Dinosaur soft tissue--just bacterial biofilm?
An interesting new paper is just out today in PLoS ONE. You recall the announcement a few years back that soft tissue that resembled organic tissue had been isolated from a Tyrannosaurus femur. This started off a huge controversy in the field (and beyond)--researchers disagreeing with each other whether the structures seen were indeed blood cells and vessels; creationists crowing about how this finding represented "proof" that the earth was indeed young and dinosaurs had existed just a few thousand years ago; and of course, talk of cloning and DNA analysis. On the side of "soft tissue = dino blood" were findings that reported identification of the iron-containing protein heme (potentially from the red blood cells) and morphology of cells and vessels similar to that seen in modern-day ostriches and emu. However, the new paper by Kaye et al. provides an alternative explanation: that the structures aren't actual vessels and cells, but are instead iron-rich bacterial biofilms. Read the rest over at Aetiology...
109 Comments
Gary Hurd · 30 July 2008
Fascinating. Maybe I will need to write an update. Thanks for the post.
chuck · 30 July 2008
The original report was spun as physical evidence for creation.
How many nanoseconds before this opposing one is spun as physical evidence for creation?
Frank J · 30 July 2008
GuyeFaux · 30 July 2008
Just pointing out a typo in the second sentence: "structures scene" should be "structures seen".
Mike Elzinga · 30 July 2008
karl · 30 July 2008
Creationists spun this a lot as "soft tissue! dna! none of this could survive 60 million years!" One needed a very long, detailed explanation as to why that was a gross over simplification.
However, it was also the best friend of evolutionists as we could point out proteins matched closest to chickens. Hence, prediction, testing, and confirmation of the birds from dinosaurs hypothesis.
chuck · 30 July 2008
Then how many nanoseconds before they complete the trifecta and spin the fact that the reports disagree as evidence for creation? ;)
Frank J · 30 July 2008
Wheels · 30 July 2008
Gary Hurd · 30 July 2008
Eric Finn · 30 July 2008
Since bacterial biofilms are formed in water-surface boundaries, we must conclude that the biofilms are ancient, but well preserved.
It this a correct statement?
Regards
Eric
Gary Hurd · 30 July 2008
Gary Hurd · 30 July 2008
Gary Hurd · 30 July 2008
OHOHOH
The amino acids are racemic! This means that the sources of the bacterial amino acids are ancient, and (IMHO) the bacteria were probably using both L- and D- aa's anyway.
Draconiz · 30 July 2008
Gary Hurd · 30 July 2008
jk · 30 July 2008
I have a small problem with this. Didn't they sequence proteins from that tissue, and positively identify it as the same 'substitute' bone tissue that female birds produce during ovulation? A form of collagen, wasn't it? I'm confused...
jk · 30 July 2008
I had missed some of those other comments. Are we talking about two different finds?
Eric Finn · 30 July 2008
Gary Hurd · 30 July 2008
Gary Hurd · 30 July 2008
Racemization would be wandering rather far form the OP. However, racemic peptides are not uncommon in bacteria. In fact L- and D- amino acids are found in all life, including humans. See my comment on this re: abiogenesis, also Here, and Here.
jk · 30 July 2008
Gary Hurd · 30 July 2008
Gary Hurd · 30 July 2008
Eric Finn · 30 July 2008
bornagain77 · 30 July 2008
The Cambrian Explosion - Darwin's Worst Nightmare
http://www.godtube.com/view_video.php?viewkey=13d268e7356e095e9cad
GuyeFaux · 30 July 2008
And the banana is the atheist's worst nightmare.
Gary Hurd · 30 July 2008
PS: There is an interesting defense by Asara and Schweitzer of their "protein" sequences against the criticism by Buckley et al.
Science 4 January 2008:
Vol. 319. no. 5859, p. 33
DOI: 10.1126/science.1147364
Technical Comments
"Response to Comment on "Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry"
John M. Asara and Mary H. Schweitzer
Science 4 January 2008:
Vol. 319. no. 5859, p. 33
DOI: 10.1126/science.1147046
Technical Comments
"Comment on "Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry"
Mike Buckley et al.
Gary Hurd · 30 July 2008
what creationists do with a bananaanana...
HR Pufnstuf · 30 July 2008
Jackelope King · 30 July 2008
Frank J · 30 July 2008
prof weird · 30 July 2008
iml8 · 30 July 2008
Tom Kaye · 30 July 2008
Hello All,
Tom Kaye from the PLoS paper signing in. I see there is the usual ID spam going on but if we can work around that I am willing to answer any reasonable questions.
Thanks
Tom Kaye
GuyeFaux · 30 July 2008
Gary Hurd · 30 July 2008
Science Avenger · 30 July 2008
James F · 30 July 2008
Tom Kaye · 30 July 2008
Howdy, Tom. I have read you paper through only once, and haven't done the close reading. I did wonder if you had sent an draft to Schweitzer for comment.
Hi Gary,
No we didn't send a final copy but Mary and I had an almost hour long conversation at my poster in 2006. There was nothing new in the manuscript and we figured for sure she would be a reviewer.
Tom
Gary Hurd · 30 July 2008
The most obvious counter argument I would expect from Schweitzer, and one I actually suspect to be true, is that you have found specimens that have been contaminated recently, and that is all. Schweitzer will reply that her samples were not contaminated recently, as demonstrated by a racemic aa mix from her extracted material.
So, she might conclude that the most you have shown is a potential mechanism for the formation of the features she has analyzed. (I mentioned this earlier in the thread.)
If you still have voucher material, I suggest a racimization check. I have no doubt about the racimization result given that your radiocarbon analysis showed a post-atomic result. But, I'd do it anyway.
Tom Kaye · 30 July 2008
Draconiz · 30 July 2008
Hello Kaye, I greatly appreciate the fact that you are here.
I just want to clarify
1. whether this research
http://www.sciencedaily.com/releases/2008/04/080424140418.htm
use the T-rex specimen or not and what are the implications of this discovery.
2.Are there currently any other Genetic or molecular evidence concerning Dinosaur-bird ancestry?
Thank you
Don
PS.
Dear Gary,
I just have to ask him again, I apologize if you feel offended.
Don.
Draconiz · 30 July 2008
Indicating Dinosaur-bird ancestry.
Sorry, it has been a long day,
iml8 · 30 July 2008
Gary Hurd · 30 July 2008
I would next expect that Asara will argue that they were looking at actual sequence data and not merely an IR. (I must say that I found your IR data most striking).
However, given the immuno data of Schweitzer, I just don't see a way that a "biofilm" has the specificity for an avian v.s. crocodilian v.s. rabbit (IIRC) result.
I am very interested in your results, as I have written a bit about this over the years.
Tom Kaye · 30 July 2008
Draconiz · 30 July 2008
Dear Tom.
Thanks, I just used the study as an evidence for common ancestry between Dinosaurs and birds. If any creotard tries to spin this study to refute me I can use your response as a reply to them.
I owe you a beer. :p
Don
Gary Hurd · 30 July 2008
I have a dinner break from the 'intertudes.' See you in an hour or so.
Tom Kaye · 30 July 2008
Gary Hurd · 30 July 2008
AMS dates are not cheap, although the price has come down a lot since the 1980s. A real problem is that they use such small samples, any contamination is going to totally blow your date. I had one kid working for me as field crew, and he insisted on smoking in or around his unit. I took one C14 sample from material he collected and it was 500 years younger than any other data from that site.
Potentially, exposure to air could contaminate an organic rich material. I prefer using charcoal, or collagen. But, your results have an important implication there as well. If there is a significant bacterial load that is actively metabolizing modern carbon, and appears to behave like bone collagen, many other C14 dates might be younger than the parent bones really are.
That might be a funding angle all by itself. (I work for 5% plus beer).
Michael J · 30 July 2008
It looks like that there are still questions unanswered but if it ends up being biofilm then using CSI and EF I make three predictions:
1. Some creationists for the next 20 years will still say "what about the soft tissue found in the dinosaur fossils"
2. Others will say that that this is another example of Darwinist Hoaxes just like the butterflies
3. Others will say that see science is wrong again, the Bible is the only source of truth
DistendedPendulusFrenulum · 30 July 2008
stevaroni · 30 July 2008
Stanton · 30 July 2008
Stanton · 30 July 2008
DistendedPendulusFrenulum · 30 July 2008
stevaroni · 30 July 2008
I am always struck by the way that an offhand comment on Pandas Thumb will, sometimes within minutes, bring out detailed information on almost any subject related to biology, physics or engineering.
In the space of maybe 4 hours, I've learned more about bananas than I have in the whole rest of my life.
Whenever one of us quoted a fact sloppily, someone else corrected it with a detailed reference.
Compare that to the typical chain of informed "discussions" over on the ID blogs, where most conversations begin and end with bronze-age religious texts as authoritative sources.
I have seen sciences "peer review" at work, and I have seen IDs "peer review" at work, and they are two distinctly different things.
Slarty Bardfast · 31 July 2008
Frank J · 31 July 2008
Frank J · 31 July 2008
iml8 · 31 July 2008
Frank J · 31 July 2008
iml8:
I should add that I don't recommend copying all, or even a majority, of "Paley's" methods. But there are a few lessons that we can even learn from - gasp - people like Dembski. The ought-to-be-obvious one is "don't take the bait." Or - pardon the mixed metaphor - "don't feed trolls."
Jon Fleming · 31 July 2008
ryan cuggy · 31 July 2008
ryan cuggy · 31 July 2008
one day, I will remember to use the appropriate tags on the for the appropriate software.
ryan cuggy · 31 July 2008
...and maybe even remember to hit backspace. /facepalm
jackstraw · 31 July 2008
iml8 · 31 July 2008
Frank J · 31 July 2008
Gary Hurd · 31 July 2008
I looked a bit into bacteria living in rock, particularly meteorite, for a review I wrote of Walt Brown's creationist book, In the Beginning: Compelling Evidence for Creation and the Flood.
Giuseppe Geraci et al., “Microbes in Rocks and Meteorites,” (Rendiconti Accademia Nazionale dei Lincei, Vol. 12, No. 9, 2001, p. 51) claims to have documented living bacterial colonies in meteors. This article was published with a long list of objections and cautions that its conclusions were provisional, and that there were many doubts regarding methods used by the principal investigators. Forty years of meteorite investigations have always found terrestrial contamination to be the source of microorganisms found in meteorites, e.g. “Bacterial Contamination of Some Carbonaceous Meteorites” J. ORO T. TORNABENE (1965 SCIENCE, VOL. 150, pg. 1047-1048). The probability of contamination increases in direct proportion to the amount of handling the samples are subjected to under unsterile conditions. The two meteorite samples examined by Giuseppe Geraci had been recovered, handled and publicly displayed in museums for many decades, one for over a century.
Tom (if you check back), my last question is, "What were the curation conditions of the examined fossils used in Kaye et al?" I don't see this data in your paper.
stevaroni · 31 July 2008
Tom Kaye · 31 July 2008
Gary Hurd · 31 July 2008
Tom Kaye replied to me in an email, and he invited me to share the details here.
He and his team excavated all the materials they tested over the course of time. The paleo speciments were stored in a warehouse in ziploc bags until they were selected for this analysis.
Thanks.
Eric Finn · 31 July 2008
Frank J · 31 July 2008
Eric Finn · 31 July 2008
Eupraxsopher · 31 July 2008
The Cambrian explosion is kind of a horrible term, as the variety of organisms likely still came about by gradual evolution. The 'sudden' appearance of myriad fauna may have more to do with the chance amount of fossiliferous rock preserved in that time. We only get glimpses.
Frank J · 31 July 2008
Eric Finn · 31 July 2008
Peter Henderson · 31 July 2008
Eric Finn · 31 July 2008
Frank J · 31 July 2008
GSLamb · 31 July 2008
Every time I read "Cambrian explosion" I imagine groups of stunned dinosaurs violently flying into bits.
I'm sure images like that would keep Darwin up at night, but this would hardly be his worst nightmare.
Kevin B · 31 July 2008
iml8 · 31 July 2008
Henry J · 31 July 2008
I.D. = evolved Creationism.
(Or would "devolved" work better there?)
I tend to use "anti-evolutionist" for the generic label.
Henry
GuyeFaux · 31 July 2008
Saddlebred · 31 July 2008
Steven Salzberg · 31 July 2008
Seven protein fragments were originally reported in 2007 (in Science) by Asara, Schweitzer, and colleagues. However, this study was poorly done and has come under criticism by other scientists who are more expert in mass spectrometry than either Asara or Schweitzer (neither of whom is an expert on interpretation of mass spec data). As a result they revised (in a letter to Science in Sept 2007) one of their interpretations, reducing the number of supposed T. rex fragments to 6. Gary Hurd points out a further discussion - printed in a technical letter to Science in January 2008 - that was pretty devastating to Asara and Schweitzer's claims. Essentially, they didn't perform adequate tests to show that the T. rex DNA was truly ancient, and it almost certainly was a contaminent. Further evidence - re-analysis of the original mass spec data - is likely to show that the protein fragments don't match birds particularly well (as the original article claimed), but instead match bacteria even better. Other articles are pending (not by me) that will make this argument more clearly.
MPW · 31 July 2008
Gary Hurd · 31 July 2008
Kevin B · 1 August 2008
Frank J · 1 August 2008
David Stanton · 1 August 2008
Frank J,
I'm with you on this. I think we should use the terms "creationism" and "creationist" and object strongly to the common usage of the terms "evolutionism" and "evolutionist". This is more important than the benefits of any shorthand usage.
I also like to refer to ID specifically as a type of creationism. While you might be correct that, technically speaking, this is not entirely accurate, given the duplicitious nature of ID advocates, it certainly is appropriate as a descriptor of the origin and true motivation of most individuals who identify themselves as ID supporters. Why should we help them perpatrate a scam?
Of course, I think we should also be very careful to use the term "hypothesis" whenever appropriate as well. That would certainly help our cause. I cringe when I hear the inapporpriate use of the term "theory" as I did on CSI last night. I love to use that show as an example of how science works.
This is a PR battle, at least in part, and we shouldn't roll over and play dead when some dipstick tries to swiftboat entire fields of science just to get the chance to brainwash young children at taxpayer expense.
Frank J · 1 August 2008
David Stanton,
I use "Darwinism/Darwinists" and "evolutionists" only in quotes. "Evolutionism" is a story in itself; I never leave it to the context to suggest that I am mocking it.
As for "creationism/creationists", the most important distinction ought to be between the anti-evolution activists and the "rank and file believers." There really is no "rank and file IDer"; they are either some "kind" of creationist (including Omphalos) or maybe a TE who has more sympathy for the political/religious ideology of the activists than with mainstream science (which has no ideology). Also, when I say "IDer" I mean "anti-evolution activist who prefers the 'don't ask, don't tell what the designer did when' approach.
Bottom line, never say "creationism/creationists" without specifying what "kind" if there are people listening/reading who define it as "honest belief/believers in a ~6000 year ago creation" and others who define it as "any strategy/strategist that misrepresents evolution and proposes a design-based alternative."
Frank J · 1 August 2008
Ouch. See how easy it is to lazily say "creationist"?!
Please change "..some 'kind' of creationist.." in the middle paragraph of my 10:21 comment to "..some 'kind' of believer of classic creationism..".
Once again in case anyone didn't notice: By "classic creationism" I mean YEC or OEC, IOW, an anti-evolution position that specifically denies common descent and makes testable statements of basic "whats" and "whens" of natural history.
Gary Hurd · 1 August 2008
Steven Salzberg http://genefinding.blogspot.com/2008/07/preserved-t-rex-or-bad-science.htmlhas some further thoughts about Schweitzer's research that I recommend.
Gary Hurd · 1 August 2008
Steven Salzberg has some further thoughts about Schweitzer's research that I recommend.
Henry J · 1 August 2008
Yeah, that "evolved Creationism" analogy doesn't really work, does it. It analogy doesn't work when somebody goes and actually examines the details - why'd somebody have to go and do that, it's like they're tying to do science or something. Oh wait...
Henry
David Willis · 15 September 2008
To Tom Kaye,
I noticed this from 7/30: "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."
What is your explanation of your getting a 135% of modern content result? And why do you think it is relevant at all to C14 test the bacterial scales taken from the surface of a dino bone (as I recall, that is where they came from)...if you intent is to prove the age of the material found deep inside a bone after it has been demineralized? Surface formations by bacteria on a dino bone would be expected to give modern C14 dates I would think and therefore would be irrelevant no matter what date you got. Sorry to say it but IMO you wasted your money.
What WOULD be useful perhaps is to get some of the actual stretchy tissue inside the bone of a dino and C14 date THAT. Of course when C14 is found, as I expect it would be, even if it is far above the sensitivity thresholds of the AMS equipment, it will "have" to be attributed to contamination. Why would that not be the explanation for your C14 date...especially since it came back with an impossible number of 135%?
David Willis · 15 September 2008
Also to Tom Kaye,
I believe that your article must do more than simply suggest SIMILARITIES to biofilms...if you are going to refute the claim the tissues are dinosaurian. Wouldn't they have to be indistinguishable rather than just similar? In other words, if we had the "blood vessels" which MS found sitting side by side with the biofilm tubes you studied, and they both were stretchy and tubular...but had other very definite distinctive differences, wouldn't we have to say that you have not successfully explained the features as being from bacteria? In my opinion based on your photos and hers, the framboids you identified as inorganic don't look much like the "blood cells" she ID'd. Those spheres you showed with no nuclei don't look much like the fat discs she found WITH nuclei.
Also, I apologize for using "scales" and 135% in my prior post. I just checked your article and you reported 139% and also said the material C14 tested was from "coatings" which "appreared to be dislodged" after being pressure fractured. I am wondering if you could identify for sure that the single sample you tested came from inside the bone, since you said "APPEARED". Also, even if some bones do have biofilms inside the vascular canal walls, which are indeed formed by modern bacteria, that would not mean necessarily that what Dr. S found was only that would it? I mean she could have found true dino tissue AND there could also be modern bacteria in her vascular spaces of her samples.
One more point. What may be the most astonishing part of her work was the 4th point in the list of the 4 things she found, but you only were able to find similarities to the first 3 (in your opinion) with your work. Do you agree that you found nothing that would resemble the 4th? Here is what you wrote:
Four categories of tissues were initially discovered in 2005 [1]: (A) Clusters of spheres that showed an iron-oxygen elemental signature appeared red under the light microscope. (B) Soft, branching, tube-like structures that contained spheres. (C) Free floating “osteocytes” complete with fillapodia and (D) a filamentous mass that remained pliable and elastic. Subsequent tests using immunochemistry showed positive for proteins [3]. Three of these structures were found commonly in this survey and discussed below.
Thanks.
Mike · 24 June 2009
The dinosaur thing is a joke at Harvard, we all know the shanigans in research misconduct that occurs frequently there. . Shitzers and Asora's research is a hoax, or certainly misrepresentation. The tissues are porous ---liquids go through them. how this collagen tissue remain for 80,000,000 years?!?!!? Can federally subsidized (tax payer, white collar welfare) can Shitzer and Asora please explain this. thanks.
Henry J · 24 June 2009
Whether the tissue stays porous after death is a different question than whether it's porous while the organism was alive.
Henry
Henry J · 25 June 2009
test
David Willis · 9 October 2009
You guys trashing MS/Asara and praising Kaye need to read the 5/09 SCIENCE. In it a separate lab CONFIRMED that MS's group were right in IDing dino collagen. "Contamination" ain't gonna save the day for you.
wile_coyote · 9 October 2009
Y'know, they REALLY oughta lock down these threads after 90 days. If you don't you just get some passerby kicking on a dead horse.
SWT · 9 October 2009
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