For a moment let's get back to the top of the OP, which were the partial preservation of "soft tissue" in fossils that are over 10 million years old.
Hypotheses are tested in huge bundles, not singly. In terms of the T. rex fossil there are 2 important hypotheses at work:
1. The T. rex fossil is 65 million years old.
2. Soft tissues do not survive after a few million years.
The authors specifically state that second hypothesis in the second paper of the series on the T. rex fossil:
"It has long been assumed that the process of fossilization results in the destruction of virtually all original organic components of an organism, and it has been hypothesized that original molecules will be either lost or altered to the point of nonrecognition over relatively short time spans (well under a million
years) (1–7)."
Now, the first author on the paper is Mary Sweitzer. She was, at the time, a graduate student under John Horner. They were looking at the femur and, specifically, at the bone lining the medullary canal (marrow cavity). There is a thin layer of trabecular bone -- the endosteal bone -- that lines the circumference of the marrow cavity just under the cortical bone.
All bone is a biphasic material: organic matrix and inorganic (rock) mineral -- hydroxyapetite. Notice that no soft tissue outside the skeleton remained: no muscles, nerves, blood vessels, heart, intestines, lungs, etc. and this is the innermost layer of the bone.
So what Dr. Schweitzer did was demineralize the bone -- removed the hydroxyapetite with a dilute solution of EDTA. This chelates the calcium in the hydroxyapetite, thus dissolving the mineral. What they are talking about is the organic matrix of the bone. The "soft tissue" is actually the organic matrix of the femur. Within the cortical bone, there are structured called "Haversian canals" and these consist of long tubes within the bone. Within the tubes are blood vessels, and
fragments these blood vessels are the ones Dr. Schweizter was able to isolate. Also embedded in the bone are cells called osteocytes, and apparently some of these were also partially intact.
What is striking when you read the papers is that the
authors do not consider that the data questions the first hypothesis. IOW, they don't consider this discovery, or previous discoveries of the organic matrix of bone in Cretaceous fossils, to be evidence that the fossils are young. Dr. Schweitzer is also an evangelical Christian and has steadfastly maintained that her discovery does NOT show the fossils to be young.
Instead, it is the second hypothesis that is falsified. Under most conditions, bacteria and other microbes have access to the interior of the bone, and it is these that destroy the organic matrix. But in some rare circumstances, this does not happen. Now, proteins -- particularly collagen (which is the major constituent of the organic matrix) -- are very stable molecules. The peptide bonds are not easily hydrolyzed by water and the very tight helix structure of collagen does not allow water into the molecule to begin with. Even if collagen is cleaved in one or two places, the structure is such that it preserves its eleasticity. Think of a very long, very thick rope. Even if you cut some of the strands in a couple of places, the rope itself is going to behave pretty much the same. Same here. For the blood vessels, the collagen is type IV.
"Mesozoic fossils, particularly dinosaur fossils, are known to be extremely well preserved histologically and occasionally retain molecular information (6, 17, 18), the presence of which is closely linked to morphological preservation (19). Vascular microstructures that may be derived from original blood materials of Cretaceous organisms have also been reported (14–16)."
That's from the paper.
In the next paper Sweitzer and Horner propose chemical mechanisms to account for the presence of the collagens. Collagens crosslink, both within a fibril and between fibrils. This increases their mechanical strength. It will also protect them from degradation.
"We hypothesize that these molecular fragments are preserved because reactive sites on the original protein molecules became irreversibly cross-linked, both to similar molecules and to mineral or exogenous organic components. These cross-linking reactions may have been initiated by unstable metal ions that formed free radicals
(30, 31), which in turn reacted with organic molecules to form polymers (6, 7, 9, 32).We propose that the unstable metal ions were derived from the post mortem degradation of iron-containing dinosaur biomolecules such as hemoglobin, myoglobin,
and possibly cytochromes (9, 31). Once stabilized by these cross-linking reactions, the molecules were no longer available as substrates for further degradative reactions."
Notice the numbers in parentheses. Those are references and refer to other papers with data that support the statement. So their hypothesis has experimental support.
They also note that preseveration of the organic matrix happens in sandstone. This is special and there is a reasons such fossilization would preserve the organic matrix:
"Another contributing factor in the retention of original mineral may be that
apatite is stabilized in the presence of calcite (33). Sandstones surrounding MOR 1125 contain abundant calcite cements."
So, the original hydroxyapetite is not replaced during fossilization. Since they propose that the organic molecules also bind to the hydroxyapetite, that retention helps the proteins survive.
It is the second hypothesis -- that "the process of fossilization results in the destruction of virtually all original organic components of an organism" -- that has been shown to be wrong. NOT the age of the fossils. It is not valid to try to use the presence of bone organic matrix to say that the fossils are "young", particularly young enough to fit into a young earth theory.
