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Published online 21 August 2008 | 454, 1035 (2008) | doi:10.1038/4541035a
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Fresh doubts over T. rex chicken link
Critics call on researchers to disclose protein spectra data.
A claim by researchers to have extracted proteins from a Tyrannosaurus rex bone and matched these to proteins found in chickens has been attacked in the same journal that published the original research.
In a withering critique, computational biologist Pavel Pevzner and his colleagues at the University of California, San Diego, say that the protein claim cannot be supported by the analytical data released so far1.
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This is very well put. Schweitzer and Asara have to release their spectra - but it seems that multiple lines of evidence already refute their results. Another important element of this discussion is that Science chose to publish the original article and a followup as regular articles - in print. In contrast, they published the two critiques as "Technical Comments", which only appeared online. Seems that Science is trying to avoid negative publicity - but they were only too happy to publicize the original story.
Although these techniques aren't as esoteric as they come...and although scientific back-and-forth is widely considered a necessity in science rigor, I wonder how accessible these discourses will become (to the people who ultimately might make decisions or be particularly influenced based on the findings) as the techniques and claims become increasingly specialized. Maybe the chicken -- T-Rex link looks academic for now, but new and past tech continue to defy convention in shifting our notions of relevance and practicality. While some people tire of these frequent tennis-like matches of research claim and counter-claim, maybe we'd do well to cherish the dialogue -- while it's still the case that there's more than one individual in a place to bring the dialogue to the research.
One thing that we should not ignore is that Science as a top scientific journal with its strict inspection and high selectivity of papers submitted to it ought to be responsible,at least partially,for the debate. This proves again that Science as a science journal sets too much eagerness on sensational claims than it should,after publishing of the faked paper by the Korean stem cell biologist years ago.
That science, as distinct from chat, is an exact science with a lot of Arguments.
Very interesting article indeed. How is one ever sure that their process is accurate and up to the standards of the community? As we learn more we change more, it's the nature of research.
If Asara et al have, as Pvzner isinuates, "cherrypicked" a randomly generated sequence among many, simply taking one that looks like chicken, we should expect other randomly generated sequences to match a target decoy which is of equal size and amino acid composition, but in which no matches are expected (random sequences or reversed target database entries). Asara et al. did these controls. The only mass spectrometric fragmentation patterns from T. rex that statistically matched anything in vertebrate protein databases (other than human keratin contamination) was collagen. Pvnezer expects us to believe that by "chance" a monkey has typed the exact word we demanded, while at the same time has somehow failed to produce any other word. Now, computer scientists may be unaware of the fact that there is no dispute within phylogenetic systematics that T.rex is closer to the chicken than to any other species it was compared to. Any OTHER position of the recovered T. rex collagen in the phylogenetic tree than that published by the Asara tema (in Organ et al 2008) would imply ridiculous morphological leaps, at odds with the opinion of entire field of paleontology. Now THAT would strongly suggest an artifact. But its not the case. Sure, "monkeys" can by chance write several words. But only ONE word? And further, it is precisely the word we were expecting to pop up according to our non-random hypothesis, according to the actual phylogenetic position of dinosaurs as established within paleontology. We'll see. When Asara is ready to release yet more data, the nay-sayers may have to eat up their words
Hi All, Just want you to be aware that we will be releasing 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. The peptides in the database 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. Hope you enjoy the data and let me know if you have any questions. Hopefully, this will convince you 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. Regards, John