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Old 07-30-2008, 03:23 PM   #119199  /  #1
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Default Dinosaur soft tissue - does it really exist? A counter argument.

Interesting paper in PLoS One. I'm sure we're all aware of the work of Mary Schweitzer (our very own Dlx2 is an enormous fan!), both because it's potentially very interesting in and of itself and also because of the creation-evolution wars. Well, given the significance of the finding a certain degree of caution and scepticism is obviously warranted. So, in this spirit, Thomas Kaye of the Museum of Natural History in Seattle has published an article arguing against the finds being actual dino soft tissue. Instead, they suggest it may simply represent bacterial biofilms.

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Kaye, T. G. et al. (2008) Dinosaurian Soft Tissues Interpreted as Bacterial Biofilms. PLoS One, 3, e2808

A scanning electron microscope survey was initiated to determine if the previously reported findings of “dinosaurian soft tissues” could be identified in situ within the bones. The results obtained allowed a reinterpretation of the formation and preservation of several types of these “tissues” and their content. Mineralized and non-mineralized coatings were found extensively in the porous trabecular bone of a variety of dinosaur and mammal species across time. They represent bacterial biofilms common throughout nature. Biofilms form endocasts and once dissolved out of the bone, mimic real blood vessels and osteocytes. Bridged trails observed in biofilms indicate that a previously viscous film was populated with swimming bacteria. Carbon dating of the film points to its relatively modern origin. A comparison of infrared spectra of modern biofilms with modern collagen and fossil bone coatings suggests that modern biofilms share a closer molecular make-up than modern collagen to the coatings from fossil bones. Blood cell size iron-oxygen spheres found in the vessels were identified as an oxidized form of formerly pyritic framboids. Our observations appeal to a more conservative explanation for the structures found preserved in fossil bone.
The paper can be read for free here:

http://www.plosone.org/article/info%...l.pone.0002808

I haven't had time to fully read the Kaye paper so I can't yet comment on the merits of their arguments (it looks interesting from a quick scan). However, we appear to be seeing science in action and potentially lots of egg on face.

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Old 07-30-2008, 03:37 PM   #119218  /  #2
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I suppose on the face of it this is a more plausible hypothesis.
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Old 07-30-2008, 03:39 PM   #119221  /  #3
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The last two paragraphs of that paper are worth reading:

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Biofilms are complex systems produced by virtually all bacteria on almost any water/surface boundary and are ubiquitous in nature [18], [19]. They provide a protective medium against changes in the broader environment from pH levels, toxins, etc. They are viscous, flexible and long lasting through mineralization. Recent biofilms would be naturally pliable and elastic while duplicating the shape of the surfaces they form on. Biofilms harbor ionic bonds which make them pre-disposed to mineralization [20] and is exemplified by calculus on human teeth. Examination of modern biofilms showed copious quantities of bacteria living in the films, however, SEM images only show a smooth undulating profile of the biofilm surface consistent with previous studies [21]. The voids in dinosaur bone provide the micro-environmental equivalent of a natural cave where the discovery of biofilms has become an area of active study.

The detection of similar structures by the previous body of work across time and taxa, suggests an overlap with this survey [2]. When biofilms coat a substrate, and that substrate is subsequently removed, the biofilm will retain much of the original morphology. This can explain the quantity and similarity of structures found in fossil bone and indicates that these structures are unlikely to be preserved dinosaurian tissues but the product of common bacterial activities.
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Old 07-30-2008, 04:03 PM   #119252  /  #4
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It would be tidy to find that the antibodies that reacted with the "dinosaur protein" also reacted with likely film-forming organisms (or their decay products)
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Old 07-30-2008, 04:26 PM   #119273  /  #5
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It would be tidy to find that the antibodies that reacted with the "dinosaur protein" also reacted with likely film-forming organisms (or their decay products)
Let's hope it doesn't. That would be a really crappy reagent to use in work like this.
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Old 07-30-2008, 04:52 PM   #119302  /  #6
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I always thought it was kind of unlikely that proteins could last for seventy million years without being eaten by bacteria, no matter how deeply buried. Bacteria are freaking everywhere, and what are the chances a tyrannosaur could die, be buried, and decay without bacteria digesting every last scrap of lizard meat?
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Old 07-30-2008, 05:32 PM   #119336  /  #7
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I don't know how related the tissues examined in the PLoS article are to those tested in a recent Science article.

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Molecular Phylogenetics of Mastodon and Tyrannosaurus rex

Chris L. Organ, Mary H. Schweitzer, Wenxia Zheng, Lisa M. Freimark, Lewis C. Cantley, John M. Asara

We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen {alpha}1(I) and {alpha}2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable.
The collage derived from these tissues were definitely not derived from microfilms.
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Old 07-30-2008, 07:27 PM   #119436  /  #8
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Quote:
Originally Posted by ofro View Post
I don't know how related the tissues examined in the PLoS article are to those tested in a recent Science article.

Quote:
Molecular Phylogenetics of Mastodon and Tyrannosaurus rex

Chris L. Organ, Mary H. Schweitzer, Wenxia Zheng, Lisa M. Freimark, Lewis C. Cantley, John M. Asara

We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen {alpha}1(I) and {alpha}2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable.
The collage derived from these tissues were definitely not derived from microfilms.
You actually believe a word of that paper? Really? HAH.

They had sequences between 6 and 20 amino acids long; most were between 8 and 10 amino acids, and they were from highly conserved regions of the protein, and were analyzed using a method highly susceptible to contamination. Then they aligned their sequence on the basis of an assumed phylogeny, and THEN, FINALLY ran the analysis ass-backwards.

I played around with their data, and the longer the amino acid chain, the more obviously it's human collagen.

In other words, their data is shit.
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Old 07-30-2008, 08:11 PM   #119462  /  #9
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Here is a nice discussion and explanation from Tara Smith:

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First, a bit about biofilms. These are the sticky structures that form when bacteria adhere to a surface and form "communities" of organisms (as opposed to their free-living, "planktonic" stage). The plaque on your teeth and tongue; the scummy ring around your bathtub; the slippery coatings on ocean rocks are all composed of biofilm, which itself is made up of not only bacterial cells but also the matrix they produce that allows them to adhere to the surface (and also provides them protection from the elements around them). Though we've studied bacteria in their planktonic state for much of the history of microbiology, this is quickly changing as we realize the ubiquity of biofilms not only in the environment around us, but also within our own bodies (where biofilm-associated bacteria are much more resistant to the effects of antibiotics, for instance).

So, biofims are everywhere--but *inside* bone? That was the question examined in the new paper.....

What they found provides an alternative hypothesis to the previous "dino blood" findings. The iron present (and thought to have come from blood cells) could be explained by the presence of iron-containing framboids: spheres commonly found in sediments. Blood vessel-like structures were found but also could be attributed to biofilm, and when compared by FT-IR to lab-grown biofilms, the chemical signature of the fossil structure more closely resembled modern biofilms than modern collagen. The authors argue that the biofilm hypothesis better explains the data, including the ubiquity of these structures in fractured fossils

http://scienceblogs.com/aetiology/20...just_bacte.php
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Old 07-30-2008, 09:04 PM   #119493  /  #10
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my gosh, why can't evos just let it go and admit the obvious?....just because dinos may have lived thousands of years ago does not necessarily eradicate their theory that dinos lived millions of years ago as well. Heck, crocodiles are still alive, yet they supposedly roamed millions of years ago......If evos just admitted what is blatantly obvious to most rational-thinking people -- that the dino meat in question could not be 70 million years old -- then they'd take a step in the right direction of making themselves at least appear to be interested in investigating the truth.
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Old 07-30-2008, 09:06 PM   #119496  /  #11
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my gosh, why can't evos just let it go?....just because dinos may have lived thousands of years ago does not eradicate their theory that dinos lived millions of years ago. If evos just admitted the obvious -- that the dino meat in question could not be 70 million years old -- then they'd make a step in the right direction of making themselves appear genuinely interested in investigating the truth.
The fact of the matter is, it is not "dino meat" and we've been saying this since Schweitzer first pulled this crap out and made a fuss about it. This is the danger of science by press release, which is why most of us prefer a seasoned debate in the literature to "gee golly willackers" in interwebnets sources.
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Old 07-30-2008, 09:10 PM   #119502  /  #12
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my gosh, why can't evos just let it go and admit the obvious?....just because dinos may have lived thousands of years ago does not necessarily eradicate their theory that dinos lived millions of years ago as well. Heck, crocodiles are still alive, yet they supposedly roamed millions of years ago......If evos just admitted what is blatantly obvious to most rational-thinking people -- that the dino meat in question could not be 70 million years old -- then they'd take a step in the right direction of making themselves at least appear to be interested in investigating the truth.
Trolling taken to new heights. Kindly desist from commenting any further in my thread.
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Old 07-30-2008, 09:16 PM   #119507  /  #13
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Quote:
Originally Posted by Dlx2 View Post
Quote:
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I don't know how related the tissues examined in the PLoS article are to those tested in a recent Science article.

Quote:
Molecular Phylogenetics of Mastodon and Tyrannosaurus rex

Chris L. Organ, Mary H. Schweitzer, Wenxia Zheng, Lisa M. Freimark, Lewis C. Cantley, John M. Asara

We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen {alpha}1(I) and {alpha}2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable.
The collage derived from these tissues were definitely not derived from microfilms.
You actually believe a word of that paper? Really? HAH.

They had sequences between 6 and 20 amino acids long; most were between 8 and 10 amino acids, and they were from highly conserved regions of the protein, and were analyzed using a method highly susceptible to contamination. Then they aligned their sequence on the basis of an assumed phylogeny, and THEN, FINALLY ran the analysis ass-backwards.

I played around with their data, and the longer the amino acid chain, the more obviously it's human collagen.

In other words, their data is shit.
Has anyone published these objections (or any objections) to the Organ et al. paper, or do they have the "last word" at this point?
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Old 07-30-2008, 09:25 PM   #119513  /  #14
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Quote:
Originally Posted by VoxRat View Post
Quote:
Originally Posted by Dlx2 View Post
Quote:
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I don't know how related the tissues examined in the PLoS article are to those tested in a recent Science article.



The collage derived from these tissues were definitely not derived from microfilms.
You actually believe a word of that paper? Really? HAH.

They had sequences between 6 and 20 amino acids long; most were between 8 and 10 amino acids, and they were from highly conserved regions of the protein, and were analyzed using a method highly susceptible to contamination. Then they aligned their sequence on the basis of an assumed phylogeny, and THEN, FINALLY ran the analysis ass-backwards.

I played around with their data, and the longer the amino acid chain, the more obviously it's human collagen.

In other words, their data is shit.
Has anyone published these objections (or any objections) to the Organ et al. paper, or do they have the "last word" at this point?
Well, concerns about contamination were published in response to the Asara et al. (2007) paper, so really the Organ et al. paper was treading on pretty dangerous ground. No one in the paleontological community believes this shit for a second, and the geneticists I've spoken to have mainly had laughing fits when the subject is broached. My girlfriend wrote a short program to snag some random (human) sequences from genbank, take short contigs, and put them into clustalx the way that this whole study did, and if I remember correctly, we could manage to take human collagen and turn it into archosaur collagen via these methods a significant percent of the time. I dunno what the complete results were, but we may end up writing it up eventually if it remains an issue.

The methods are available for anyone to see, and most people who've seen them agree that they're shit. Schweitzer et al. just aren't letting it die quietly, because they see an opportunity to maintain some degree of fame. Science publishes it because they know it'll end up in the newspapers. When it ends up in newspapers, the creationists masturbate to it, so it gets smeared all over the blogosphere. Doesn't mean there's a drop of reproducible science in it, though.
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Old 07-30-2008, 09:59 PM   #119537  /  #15
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Quote:
Originally Posted by Dlx2 View Post
Quote:
Originally Posted by ofro View Post
I don't know how related the tissues examined in the PLoS article are to those tested in a recent Science article.

Quote:
Molecular Phylogenetics of Mastodon and Tyrannosaurus rex

Chris L. Organ, Mary H. Schweitzer, Wenxia Zheng, Lisa M. Freimark, Lewis C. Cantley, John M. Asara

We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen {alpha}1(I) and {alpha}2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable.
The collage derived from these tissues were definitely not derived from microfilms.
You actually believe a word of that paper? Really? HAH.

They had sequences between 6 and 20 amino acids long; most were between 8 and 10 amino acids, and they were from highly conserved regions of the protein, and were analyzed using a method highly susceptible to contamination. Then they aligned their sequence on the basis of an assumed phylogeny, and THEN, FINALLY ran the analysis ass-backwards.

I played around with their data, and the longer the amino acid chain, the more obviously it's human collagen.

In other words, their data is shit.
Have you or anyone else formally challenged this paper? Have there been published critiques of this work in Science or elsewhere?

ETA - I submitted this before realizing that Voxrat had asked the same question.

In response to your response to that question:

It seems to me that it does not matter how many analyses you and your girlfriend do, or what you think other professional paleontologists have to say, if none of you are willing to publish your critiques and subject those critiques to public review.

Until you (or someone else) does so, the results stand.

Last edited by ck1; 07-30-2008 at 10:04 PM.
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Old 07-30-2008, 10:04 PM   #119545  /  #16
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Jerry Harris comments at Tara's blog:

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Tara, be very careful in accepting that this paper is the last word on the subject! Some of the new findings do contradict some of the older findings, but there is much about this new paper that isn't satisfactory (and doesn't address admitted problems with the older findings). For example, why are the framboids not nucleating around iron-rich sources, such as blood cells? Wherever there's a source of iron (be it blood or anything else), iron crystals can form diagenetically. Why are these biofilms dating so recently, despite all the different ages of the source materials? Did they all somehow predict "Hey, in the next couple hundred years, someone's going to break us open and look for biofilms -- better get some!" How did the biofilms form such uniform tubular structures, especially if water levels inside the bones fluctuated and varied? Why did the previous collagen findings have chemical signatures more similar to chickens than anything else (reacted with chicken antibodies)...are we now supposed to accept that this reaction indicates that tyrannosaurs are more closely related to Rhodococcus bacteria than to chickens?

I'm not saying this new paper is bad; certainly it's a good attempt to come at some previous conclusions another way, which is what science is supposed to do. But this new approach examines structures; much of the previous work examined chemistry, and I don't think one can adequately contradict the other. That they point at different results only means that there's a lot more work to do. The field of examining fossilization at this scale is so new that there's basically now two data points. Would any scientist be comfortable making pronouncements on such tiny quantities of data?
The author of the paper will also apparently answer questions at Tara's place.
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Old 07-30-2008, 10:14 PM   #119552  /  #17
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my gosh, why can't evos just let it go and admit the obvious?....just because dinos may have lived thousands of years ago does not necessarily eradicate their theory that dinos lived millions of years ago as well. Heck, crocodiles are still alive, yet they supposedly roamed millions of years ago......If evos just admitted what is blatantly obvious to most rational-thinking people -- that the dino meat in question could not be 70 million years old -- then they'd take a step in the right direction of making themselves at least appear to be interested in investigating the truth.
Here's the problem, Guzman: no evidence that any non-avian dinosaurs were alive at any time in the last 65 or so million years. That's what's obvious.

The "dino meat in question" appears not to be "dino meat," but rather either mineralized biofilm or modern contamination.

Scientists are investigating the truth, Guzman. Hence the research. You will notice the complete and utter lack of research on the part of creationists.
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Old 07-30-2008, 10:22 PM   #119555  /  #18
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Science publishes it because they know it'll end up in the newspapers. When it ends up in newspapers, the creationists masturbate to it, so it gets smeared all over the blogosphere. Doesn't mean there's a drop of reproducible science in it, though.
This is certainly as extreme an anti-science statement as anything said by supersport or Dave.
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Old 07-30-2008, 10:25 PM   #119557  /  #19
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This is the critique of the Asara paper:

http://www.sciencemag.org/cgi/conten...t/319/5859/33c

a free copy can be seen here:

http://www.simonho.org/papers/science08_buckley.pdf
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Old 07-30-2008, 10:58 PM   #119572  /  #20
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I always thought it was kind of unlikely that proteins could last for seventy million years without being eaten by bacteria, no matter how deeply buried. Bacteria are freaking everywhere, and what are the chances a tyrannosaur could die, be buried, and decay without bacteria digesting every last scrap of lizard meat?
Or simply just deteriorating on their own. Tissues are not known for their durability, especially when they have ceased being alive.
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Old 07-31-2008, 01:59 AM   #119668  /  #21
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Living critters composed of tissues are not known for their durability, which is why they always end up dying.
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Old 07-31-2008, 03:51 AM   #119712  /  #22
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Originally Posted by ck1 View Post
It seems to me that it does not matter how many analyses you and your girlfriend do, or what you think other professional paleontologists have to say, if none of you are willing to publish your critiques and subject those critiques to public review.

Until you (or someone else) does so, the results stand.
Well, as I said, there's already been one major criticism published, and here's a second. This is a case right now where all of their results are highly questionable; their data is highly susceptible to contamination, and a more likely explanation has been proposed in the literature. At this point, any additional criticism is beating a dead horse. Perhaps a criticism of Organ et al.'s methods is in order, but that criticism honestly would have to take the stance of "hey, look, Organ doesn't know the first thing about phylogenetic analysis and biased his analysis from the get-go," not a particularly sexy piece of information, and something that anyone who knows two or three things about the field would be able to pick up without needing it spelled out. The only reason we wrote the program in the first place was because we were bored and we wanted to know with what sort of certainty we could say that the sequence fragments were human contaminants. The response to the Asara et al (2007) paper was sufficient to demonstrate that there was a significant risk of contamination.
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Old 07-31-2008, 04:07 AM   #119714  /  #23
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Science publishes it because they know it'll end up in the newspapers. When it ends up in newspapers, the creationists masturbate to it, so it gets smeared all over the blogosphere. Doesn't mean there's a drop of reproducible science in it, though.
This is certainly as extreme an anti-science statement as anything said by supersport or Dave.
Bullshit. Plenty of journals make editorial decisions that have nothing to do with the quality of the research being published. Science is one of these, and extraneous requirements, such as the requirement that you have not presented the material already in meeting format at any stage of the research. The research that ends up in these journals is generally not the top top quality research in the field, but it generally is the research that has the greatest public interest.

Pointing out that the journal Science tends to be overly enthusiastic about publishing newsworthy studies and emphasizes results while underemphasizing methods and data is like pointing out that there are certain scientists who routinely publish large portions of their work in their own journals or journals where they serve on the editorial board. It happens, and generally it's not an issue, but sometimes shit gets through. There were assertions made in a number of the papers from the Schweitzer groups that were not backed up in any meaningful way, such as the fact that none of the fossils were contaminated when anyone who has worked with DNA, RNA, and protein knows how very fucking easy it is to contaminate a sample. These sorts of things should have been caught in review. They weren't.
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Old 07-31-2008, 07:47 AM   #119774  /  #24
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It would be tidy to find that the antibodies that reacted with the "dinosaur protein" also reacted with likely film-forming organisms (or their decay products)
Let's hope it doesn't. That would be a really crappy reagent to use in work like this.
I can't just bring to mind whether they used monoclonal antibodies or polyclonals.

Polyclonals or hyperimmune antisera can often have unexpected reactivities, and even monoclonal antibodies sometimes do - I had one supposed to be specific to the lipopolysaccharide of a certain bacterial genus, and it cross-reacted strongly with a non-LPS antigen of one species of a totally unrelated genus

I've learnt to maintain due skepticism when dealing with immunochemistry
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Old 07-31-2008, 08:29 AM   #119782  /  #25
SteveF
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Our study was first and foremost a physical survey of these specimens because SEM’s etc. were the tools at our disposal. The intricate geochemistry/biochemistry is not our area of expertise and hence we have not commented on this. We are quite happy to accept the protein work at face value.

The only thing we questioned is the quantity of detected dino protein. A femptogram of protein does not seem to be enough to make the branching tubes we have both shown.

One carbon date is not enough to hang your hat on. We found that out when we called and they said “you only want one!?”. We had to spend our own money so one was it. We reported what came back and as you see, we didn’t say much more about it. Once a biofilm is mineralized it could be any age in our opinion. Since the biofilms cover the framboids, we think the framboids came first and could be REALLY old.

I think realistically it’s going to take a third party to come in with the proper team that can look at both sets of data and formulate the proper tests (as your already discussing). It’s not within our capability to take it much farther and we welcome others to do so. Our SEM stubs will be available at the Burke in a few weeks and if anyone wants a piece of our bones just email me.
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biofilms vs collagen, john asara, peer review, preserved dinosaur tissue, quality of journals, quality of papers, reviewing papers, science by press release

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