Even though all sciences are greatly concerned with ‘structure’, standard mereology cannot deal with ‘structured’ wholes. Structured wholes, such as
chemical molecules, generally have causal efficacy in virtue of their ‘connec-
tivity’– in addition to the causal powers of their constituent atoms. (Levoro-
tatory amino acids are nutritious, corresponding dextrorotatory amino acids
are poisonous – although both sorts of molecules have exactly the same
Inclusion in a chemical molecule clearly causes significant changes in each
of the components that are so included. For example, organic molecules gen-
erally contain many hydrogen centers (‘protons’). Ethyl alcohol (CH3CH2
OH) has five hydrogen centers (‘atoms’). Those hydrogens are not all the
same, however. There are three distinct sorts of hydrogen centers in the
ethanol molecule. If a sample of ethanol is placed in a magnetic field and sub-
jected to appropriate radio-frequency radiation of varying frequency, energy
may be absorbed in bringing about a change in the relationship between the
‘spin’ of a proton (hydrogen nucleus) and direction of the imposed magnetic
field – what is sometimes called a ‘spin-flip’. In such experiments, sharp ab-
sorption bands are observed at three separate frequencies (‘chemical shifts’)
corresponding to differing detailed characteristics of the electromagnetic en-
vironments that characterize the several types of hydrogen nuclei within the
ethanol molecule. The intensities of those three absorptions correspond to
the numbers (1 and 2 and 3) of hydrogen centers of each of the three struc-
tural types that are present in ethanol....
Those hydrogen centers are strongly influenced by being parts of the ethanol
molecule, and by the details of their relative locations in the molecule....
John Earley, Sr., How Philosophy of Mind Needs Philosophy of Chemistry (PDF). The example could be stated a bit more clearly, but the basic point is that even though the hydrogen atoms in ethanol are all hydrogen atoms, they have very importantly different behaviors depending on their 'locations' in the molecule, that is, depending on how they link up with other atoms. Earley has argued that this is quite common for chemical substances: parts that are, in some sense, of the same kind nonetheless differ considerably depending on the structures (or structured processes) in which they are participating. Chemistry is a field in which mereology, i.e., parts and wholes in relation, is extraordinarily important, but most discussions of mereology don't give us an account of how parts relate to wholes that is useful for explaining reasoning about chemical reactions and substances. What is needed is an account of mereological structure or forms of integration.
Earley goes on to make the argument, which is a somewhat different issue, although interesting in its own right, that the major forms of physicalism and reductionism regularly assume mereological principles that are too simplistic to account for chemical substances and processes.