On the classical Aristotelian metaphysics inherited by the medieval scholastics, every primary substance ... has a secondary substance-kind ... that pertains to it and without which it could not exist. ... (Thomas H. McCall, An Invitation to Analytic Christian Theology, 104)
Metaphysics is the branch of philosophy that seeks to deal with the nature of reality. Part of that is the nature of all reality, thus they deal with questions involving whether reality is actually real in a material sense or not. That level of metaphysics goes beyond scientific examination because it deals with the ultimate reality of things beyond that of science. However, there is another level of metaphysics which in the modern world has mostly gone obsolete, that of Aristotelian substances and accidents, where that level of metaphysics seek to discover the nature of things as they are present in real life. In the modern world, science in the fields of physics, chemistry, and biology have supplanted this level of metaphysics, and have provided answers to these questions that are far more practical and much better approximations to the truth. Nevertheless, a new level of interest in Aristotelianism has arisen recently. Perhaps such is due to the failure of modern philosophy to provide a unitary vision of the truth. Perhaps it is due to an interest in virtue ethics of which Aristotle has much to contribute. Or perhaps it is due to influence from certain fields of theology where Aristotelianism has laid dormant and are now uncritically accepted due to a unbiblical view of what theological retreival should mean for a Reformed Christian. Needless to say, this resurrection of Aristotelian metaphysics is deeply troubling. Part of that of course is that the notion of Aristotelian substance and accidents are just plain wrong; science has shown that to be the case. The same people who are resurrecting Aristotle, either Aristotle himself or Aristotle as mediated through Aquinas, are the same people who are benefitting from the applications of modern science, science that would not be possible if scientists stuck with Aristotelian metaphysics!
Reality can be described and explained in many ways. There is therefore nothing wrong with using Aristotelian categories if one understands them to be mere descriptions. However, the claim that these are true of reality is an ontic claim, and that is a problem because such claims are demonstrably false. For example, a dog as substance would possess the "substance-kind" dogness or caninity. But there is no such ontological thing as "dogness." A dog is an emergent substance formed by the expression of instructions found in the canine DNA of dog cells. "Dogness" is at best information encoded by DNA. That information in turn does not produce an ontological substance called "dog" but rather a bunch of phenotypes that we collectively called "dog." Platonism with its view of forms is more amenable to modern science here, since dog phenotypes can be called its "form." Even then, there is no "dog substance" that is combined with a "dog form," since the substance of DNA, proteins, and carbohydrates are common to all animals.
The substance of living things are the molecules that form the thing, or the particular permutation of molecules in various cellular structures. The substance of all living things are therefore the same, since all living things have DNA, proteins, carbohydrates and so on. There is no "dog substance," no "human substance" and so on. Dog cells and human cells, the fundamental living unit of dogs and humans respectively, are emergent substances that form as the "form" from the instructions on the DNA imprints unto the cells to form these different dog and human cells. Dogs are made of dog cells, tertiary substances that can only emerge from the imprint of dog DNA information unto them. There is no primary substance called "dog"‐ never has been and never will be.
With the resurrection of Aristotle, we can expect to see bad philosophy, bad science and bad theology. In philosophy, one can obviously find alternatives to Aristotelianism. That cannot be said to be true of much of classical Christian theology, which needs a good round of de-Aristotelianism to bring it out of captivity to this false philosophy.