Some things are largely guesses or extrapolations from what characteristics we can find in preserved samples/fossils and such, but in many cases, there’s good evidence and level of detail still remaining in fossils/remains to base these extrapolations and guesses on. For example, you can sometimes get fossils that shed light on muscle composition, connective tissues, bacteria, cells responsible for pigment (?), and finer structures such as feathers or wings. However, this depends a good bit on the fossil itself, and conditions surrounding its preservation.
Fossilization is a sort of mineralization process of remains that *does not* exclude soft tissues, but generally soft tissues and the like are much less likely to be preserved. The less it decays the better. Hard things like bones/shells/teeth, stand a much better chance to be found relatedly. But, you can still get fossils that have a lot more to show. And, from what I understand, better tools and more precise analysis has helped a *lot* with resolving the less clear signs of other structures and parts of the remains that give additional detail about their body process.
But, often it is still an educated guess based around all the data we have found. But an educated guess on really good science and information can still be really damn good.
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