Editing Tyrannosaurus (section)

===Soft tissue===
[[File:Tyrannosaurus peptides.jpg|thumb|upright|''T.&nbsp;rex'' femur (MOR 1125) from which demineralized matrix and [[peptides]] (insets) were obtained]]
In the March 2005 issue of ''[[Science (journal)|Science]]'', [[Mary Higby Schweitzer]] of [[North Carolina State University]] and colleagues announced the recovery of soft tissue from the marrow cavity of a fossilized leg bone from a ''T. rex''. The bone had been intentionally, though reluctantly, broken for shipping and then not preserved in the normal manner, specifically because Schweitzer was hoping to test it for soft tissue.<ref name="smithsonian-fields">{{Cite magazine |last=Fields |first=H. |date=2006 |title=Dinosaur Shocker |url=http://www.smithsonianmag.com/science-nature/10021606.html |magazine=[[Smithsonian Magazine]] |access-date=October 2, 2008 |archive-date=October 14, 2008 |archive-url=https://web.archive.org/web/20081014011547/http://www.smithsonianmag.com/science-nature/10021606.html  }}</ref> Designated as the Museum of the Rockies specimen 1125, or MOR 1125, the dinosaur was previously excavated from the [[Hell Creek Formation]]. Flexible, bifurcating [[blood vessel]]s and fibrous but elastic [[bone]] matrix tissue were recognized. In addition, microstructures resembling [[blood cell]]s were found inside the matrix and vessels. The structures bear resemblance to [[ostrich]] blood cells and vessels. Whether an unknown process, distinct from normal fossilization, preserved the material, or the material is original, the researchers do not know, and they are careful not to make any claims about preservation.<ref name="MHSetalb">{{Cite journal |last1=Schweitzer |first1=M. H. |last2=Wittmeyer |first2=J. L. |last3=Horner |first3=J. R. |last4=Toporski |first4=J. K. |s2cid=30456613 |date=2005 |title=Soft-tissue vessels and cellular preservation in ''Tyrannosaurus rex'' |journal=[[Science (journal)|Science]] |volume=307 |issue=5717 |pages=1952–5 |bibcode=2005Sci...307.1952S |doi=10.1126/science.1108397 |pmid=15790853 |author-link=Mary Higby Schweitzer}}</ref> If it is found to be original material, any surviving proteins may be used as a means of indirectly guessing some of the DNA content of the dinosaurs involved, because each protein is typically created by a specific gene. The absence of previous finds may be the result of people assuming preserved tissue was impossible, therefore not looking. Since the first, two more tyrannosaurs and a hadrosaur have also been found to have such tissue-like structures.<ref name="smithsonian-fields" /> Research on some of the tissues involved has suggested that birds are closer relatives to tyrannosaurs than other modern animals.<ref>{{Cite news |url=http://news.bbc.co.uk/2/hi/science/nature/6548719.stm |title=Protein links T. rex to chickens |last=Rincon |first=P. |date=April 12, 2007 |work=[[BBC News]] |access-date=October 2, 2008 |archive-date=September 7, 2018 |archive-url=https://web.archive.org/web/20180907082950/http://news.bbc.co.uk/2/hi/science/nature/6548719.stm |url-status=live }}</ref> The original endogenous chemistry was also found in MOR 1125 based on preservation of elements associated with bone remodeling and redeposition (sulfur, calcium, zinc), which showed that the bone cortices are similar to those of extant birds.<ref>{{Cite journal|last1=Anné |first1=J. |last2=Canoville |first2=A. |last3=Edwards |first3=N. P. |last4=Schweitzer |first4=M. H. |last5=Zanno |first5=L. E. |title=Independent Evidence for the Preservation of Endogenous Bone Biochemistry in a Specimen of ''Tyrannosaurus rex'' |year=2023 |journal=Biology |volume=12 |issue=2 |at=264 |doi=10.3390/biology12020264 |pmid=36829540 |pmc=9953530 |doi-access=free }}</ref>

In studies reported in ''Science'' in April 2007, Asara and colleagues concluded that seven traces of [[collagen]] proteins detected in purified ''T. rex'' bone most closely match those reported in [[chicken]]s, followed by frogs and newts. The discovery of proteins from a creature tens of millions of years old, along with similar traces the team found in a mastodon bone at least 160,000 years old, upends the conventional view of fossils and may shift paleontologists' focus from bone hunting to biochemistry. Until these finds, most scientists presumed that fossilization replaced all living tissue with inert minerals. Paleontologist Hans Larsson of McGill University in Montreal, who was not part of the studies, called the finds "a milestone", and suggested that dinosaurs could "enter the field of molecular biology and really slingshot paleontology into the modern world".<ref>{{Cite news |url=https://www.usatoday.com/tech/science/discoveries/2007-04-12-trex-protein_N.htm |title=Yesterday's T. Rex is today's chicken |last=Vergano |first=D. |date=April 13, 2007 |work=[[USA Today]] |access-date=October 8, 2008 |archive-date=April 19, 2012 |archive-url=https://web.archive.org/web/20120419005821/http://www.usatoday.com/tech/science/discoveries/2007-04-12-trex-protein_N.htm |url-status=live }}</ref>

The presumed soft tissue was called into question by Thomas Kaye of the [[University of Washington]] and his co-authors in 2008. They contend that what was really inside the tyrannosaur bone was slimy [[biofilm]] created by bacteria that coated the voids once occupied by blood vessels and cells.<ref>{{Cite journal |last1=Kaye |first1=T. G. |last2=Gaugler |first2=G. |last3=Sawlowicz |first3=Z. |date=2008 |editor-last=Stepanova |editor-first=A. |title=Dinosaurian Soft Tissues Interpreted as Bacterial Biofilms |journal=PLOS ONE |volume=3 |issue=7 |pages=e2808 |bibcode=2008PLoSO...3.2808K |doi=10.1371/journal.pone.0002808 |pmc=2483347 |pmid=18665236|doi-access=free }}</ref> The researchers found that what previously had been identified as remnants of blood cells, because of the presence of iron, were actually [[framboid]]s, microscopic mineral spheres bearing iron. They found similar spheres in a variety of other fossils from various periods, including an [[ammonite]]. In the ammonite, they found the spheres in a place where the iron they contain could not have had any relationship to the presence of blood.<ref>{{Cite press release |title=New Research Challenges Notion That Dinosaur Soft Tissues Still Survive |date=July 24, 2008 |publisher=Newswise |url=http://newswise.com/articles/view/542898/ |access-date=October 8, 2008 |archive-date=July 30, 2017 |archive-url=https://web.archive.org/web/20170730134938/http://newswise.com/articles/view/542898/ |url-status=live }}</ref> Schweitzer has strongly criticized Kaye's claims and argues that there is no reported evidence that biofilms can produce branching, hollow tubes like those noted in her study.<ref>{{Cite press release |title=Researchers Debate: Is It Preserved Dinosaur Tissue, or Bacterial Slime? |date=July 30, 2008 |publisher=Discover |url=http://blogs.discovermagazine.com/80beats/2008/07/30/researchers-debate-is-it-preserved-dinosaur-tissue-or-bacterial-slime/ |access-date=September 4, 2008 |archive-date=August 7, 2008 |archive-url=https://web.archive.org/web/20080807005940/http://blogs.discovermagazine.com/80beats/2008/07/30/researchers-debate-is-it-preserved-dinosaur-tissue-or-bacterial-slime/  }}</ref> San Antonio, Schweitzer and colleagues published an analysis in 2011 of what parts of the collagen had been recovered, finding that it was the inner parts of the collagen coil that had been preserved, as would have been expected from a long period of protein degradation.<ref>{{Cite journal |last1=San Antonio |first1=J. D. |last2=Schweitzer |first2=M. H. |last3=Jensen |first3=S. T. |last4=Kalluri |first4=R. |last5=Buckley |first5=M. |last6=Orgel |first6=J. P. R. O. |date=2011 |editor-last=Van Veen |editor-first=H. W. |title=Dinosaur Peptides Suggest Mechanisms of Protein Survival |journal=PLOS ONE |volume=6 |issue=6 |pages=e20381 |bibcode=2011PLoSO...620381S |doi=10.1371/journal.pone.0020381 |pmc=3110760 |pmid=21687667|doi-access=free }}</ref> Other research challenges the identification of soft tissue as biofilm and confirms finding "branching, vessel-like structures" from within fossilized bone.<ref>{{Cite journal |last1=Peterson |first1=J. E. |last2=Lenczewski |first2=M. E. |last3=Scherer |first3=R. P. |date=October 12, 2010 |title=Influence of Microbial Biofilms on the Preservation of Primary Soft Tissue in Fossil and Extant Archosaurs |journal=PLOS ONE |volume=5 |issue=10 |pages=e13334 |bibcode=2010PLoSO...513334P |doi=10.1371/journal.pone.0013334 |pmc=2953520 |pmid=20967227 |quote=[T]he interpretation of preserved organic remains as microbial biofilm [is] highly unlikely|doi-access=free }}</ref>