Spectroscopy has been used to get a handle on diagenesis, and many different techniques have been developed to assess diagenetic alteration of fossils. Despite the range of options, and partially because of it, a tendency has arisen to treat spectroscopic instruments as “black boxes” that produce diagenetic conclusions. Or, otherwise put, when all you have is a hammer, every problem looks like a nail. You can imagine how bad this might be when you build a skyscraper using nothing but nails…
Part of the problem is semantics. Diagenesis refers to chemical and physical changes that occur during burial. Diagenetic alteration of fossils therefore refers to changes in the chemistry or structure of a fossil once it has been buried. This is basically an open book, and you can pretty much expect every fossil to have been diagenetically altered. Got no collagen? Altered. Increased your fluoride? Altered. Slightly warped? Altered. This is where we have to get a bit picky, and ask whether diagenetic alteration of a fossil has been significant. Significant diagenetic alteration is when a chemical or physical parameter you wish to measure is distinct (statistically distinguishable) from the original, biogenic composition. So, a fossil can be diagenetically altered, and they almost all are, and you might not care less. On occasion though, diagenetic alteration can be a real [bother], with significant changes to the chemistry of the bone actually obscuring any biological information.
A second issue lies in perspective. There appears to be two schools of thought regarding the priority of diagenesis. One approach is to carefully select the fossil to be studied, to carefully select a region of that fossil, to eliminate as much interference from that sample as possible, and then physically or chemically measure the sample. As all possible care has been taken and a sound methodology has been followed, the results can then be interpreted as a biogenic signal. Take the measurement of carbon and oxygen isotopes from apatite carbonate, for example. You select a fossil tooth with clean, thick enamel, you sample only the enamel, and you treat the sample for secondary carbonates: interpretations about diet and environment can then be made from the measured isotopic compositions. Any evidence for diagenetic alteration is left to compete with biological explanations for the dataset. This is akin to logical positivism.
The second approach is to follow the same methodology as the first, but instead of assuming that your careful sampling and preparation has netted biological values, you simply assume that you are measuring a completely altered sample. This might seem like fatalism, but bear with me. The burden of proof is now on you to disprove your assumption, and in so doing, find empirical reasons why your samples reflect biology and not diagenesis. Here instead we are working with critical rationalism.
This will bring us back to spectroscopy, and how it has been used to identify alteration.