The word metaphysics typically induces boredom or incomprehension, and most definitions seem unhelpful to most people - so what is it?
Metaphysics can be thought of as the default hypothesis.
The Null Hypothesis
One well known default hypothesis is the null hypothesis in Frequentist (Fisherian) statistics - this is the assumption that two samples being compared are drawn from the same population. In everyday practise, the null hypothesis assumes that there is no difference between two groups unless proven otherwise, or there is no correlation between two variables unless proven otherwise, or that nothing has changed unless proven otherwise.
Many people assume that this assumption is merely 'rigorous' scientific practice, and has been proven to be correct by vast amounts of observation and experiment. But it is nothing of the sort - the Null Hypothesis is an assumption, it is a metaphysical framework for research, and it cannot be proven, or disproven, by any amount of empirical research - because the Null Hypothesis itself frames the conduct and interpretation of empirical research.
Natural Selection as the cause of evolution
Evolution by Natural Selection is another such default hypothesis. Natural selection frames biology as the primary assumption which is the basis for the definition and coherence of biology; such that biology can neither prove nor disprove natural selection.
Whatever happens in biology is either explained as due to natural selection or not-explained and instead put down to some 'random'/ undirected factor (examples of such 'random' non-explanations would be 'genetic drift' or the stochastic extinction of small populations by the spontaneous oscillations of population size).
Although there is no biological reason for this; the assumption in 'modern' biological reasoning (i.e. since the Neo-Darwinian synthesis of the mid-twentieth century) is therefore that the default hypothesis for evolution is that we can take-for-granted (for instance) selfishness, short-termism and competition (which are intrinsic to the metaphysics of natural selection) - and what needs to be explained (using natural selection) is altruism, long-termism and cooperation.
An alternative default hypothesis for evolution
To illustrate how natural selection operates as a default hypothesis, imagine for a moment that evolution was seen as a developmental process ('ontogeny') resembling the differentiation and growth of an organism.
With development as the null hypothesis - and if we think of the growth of a human from the fertilized cell (zygote) - the assumption is that we will normally see a process of division, differentiation (specialisation), and coordinated growth - this is how development proceeds.
When looking at development, altruism, long-termism and cooperation are normal, expected, they are the processes by which development operates. It is the failure of these processes which disrupt development and which need explaining.
So, if the basic mechanism (the metaphysical foundations, the default hypothesis) of evolution were developmental instead of selectional; then we would expect to find (for instance) altruism and cooperation - and we would need to explain selfishness and competition.
In other words, one default hypothesis takes for granted what the other needs to explain - and vice versa.
Conclusion
The metaphysical foundations of biology are assumptions, not discoveries; they operate as a set of default hypotheses - and switching a different metaphysical basis will have profound effects on the nature of biology - by changing what is assumed, and thereby what needs to be explained in terms of what is assumed.
