hope they're compiling them for another paper on their proposed mechanism, and I'm eager to see what they've found. But one must simply wait and see.
Last edited by itsdemtitans on Wed Jan 20, 2016 12:17 am, edited 5 times in total.
Thu Dec 10, 2015 4:12 am
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Post Re: Dinosaur Soft Tissue

he_who_is_nobody wrote:
Isotelus wrote:I also found this from an Archaeologist who made some of the same observations: http://www.antievolution.org/cgi-bin/ik ... ntry236761


Dr. Gary Hurd, one of my heroes. I wish he would start blogging again.

Isotelus wrote:That beings said, there was the issue on if they can show unequivocally that they are Ceratopsian osteocytes; that is, is this actually a Ceratopsian horn. As I just read, that Archaeologist I linked to had the same thought


Is this the best picture of the fossil or is there a better one in the paper? To me, it looks bovid, but that is from looking at it stuck in the ground and not cleaned off (and Hurd’s opinion tainting mine).


Their paper can be found here, and yeah, that's the best pic I was able to find.
Thu Dec 10, 2015 4:15 am
DutchLiam84User avatarPosts: 382Joined: Sun Jun 13, 2010 2:27 pmLocation: Eurasian Plate Gender: Time Lord

Post Re: Dinosaur Soft Tissue

Here's my gift to you, a "new" video to rip into!

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ldmitrukUser avatarPosts: 229Joined: Thu Sep 26, 2013 2:47 pmLocation: Edmonton, Alberta Gender: Cake

Post Re: Dinosaur Soft Tissue

DutchLiam84 wrote:Here's my gift to you, a "new" video to rip into!


The biggest misconception in the video is science proving the bible to be correct.
Tue Jan 05, 2016 11:57 pm
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Post Re: Dinosaur Soft Tissue

DutchLiam84 wrote:Here's my gift to you, a "new" video to rip into!


It's the same old unsubstantiated claim.

"Oh this soft tissue could not last 100 thousand years, much less the millions required for evolution."

Which is wrong. First, it's misrepresenting the nature of the verified discoveries. All of Schweitzer's finds (and others), while certainly interesting, have nothing to do with the age of the bones. Sure, creationists can howl otherwise, but anyone who's studied the finds, or any other geologic evidence apart from soft tissue, will understand their screams of "SOFT TISSUE!! B-B-B-UT THERE'S SOFT TISSUE," are nonsense.

Why?

First, the remnants of the finds are highly degraded, and more importantly, highly crosslinked. The second is equally important because. among other things, cross-linking retards hydrolysis, oxidation, degradation from enzymes, etc. She found no undegraded, original tissues. Original material, yes, but they were decayed remnants of what once was. I'd bet my money on the hypercrosslinking observed in the tissues is one of the biggest reasons why they've lasted so long. We're still trying to figure out how this crosslinking happened, but the fact that it did means creationists claiming "Uh, what you think caused it does not work" is irrelevant. It's there, it's a big reason why it's there. Deal with it.

Second, as Isotelus pointed out, we're now seeing the REAL value of these finds (Hint: Real does not mean proving YEC and Flood Geology), namely, they're confirming evolutionary relationships found in the fossil record, as the protein sequences recovered place them basal to birds. Sure, they'll cry "THAT'S JUST COMMON DESIGN", but because evolution requires we see something like that, and creationism does not, it's indicative of evolution.

Third, it disregards the established dates of the sediments. This is the entire reason creationists care about soft tissue. There original objections to Radiometric dating are easily falsified, and their case for "Accelerated Nuclear Decay" is likewise falsified. Really, they did nothing to prove it wrong, and since it mandates and old earth, they need any reason they can to give even the slightest hint the dates are wrong. Hence why conspiracy is constantly a last resort, as they'll never bring themselves to admit the dates are accurate.

This is a prime example. They have no other evidence to debunk radiometric dates, and as such are grasping at this one straw at the bottom of the haystack, but ignore the rest of the haystack. Then, when people like me consider all the evidence, such as tests showing the accuracy of the methodology used in radiometric dating and independent confirmations, both from non-radiometric dates and radiometric dates, and say "Well, it's pretty clear these work, so saying the rocks are young is out of the question," they say all that evidence is a lie perpetrated by scientists to cover up YEC, then run back to their flock and whine about how nobody is listening to their immensely powerful evidence for a young earth.

When I first started studying YEC arguments, soft tissue was one of the things that got me. I honestly thought, misrepresentations aside, they had a valid point. UNTIL, that is, I began studying Geology. I began reading papers, studying the methodology, reading the papers where completely independent methods verify radiometric dating, etc. Then, it became clear to me that their claims the bones, and therefore the rocks, are young are false. The soft tissue debate guided me to my interest in Geology, and for that I am very thankful. But I don't personally care anymore about the soft tissue debate. Unfortunately for the creationists, all it showed me was the lengths creationists will go to grasp at straws and manipulate data. Not only did it lead me to see the vast evidence for an ancient world, but it showed me the depravity of creationism and their willingness to discard any other data at the drop of a hat far more than anything else could have.

And, as a final note, even if it did mean the bones were young, we can, and have, already falsified flood geology. That falsifies YEC. So regardless of the implications of these finds, we can still prove they're wrong too, and the origins "debate" goes back to square one.

So much for "immensely powerful" evidence.
Thu Jan 07, 2016 2:30 am
DutchLiam84User avatarPosts: 382Joined: Sun Jun 13, 2010 2:27 pmLocation: Eurasian Plate Gender: Time Lord

Post Re: Dinosaur Soft Tissue

Now tell that to the guy in the video! :P
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IsotelusBloggerUser avatarPosts: 317Joined: Tue Nov 02, 2010 12:59 am Gender: Tree

Post Re: Dinosaur Soft Tissue

itsdemtitans wrote:Second, as Isotelus pointed out, we're now seeing the REAL value of these finds (Hint: Real does not mean proving YEC and Flood Geology), namely, they're confirming evolutionary relationships found in the fossil record, as the protein sequences recovered place them basal to birds. Sure, they'll cry "THAT'S JUST COMMON DESIGN", but because evolution requires we see something like that, and creationism does not, it's indicative of evolution.


Another issue with common design is what goes on embryonically in birds. I find it odd that a designer would have chickens grow tooth buds only to be reabsorbed prior to hatching. Or a long bony tail and five manual digits. Has anyone here ever seen an explanation provided by a creationist?
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Tue Jan 12, 2016 5:24 am
Steelmage99Posts: 150Joined: Thu May 28, 2015 9:43 am Gender: Male

Post Re: Dinosaur Soft Tissue

Isotelus wrote:
itsdemtitans wrote:Second, as Isotelus pointed out, we're now seeing the REAL value of these finds (Hint: Real does not mean proving YEC and Flood Geology), namely, they're confirming evolutionary relationships found in the fossil record, as the protein sequences recovered place them basal to birds. Sure, they'll cry "THAT'S JUST COMMON DESIGN", but because evolution requires we see something like that, and creationism does not, it's indicative of evolution.


Another issue with common design is what goes on embryonically in birds. I find it odd that a designer would have chickens grow tooth buds only to be reabsorbed prior to hatching. Or a long bony tail and five manual digits. Has anyone here ever seen an explanation provided by a creationist?


Nothing beyond; "Gawd designed it that way - and who are you to question the ways of the Almighty?!?", it seems.
Blunder that theists make all the time;

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Tue Jan 12, 2016 2:04 pm
VisakiUser avatarPosts: 719Joined: Fri Nov 12, 2010 12:26 pmLocation: Helsinki, Finland Gender: Male

Post Re: Dinosaur Soft Tissue

Steelmage99 wrote:Nothing beyond; "Gawd designed it that way - and who are you to question the ways of the Almighty?!?", it seems.

Well there is the old canard that those, and lots and lots of other things, are proof of the degradation of life caused by the fall of man and exile from Eden. After all the original edenese birds had teeth and teeth are better than no teeth, right? Though it seems unlikely that ID proponents would use that so called argument.
Tue Jan 12, 2016 2:09 pm
Dragan GlasContributorUser avatarPosts: 2914Joined: Mon Dec 14, 2009 1:55 amLocation: Ireland Gender: Male

Post Re: Dinosaur Soft Tissue

Greetings,

Interesting update on the "soft-tissue in dinosaur bones" kerfuffle:

Collagen from a Tyrannosaurus rex bone proves Jurassic Park will never exist

Kindest regards,

James
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Thu Jun 01, 2017 1:36 pm
VisakiUser avatarPosts: 719Joined: Fri Nov 12, 2010 12:26 pmLocation: Helsinki, Finland Gender: Male

Post Re: Dinosaur Soft Tissue

Although this is another example on why science works (bitches!), I'm sure creationists will manage to mangle it and use it to attack the validity of science. Again. Which is a bit ironic because those same creationists used the original find to discredit deep time and evolution.
Fri Jun 02, 2017 7:57 am
Dragan GlasContributorUser avatarPosts: 2914Joined: Mon Dec 14, 2009 1:55 amLocation: Ireland Gender: Male

Post Re: Dinosaur Soft Tissue

Greetings,

Visaki wrote:Although this is another example on why science works (bitches!), I'm sure creationists will manage to mangle it and use it to attack the validity of science. Again. Which is a bit ironic because those same creationists used the original find to discredit deep time and evolution.

Agreed.

I wonder if the two "Bobs" - Enyart and Dutko - will mention this?! :roll:

Kindest regards,

James
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Fri Jun 02, 2017 1:21 pm
itsdemtitansBloggerUser avatar
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Post Re: Dinosaur Soft Tissue

Full paper here:

http://rspb.royalsocietypublishing.org/ ... 5/20170544

I honestly feel really bad for Schweitzer's team. These results are pretty damning if you ask me, at least with regards to proteins. Maybe they can still learn how cell structure can be preserved over deep time, but I cant imagine having all my work trashed like that. They seemed to make really obvious mistakes in hindsight.
Thu Jun 08, 2017 2:57 pm
he_who_is_nobodyBloggerUser avatarPosts: 3245Joined: Tue Feb 24, 2009 1:36 amLocation: Albuquerque, New Mexico Gender: Male

Post Re: Dinosaur Soft Tissue

itsdemtitans wrote:Full paper here:

http://rspb.royalsocietypublishing.org/ ... 5/20170544

I honestly feel really bad for Schweitzer's team. These results are pretty damning if you ask me, at least with regards to proteins. Maybe they can still learn how cell structure can be preserved over deep time, but I cant imagine having all my work trashed like that. They seemed to make really obvious mistakes in hindsight.


Well damn, that sucks. I am still holding out hope that Schweitzer et al. are right, but how I want the world to work does not factor into how the world actually works.
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