Dinosaur soft tissue–just bacterial biofilm?

| 109 Comments

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

Fascinating. Maybe I will need to write an update. Thanks for the post.

The original report was spun as physical evidence for creation.

How many nanoseconds before this opposing one is spun as physical evidence for creation?

chuck Wrote:

How many nanoseconds before this opposing one is spun as physical evidence for creation?

Not many, but when it happens it will be another opportunity to (1) get YECs and OECs/IDers to challenge each other, or (2) not let another evasion of their irreconcilable differences go unnoticed.

Just pointing out a typo in the second sentence: “structures scene” should be “structures seen”.

chuck said:

The original report was spun as physical evidence for creation.

How many nanoseconds before this opposing one is spun as physical evidence for creation?

And you can bet that, if they do try to spin it, they will make it appear that science is in disarray and that ID/Creationists noticed this first.

They will not mention that this is the normal process of scientific vetting, and they certainly will cover up the fact that ID/Creationists never ever admit contrary evidence once their own “research” has concluded that the data support ID/Creationism.

(Sorry if this double posts. The screen locked up the first time through)

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.

Then how many nanoseconds before they complete the trifecta and spin the fact that the reports disagree as evidence for creation? ;)

Mike Elzinga Wrote:

And you can bet that, if they do try to spin it, they will make it appear that science is in disarray and that ID/Creationists noticed this first.

IDers might quote mine it to support their “‘Darwinists’ are in disarray” nonsense, but will conveniently leave out the fact that they do not consider it evidence for a young Earth or a young biosphere. And they will of course leave out the fact that the mismatched spin is clear indication that it is the ID/Creationists who are in hopeless disarray. Except in the area of fooling the public, alas, where they have “self-organized” into a “conspiracy” (the big tent) without overarching “design.” IOW, despite the occasional criticism of the ID strategy by YEC groups.

karl said: 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.

Yeah, I was wondering about that: the comparison between the organic materials and chicken collagen proteins. I guess that throws the chicken/T. rex comparison into question?

chuck said:

The original report was spun as physical evidence for creation.

How many nanoseconds before this opposing one is spun as physical evidence for creation?

Alternately, the creationists might insist this is an effort to supress the “damage” that so-called soft tissue preservation does to science. Schweitzer, and her colleagues will undoubtedly defend their results, which creationists will distort into the evilutionist thought police attempting to silence Schweitzer (who happens to be an evangelical Christian).

There were two early papers by Schweitzer that I recall to have addressed some of the arguments in the PLOS article, specifically pyritic framboids were discussed in one of the PNAS articles. The new energy dispersive spectroscopy (EDS) results seem conclusive that the “blood cells” were framboids. I asked Schweitzer if she would be interested in a trace element analysis by scaning tunneling microsopy of her dissertaion material, but she had basically used it all up, and there were no voucher specimens for further analysis. This was too bad, but not a surprise given the number of different studies that had been done on what was very little bone.

There was also an amino acid racemization result that I thought clearly argued against modern contamination. Also several times she (or coauthors) have at least mentioned the notion that bacteria could have “reworked” the original material (IIRC). The new paper does not seem to account for the immunological data, either from her dissertation or the later work she published. However, the infrared spectra in Fig 9 of Kaye et al 2008 holds considerable interest with implications to other studies of fossil collagen, eg;

Embery G, Milner AC, Waddington RJ, Hall RC, Langley MS, Milan AM. 2003 “Identification of proteinaceous material in the bone of the dinosaur Iguanodon” Connect Tissue Res Vol. 44 Supplement 1: 41-6.

Gurley, L., Valdez, J.G, Spall, W.D., Smith, B.F., and Gillette, D.D. 1991 “Proteins in the fossil bone of the dinosaur, Seismosaurus” Journal of Protein Chemistry, 0(1): 75-90.

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

As I recalled:

Schweitzer and Horner (1999) addresses this issue of cellular preservation directly. The observed structures are not red blood cells -

Clearly these structures are not functional cells. However, one possibility is that they represent diagenetic alteration of original blood remnants, such as complexes of hemoglobin breakdown products, a possibility supported by other data that demonstrate that organic components remain in these dinosaur tissues.

And

Although they are not consistent with pyrite framboids, they may indeed be geological in origin, derived from some process as yet undefined; they may have their origin as colonies of iron-concentrating bacteria or fungal spores, or they may be the result of cellular debris, which clumped upon death, became desiccated, and then through diagenetic processes such as anion exchange or others not yet elucidated, became complexed with other, secondary degradation products. Schweitzer and Horner (1999: 189).

Schweitzer, Mary Higby, John R. Horner 1999 Intrasvascular microstructures in trabecular bone tissues of Tyrannosaurus rex, Annales de Paléontologie Volume 85, Issue 3, July-September , pg.179-192.

See also Dino-blood and the Young Earth

Eric Finn said:

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

Well, how about this: The organics, including bacteria, were of ancient source. The bacteria persist as spores over vast periods of time whe nthe bone is dessicated, but periodically the bone is saturated and they reactivate with less and less success due to our old friend, the second law. The resulting biofilm is unusually hardy more like a massively cross linked plastic than a tissue.

I like it!

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.

Wheels said:

karl said: 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.

Yeah, I was wondering about that: the comparison between the organic materials and chicken collagen proteins. I guess that throws the chicken/T. rex comparison into question?

I think it was a separate experiment. For the chicken-T-rex experiment,the scraps of dinosaur protein were wrested from a fossil femur discovered in 2003. While the Femur was discovered in 2005.

Hope it helps

Draconiz said:

I think it was a separate experiment. For the chicken-T-rex experiment,the scraps of dinosaur protein were wrested from a fossil femur discovered in 2003. While the Femur was discovered in 2005.

Hope it helps

Actually, Schweitzer has immuno data for both MOR 1125 T. rex, and from her dissertation’s material from entirely separate bone (See Dino-blood and the Young Earth)

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…

I had missed some of those other comments. Are we talking about two different finds?

Gary Hurd said:

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.

I am not sure I understand this.

I thought that only L-enantiomers were used since much earlier than 100 million years ago. Are there other explanations for the amino acid racemization?

Regards

Eric

jk said:

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…

Yep, you are confused. No proteins were ever sequenced. The medulary bone is a hard tissue, not a protein and is obvious to visual and micorscopic examination.

I have tried to make a simplified version of the results, plus refuting the creationist dribble of Schweitzer’s last round of papers in Dino Blood Redux. You will also find the references to the original papers relevant to the “soft tissue.”

The Medulary bone papers were in Science and PNAS, and are free to download.

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.

this is why I’m confused:

http://news.nationalgeographic.com/[…]tissues.html

…this article is totally erroneous?

Gary Hurd said:

jk said:

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…

Yep, you are confused. No proteins were ever sequenced. The medulary bone is a hard tissue, not a protein and is obvious to visual and micorscopic examination.

I have tried to make a simplified version of the results, plus refuting the creationist dribble of Schweitzer’s last round of papers in Dino Blood Redux. You will also find the references to the original papers relevant to the “soft tissue.”

The Medulary bone papers were in Science and PNAS, and are free to download.

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jk said:

this is why I’m confused:

http://news.nationalgeographic.com/[…]tissues.html

…this article is totally erroneous?

I see where you are comming from now. The key quote is (IMNHO), “Asara’s team isolated seven fragmentary chains of amino acids.” These were exactly that and no more- 7 fragments of something with amino acids. They were not exclucively attributable to proteins, and so I won’t call them proteins. That didn’t stop Asara, and it might come back to bite him. (Not hard- he has tenure).

The gross irony is that in Schweitzer’s dissertation material, she actually had something that was probably a 20 to 30 aa residue. But no sequencing was done.

Gary Hurd said:

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.

OK, thanks for taking the time to reply!

Regards

Eric

The Cambrian Explosion - Darwin’s Worst Nightmare

http://www.godtube.com/view_video.p[…]356e095e9cad

And the banana is the atheist’s worst nightmare.

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.

The propagandists for the religion of evolutionism thought that the existence of soft dinsaur tissue would win them more converts until Christians pointed out what that would mean for their “millions of years” fantasy–so now, they are in backtrack mode!

From the paper:

An experiment was conducted to compare infrared spectra of modern biofilms with modern collagen and fossil bone coatings. Modern biofilms were grown on microscope slides from local pond water with high iron content. These slides developed EDS signatures of iron contamination within 2 weeks of formation. Sample coatings from fossil turtle carapace were submitted to infrared spectroscopy and compared to spectra of modern biofilms and modern collagen (Fig. 9). Fourier cross-correlation showed an 83% match between modern biofilms and fossil specimen with only a 37% correlation to modern collagen. This experiment suggests that modern biofilms share a closer molecular make-up than modern collagen to the coatings from fossil bones.

What a bunch of rubbish! They are just emissions from the part of the spectrum that confirms their pre-conceived conclusion! Why not visible? Why not ultraviolet? Why not x-ray? Hmmmm

Of course, the real reason comes through later on:

The third structures recovered from the acid baths, were free floating osteocytes complete with fillapodia . (Fig. 10, A and B). Freshly fractured bone shows cross sections though many lacunae. SEM investigation of these lacunae before acid dissolution yielded the following results. Figures 10, C, D and E are several examples of material contained in the original lacunae. The variety of forms found (even in the same bone), indicates that the lacunae are not isolated pockets of exceptional preservation. The structures present are sub-micron spheres and rods, which are morphologically consistent with bacterial structures.

We have an assumption that anything preserved from the so-called dinosaur age requires some “extraordinary preservation” requiring “millions of years.” What a crock! Old-earth, evolutionary question begging at its finest!

Gary Hurd said:

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.

Seriously?

Where’d you bury the body?

MPW said:

Gary Hurd said:

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.

Seriously?

Where’d you bury the body?

I just reported the data in a footnote, and never hired him again. Years later, the same sort of sloppy work caused me to sever a partnership. I did OK on the money end, and avoided being professionally associated with fools.

Henry J said:

I.D. = evolved Creationism.

(Or would “devolved” work better there?)

I tend to use “anti-evolutionist” for the generic label.

Henry

I thought it was firmly established that ID didn’t “evolve” from creationism. It was done by conscious design by the authors of “Of Pandas and People” with a text editor.

GyueFaux Wrote:

It’s slightly perverse but we should just start calling them “Darwinists”. After all, they’re the ones religiously obsessed with what Darwin said or believed. It’s always them prefacing with “Darwin thought this”, “Darwin never knew that”, “Darwin’s Black Box”, “Was Darwin Wrong?”, etc. etc. It’s a masochistic sort of idolatry.

I’d be your biggest backer. But alas, you have less of a chance of than happening that I have of fellow critics agreeing that ID is not “creationism” (but nevertheless a pseudoscience that indirectly promotes it). I can’t even get pro-science people to stop using the word “Darwinism.” They don’t just ignore me, but even defend it’s use; their defense reads like “it’s my foot, and I’ll shoot it if I want to.”

The bigger issue is how words and definitions are established. Even those who reject “memetics” will admit that it’s a “bottom up” approach, and not by overarching “design”. It starts small and unnoticed, then “catches on.” Sound familiar? Many “Darwinists” (pro- and anti-evolution “kinds”) will disagree, but I think that linguistic evolution is more than just an analogy of biological evolution - it’s part of it. On that note…

Henry J Wrote:

I.D. = evolved Creationism.

While the post-Dover (and “cdesign proponentsists”) books apparently analyze it in more detail, the “speciation” of creationism into classic creationism and ID is outlined in “Tower of Babel” (Robert T. Pennock, 1999). In the same book he discusses linguistic evolution as a way introduce biological evolution to those who object to it but are not beyond hope.

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.

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.”

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.

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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

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%?

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.

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.

Whether the tissue stays porous after death is a different question than whether it’s porous while the organism was alive.

Henry

test

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.

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.

wile_coyote said:

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.

Well, we are back in the academic year … time for a new batch of students to earn their creationist course credits. What safer way to enter the lion’s den than to wait until the lions have moved on to another den?

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