Sadly not all of the information you might want from a fossil can be obtained just by looking at it. No matter how technological your approach (microscopes, SEM, X-rays, CT scans, synchrotron and the rest) some things, while present, will remain inaccessible. For a start, most vertebrate specimens won’t fit into a scanning electron microscope. CT scanners can only penetrate so much matrix or so much bone. X-rays will only give you a certain level of resolution and so on.
Therefore if you really want to count the LAGs in that femur, or look at those melanosomes in that feather then destructive sampling may be your only option. If you want to do some form of geochemical analysis such as looking at the isotopes then this certainly is your only option. The term might sound rather drastic and imply that you won’t be left with much at the end of it, which while far from the truth, is certainly descriptive. The aim of destructive sampling is to extract the necessary information with the minimum amount of damage, but the crucial point here is that the fossil will be irreparably damaged by this process.
This is typically and understandably seen as a necessary evil in most cases. The damage can be minimised and the information gained can be massive. And of course in many cases it need hardly be noticeable. Isolated dinosaur teeth are for example exceptionally common and in most cases damaged or incomplete, and only the smallest of sample (a few milligrams) is needed to do an oxygen isotope analysis say. It is therefore hand not to justify the sampling of teeth for this purpose.
However, as the specimens become more important and better preserved (and rarer) it becomes harder to justify. It’s no surprise that the first destructive work ever done on Archaeopteryx was only published last year, though it’s still more impressive that several specimens were sampled. Similarly, although there are various feathered dinosaurs, it was hard to justify the destructive sampling necessary to look at the colour of Anchiornis until the method had been well established and it was likely good results would be obtained, and that there were several specimens known so that the loss of information on one does not mean that our only record of this is gone for good.
It might be tempting to argue that anything that possibly damages any fossil (or any scientific specimen) irreparably should not be carried out. After all, technology always increases in scope and accuracy and it is only a matter of time before we could put a whole T.rex under and SEM or put a 5 ton block into synchotron to see what is inside. Science is a steam-roller of a methodology – it takes forever with constant checks, rechecks, corrections, restarts and revisions. A few years or decades will not make so much difference, then will it?
Well, that might be true to a degree, but the obvious counterargument to this approach is that this ensures nothing will ever be done. There will always be another method that’s less invasive, or faster, or cheaper, or provides greater detail coming around the corner and if you wait for one, you’ll wait for the next and the next and the next and no research will ever be performed. In palaeontology we don’t have the luxury of infinite resources or to a degree, such time. We have to get some work done, and if a few specimens have to suffer a little damage to produce a great deal of information, that’s probably no great loss (indeed, on average it’s a gain). So while destructive sampling is hardly the first choice for any specimen, and certainly not ever the choice for some of exceptional historical or scientific importance, it’s a necessary tool in our arsenal and one that is used with care, when appropriate.