i-c06ff96a2dc1f3c426ffc100f1ec4490-ugly_fact_kills_beautiful_hypothesis.jpg

An ugly fact killing a beautiful hypothesis
I’m not mentioning any names, and don’t ask me any details. In fact, don’t repeat this story.

Some years ago, when I was a mere graduate student, a fellow student working in an unnamed country in Africa discovered a very very old stone artifact. To this day, this bit of chipped stone debris, representing the activities of an ancient very pre-human hominid, is one of the oldest well dated, in situ objects of its kind known.

The stone had some yeck on it, and for giggles, this stone got passed on to a physicist who had invented a new way of looking at small things. He was going to look at the tool to see what the yeck was. I should point out that this physicist had no knowledge to speak of of either archaeology or geology.

Right away results came back clearly indicating that the yeck was made of apatite. Apatite is, of course, the primary mineral constituent of bone. Was this a piece of ancient bone jammed into the micro-bumpy surface of an ancient stone tool?

My colleague, the student who had found this bone, knew that this was very unlikely. He had reasons to believe that this was not going to go anywhere, and he indicated those reasons to his adviser, a gentleman we shall refer to here as … let’s see … Bruce. Bruce did not want to hear the student’s objections … this was too exciting of a find to not blunder ahead with! Indeed, Bruce gathered up two highly respected level headed experts on related topics (me and someone else) and dragged us over to meet the physicist and get the story straight from him. The five of us sat in the physicist’s office …. The student, we two experts, the physicist, and Bruce …. and heard the story, learned about the technique, reviewed the data, discussed the findings. Then we left.

Blogging on Peer-Reviewed Research

On the way back, the other expert knew enough to keep silent. I, however, did not. I said “Bruce, you know, the chances of this apatite being from animal bone are about zero. How much apatite is in the geological formation these artifacts are from, do we know?

That was the last time Bruce would listen to my advice on anything. He begrudgingly let me hang around on the project that I was still working on, but the next iteration of a jointly authored paper that I had worked on (far more than Bruce had) suddenly did not have my name on it any more. I was disinvited to further meetings to discuss the research program. I had become persona non gratis in Bruce’s eyes.

A month later, I was in an unnamed African country …. the same country that these artifacts had been found. I had been sent by Bruce to deliver some stuff (or pick up some stuff, can’t remember) to a particular location where I ran into the gentleman who at the time was probably the most authoritative expert on the geology of the region. When he saw me, he said “SO, what’s this big secret Bruce has … some great find or another?” Not considering what we were doing a particular secret, I said “Oh that. So and so has a stone tool that this and that technique indicates has bits of apatite smeared into it. Bruce is pretty sure it’s bone.”

Mr Famous Geologist laughed and laughed. When he recovered from this bit of news he said what I, by that time, already knew: “Bruce …. he can be a dumb as a sheep. Apatite is the most common mineral in those deposits. Even with a good scrubbing, there’s going to be bits of Apatite on everything.”

i-f1cec05bdd72c0c9daf4a85cd5f8fc65-not_blood_cells.jpg

An iron oxide framboid cluster (a natural geological thingie) in dinosaur bone. These clusters resemble red blood cells in size and shape, but they are mineralogical, not biological, phenomena. They are found commonly in dinosaur bone.
The moral of the story? Before you invest anything … any. thing. … time, money effort, relationship building, whatever, with anyone working on a science project, make sure the person you are investing in is an actual scientist, and not a dumb sheep.

Now, let us turn our attention to a paper just out, moments ago, in PLoS. This is very simple. Previously, yeck thought to have been original tissue preserved inside dinosaur bones may not be ancient yeck after all. It radiocarbon dates to recent times, and there are perfectly good geological explanations for this yeck.

Back in 2005, research published in Science claimed that blood vessels and blood cells were found inside fossil bone of a Tyrannosaurus rex.

But now, researchers, in the current paper in PLoS, claim that the substance observed inside the dino bones is dried up biofilm. Bioflim is the brown yeck that forms on surfaces under water. Do you have a fish tank? That brown stuff that the snails eat. Since biofilm forms on surfaces, it can actually form the basis of an endocast … a fossil of the inside shape of something. In addition to endocasts, mineralogical accretions can also form inside bone tissues to resemble biological tissues.

According to Thomas Kaye, one of the study’s authors and an associate researcher at the Burke Museum of Natural History and Culture at the University of Washington, ”I believed that preserved soft tissues had been found, but I had to change my opinion…. You have to go where the science leads, and the science leads me to believe that this is bacterial biofilm.”

Kaye was not part of the original team to make the claim about preserved dinosaur tissue, but he did get on board with the idea and did some research on it. We don’t know if any graduate students got stomped on for disagreeing with The Man, but we should assume not.

source

Kaye, T.G., Gaugler, G., Sawlowicz, Z., Stepanova, A. (2008). Dinosaurian Soft Tissues Interpreted as Bacterial Biofilms. PLoS ONE, 3(7), e2808. DOI: 10.1371/journal.pone.0002808

Comments

  1. #1 megan
    July 29, 2008

    i think it’s so important for people to publish papers like this. Aside from just being good science, it shows students that it’s okay to change your mind, and that science is not, in fact, ‘fact’. it is a collection of data with the best conclusions possible at the time.

  2. #2 MikeG
    July 29, 2008

    I haven’t had to do it for such a hugely publicized case, but I hate that “Well, crap. Screwed the pooch on that one, didn’t I?” moment.

    Well, that’s why we have this self-correcting science thing set up, ain’t it?

  3. #3 Laelaps
    July 29, 2008

    Just has to come out on a day I have a paper due, doesn’t it?

    I haven’t seen it yet but I’m a little skeptical, especially since the “yeck” inside the Tyrannosaurus bones contained proteins (which can last a long time) which more closely matched that from chickens than anything else. This makes sense being that rexie was a coelurosaur and birds evolved from coelurosaurs; if it’s just “biofilm” then why are the molecular tests supporting what we know from the morphological data?

  4. #4 Karen
    July 29, 2008

    A healthy dose of “that’s waaaayyyy too good to be true” in one’s attitude also helps avoid such oopses.

  5. #5 themadlolscientist, FCD
    July 30, 2008

    Just shows to go ya, you can’t trust that yeck. It’s sneaky stuff.

  6. #6 Sigmund
    July 30, 2008

    The original research was not based on purely mass spec analysis, if I recall correctly, but on additional evidence such as immunocytochemical analysis – using monoclonal antibodies to detect the presence of protein specific epitopes. This gave far greater weight to the mass spec results. Could those vertebrate specific proteins also be present in biofilm? (I guess the alternative is that the antibody test threw up a false positive).

  7. #7 Greg Laden
    July 30, 2008

    Sigmund: Indeed. I don’t think this story is going to go to bed nice and quiet-like.

  8. #8 qbsmd
    July 30, 2008

    What is “yeck”? Google and Wikipedia aren’t being helpful.

  9. #9 megan
    July 30, 2008

    hmm. laelaps, you have me intrigued. do you know if archaeologists are using proteins in their research? and if so – how could we use them? i know nothing about them, so would finding them in pots be particularly helpful? or would it just say ‘an animal was cooked here!’

  10. #10 SteveF
    July 30, 2008

    This isn’t the only paper that has been critical of their work. For example:

    http://www.sciencemag.org/cgi/content/abstract/319/5859/33c

    Available to read here:

    http://www.simonho.org/papers/science08_buckley.pdf

  11. #11 J-Dog
    July 30, 2008

    Thanks for the post…. even though I REALLY wanted to believe in the dino blood. :(

  12. #12 Sigmund
    July 30, 2008

    Laelaps, having been involved in several mass spec experiments aimed at identifying unknown proteins I can assure you that what you mostly get are false positives.
    These are usually removed from your results to produce a ‘results’ table of putative peptide fragments. I’m pretty sure that the ‘collagen’ fragments reported in the original paper were rare overall amongst all the initial results thrown up by the analysis. As well as that only one or two of the fragments had a bird-specific sequence – at least one of the others matched lots of other species (including man!).
    This doesn’t mean its false but we are talking about extremely rare and very short sequences here that may have other possible explanations. It was the antibody evidence that looked most convincing to me.

  13. #13 gary
    July 30, 2008

    I think the real moral of the story is to try to never have a boss like Bruce! I once had a boss who got mad at me because I told him something he didn’t believe. When he found out I was right, which I knew he would, he came and apopogised.

  14. #14 themadlolscientist, FCD
    July 30, 2008

    What is “yeck”? Google and Wikipedia aren’t being helpful.

    Icky, gross, usually slimy and smelly stuff you wouldn’t want to step in, or even touch without 3 layers of surgical gloves and possibly a full-face breathing mask.

    You know, stuff like The Blob, doggy doo, and the so-called brains of Fundy Mental Cases, cdesign proponentsists, Bill DonoWTF and his one-man Catlick League (although I can’t imagine that any self-respecting cat would lick him), G-Dub-the-Shrub & Co., and Faux News wingnut commentators pundits blathering blowhards and nattering nabobs.

  15. #15 Jason Malloy
    July 30, 2008

    But now, researchers, in the current paper in PLoS, claim that the substance observed inside the dino bones is dried up biofilm.

    I suppose I should read the paper, but does it address why or how at least two papers last year found the “biofilm” contained proteins that were related to chickens?

    “The sequences are clearly from T. rex,” said John Asara of Harvard Medical School in Cambridge, Massachusetts, who led one of the studies.

    In addition, both studies found similarities between the dino sample and the bone collagen of chickens, providing molecular support for the hypothesis that modern birds are descended from dinosaurs.

    http://news.nationalgeographic.com/news/2007/04/070412-dino-tissues.html

  16. #16 AnneT
    July 30, 2008

    Yeck can be produced from chicken soup.

  17. #17 Qwerty
    July 30, 2008

    AnneT: Chicken soup is Yeck. (At least when it is from a can.)

    themadlolscientist: Kudos on the explanation of Yeck. (I think we have to capitalize it now!) I would have just said that Yeck is Yeck. (What the heck.)

  18. #18 Qwerty
    July 30, 2008

    AnneT: Chicken soup is Yeck. (At least when it is from a can.)

    themadlolscientist: Kudos on the explanation of Yeck. (I think we have to capitalize it now!) I would have just said that Yeck is Yeck. (What the heck.)

  19. #19 Steven
    August 1, 2008

    Great post, Greg! This is exactly what happened with the supposed T. rex proteins. The comment from John Asara above – “the sequences are clearly from T. rex” – is just Asara defending his own studies, not surprisingly.
    Asara is a relative novice at ancient DNA and at mass spec analysis, and his analysis of their peptide fragments was pretty clearly flawed. They still got it published in Science – but that just shows that Science sometimes publishes sloppy work if it seems exciting enough. (Sad, but true.)
    Wishful thinking doesn’t make it so. The T. rex protein fragments were almost certainly bacteria.

  20. #20 Greg Laden
    August 1, 2008

    But at least we have confirmed the relationship between Bacteria and T.Rex….. :)

  21. #21 John Asara
    September 16, 2008

    Hi All,
    Just want you to be aware that we have released the entire T. rex MS/MS dataset on the PRIDE proteomics repository at EMBL. The dataset contains 48,216 spectra and is the same dataset that was used in the recent response to Pevzner et. al. that appeared in last week’s Science. As some of you may know, he has made his discontent with the unavailability of dataset a very public display and is convinced that collagen is statistically insigificant. I wish that all of you will download the data and run your database search engine(s) of choice against an all-species database. Trypsin was used for digestion (red./alk. with iodoacetamide) and these data are from a LTQ ion trap mass spectrometer. The peptides in the database that that we know are contaminants from our lab are human keratin, BSA, IgG and casein, so you can ignore those. Besides the collagen peptides (which do not show up as contaminants in dry runs) we see a few, but not that many bacterial proteins. Not surprisingly we see a lot of masses from these rock-like structures that are almost certainly not peptidic and probably not even organic. Their fragmentation patterns match nothing in any of the forward or reverse protein data bases and the mass separations of the fragments aren’t consistent with amino acids. I hope that you enjoy the data and let me know if you have any questions. Hopefully, this will convince the naysayers that we are not hiding anything as we tend to only believe protein data that we can verify biochemically through synthetic peptide comparisons of MS/MS data and evidence with antibodies. Please let me know if you have any questions and I look forward to hearing about your results.
    Regards,
    John

  22. #22 Dr Vector
    April 30, 2009

    I’m curious to see if the new research falsifying the biofilm hypothesis and supporting the cells and proteins as being genuinely dinosaurian will be covered here. And if the “I knew it was too good to be true” crowd would like their crow raw or cooked.

  23. #23 Jason Thibeault
    June 24, 2009

    Y’all got spammed.

  24. #24 google seo optimizasyonu
    October 2, 2009

    The peptides in the database that that we know are contaminants from our lab are human keratin, BSA, IgG and casein, so you can ignore those. Besides the collagen peptides (which do not show up as contaminants in dry runs) we see a few, but not that many bacterial proteins.

  25. #25 turbotuning
    March 7, 2010

    I think the real moral of the story is to try to never have a boss like Bruce! I once had a boss who got mad at me because I told him something he didn’t believe. When he found out I was right, which I knew he would, he came and apopogised.

  26. #26 bedavatelevizyon
    March 7, 2010

    Great post, Greg! This is exactly what happened with the supposed T. rex proteins. The comment from John Asara above – “the sequences are clearly from T. rex” – is just Asara defending his own studies, not surprisingly.

  27. #27 güzelünlüler
    March 7, 2010

    Laelaps, having been involved in several mass spec experiments aimed at identifying unknown proteins I can assure you that what you mostly get are false positives.

  28. #28 sohbet
    April 22, 2010

    Crap, didn’t realise that would happen :-)
    If I remove the li tags then the link works.

  29. #30 astin
    July 9, 2010

    Davutoğlu’na Londra’da Doğan-İsrail tuzağı!
    CHP’den Şahin’e sert çıkış!
    ABD ile Rusya arasında büyük takas
    01:59 Nusaybin’de gerginlik: 1 polis yaralı
    01:57 Antalya’da ABD uçak gemisine tepki

  30. #31 cam mozaik
    July 19, 2010

    The stone had some yeck on it, and for giggles, this stone got passed on to a physicist who had invented a new way of looking at small things. He was going to look at the tool to see what the yeck was. I should point out that this physicist had no knowledge to speak of of either archaeology or geology.

    Great..!

  31. #32 TemaTurk
    July 23, 2010

    Great post, Greg! This is exactly what happened with the supposed T. rex proteins. The comment from John Asara above – “the sequences are clearly from T. rex” – is just Asara defending his own studies, not surprisingly.

  32. #33 steve
    July 24, 2010

    Hi! I’am about to publish my findings after 8years of research.This is going to shock you all. Every formed rock is a left-over from dino feeding activity.

  33. #34 konteyner
    August 4, 2010

    Hi! I’am about to publish my findings after 8years konteyner

  34. #35 kabin
    August 18, 2010

    As we might expect, and there’s the predictable upsell. But that’s okay. We’ve seen it, we’ve used it,

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