This series is about the nature of reality and what is loosely referred to as metaphysics, the idea of reality above, apart from, or somehow different from material, real reality. When abstractions about things of this sort, like 'the human genome,' are understood as no more than practical working baselines, there may be no problem. But when what we have in mind, so to speak, are processes or theories rather than things, the situation is far less clear.
What is the reality of a theory? When is a theory an assertion....or a belief?
A theory in our context is a general principle or 'law' of nature of some sort. The theory of gravity states that objects have specific quantitative relationships with each other, that are universal no matter what the objects are or where they are--in the entire universe! We may have a difficult time falsifying a theory like that, because if there is even one single minor exception that would show the theory is not literally true, we may never come across that exception.
On the other hand, there are so many direct tests, experimental and otherwise, of such a theory, that we have very good reason to believe it. At that point the theory is accepted as an abstraction of reality, essentially in some Platonic sense. All we can directly see are specific manifestations of the theory, but we assume in essence that every single possible instance would obey the theory--even instances that have not yet arisen.
If a theory is just an approximation, what's it an approximation of?
In some instances we agree that the theory is an approximation of reality, at least insofar as we can measure it. Thus, we may not know the exact speed of light, but we assume there is such a speed, whether or not we can measure it perfectly, and that this speed--this ultimate limit--somehow exists above and beyond any instances we might observe. So even our imperfect measures are, in a sense, given metaphysical meaning. They tell us about the real speed limit.
The human genome sequence may be an easily recognized abstraction rather than any sort of metaphysical (in the sense of unreal or mystical) view of existence. But the speed of light is rather different. So, what about the theory of evolution and, in particular for our purposes, the theory that it is due to divergence from common ancestry as a result of natural selection?
Darwin used barnacles, among other groups, to argue for these points. He found shared traits among different types of barnacles, and shared traits between barnacles and crustaceans. He compared the organization of their bodies, their segments and so on. He reconstructed an hypothetical ancestor based on the idea of common ancestry. There is no problem about his reasoning from instance back up to principle.
Among the traits he studied were the various aspects of sexual reproduction among barnacle species. In particular, the differences between separate sexes, females with separate but dependent degenerate males (well, most males are degenerate, you might say!), and those who were complete hermaphrodites (both sexes in one animal). He inferred this as being due to selection clearly showing that he meant this to reflect instances of the concept (and we can ask if it is metaphysical) that applies more broadly.
But he also inferred, at least implicitly in what we're familiar with, that barnacles with partial hermaphrodism were on the way to complete hermaphrodism. His reasoning was that he's seen some modern hermaprhodites, and these intermediates could be seen as....intermediates! That builds into an instance, his metaphysical or Platonic ideal. Rather than the instance showing the idea, in the way your genome is an instance of 'the human genome', Darwin imposed the theory onto the data. That, in many ways, makes it fundamentally metaphysical, something science doesn't like to acknowledge.
Darwin knew that his idea of inheritance (called pangenesis) did not fit the data, and he wriggled about that, but it made problematic his theory of ubiquitous natural selection. His estimate of the age of geological formations, such as the valley near his home in Kent, was far too old for what astronomers were estimating. But he stuck to his guns! He believed he was right. That in many ways is a commitment to metaphysical truth in the absence of the required evidence.
Then he extended this to human evolution, human racial variation, and our relationship to other modern primates. We agree with Darwin in general, but not with the kind of racial hierarchy he invoked as being due to natural selection. So we would say Darwin was extending his theory too broadly (some argue still today that in many ways there is a racial hierarchy--again raising the same kinds of issues about whether natural selection is a real 'law' or just something that can happen and that has to be shown separately in each case).
One might say he knew he was right about the process (the
Platonic ideal of evolution?), and just that his measurements were
wrong. But was he right about barnacles being 'on the way' to
hermaphrodism? Or about racial hierarchies?
truth is that all we have are instances rather than universal law, how
can we know that? How can we know whether our knowledge is incomplete
or our ideas (our theory) is wrong? Or, if we accept that theory may
only be approximate, how can we know that, as opposed to the theory
being simply wrong?
When and why should a theory be abandoned?
This raises the metaphysical question in a somewhat new way. If a theory, like gravity or evolution, is truly universal, then that is somehow a metaphysical concept of which we can only see instances. It seems a bit less clear than the idea of 'chair' accepted to stand for the various actual chairs that we see.
And in science other questions arise here. We can look at an object and see if it is an instance of chair or not, because chair is a human-defined symbol. But universal principles or laws of nature are human-discovered and their universality is effectively assumed as an ideal. If we assume a theory, and don't find the evidence for it, when do we abandon it and admit we were wrong, and when do we just say that the evidence simply is still flawed?
We see the problem in areas we write a lot about here on MT: evolution and genetic causation. GWAS attempt to identify 'the' genes responsible for a particular trait, with the clear if sometimes unstated expectation that it's tractable in the number of genes and rather stable, replicable, and quasi-deterministic (high predictability). What that's not what's found--as is routinely the experience--then why don't we abandon the idea of simple causation, or that we can use enumerative approaches to find 'the' causes? Why do we cling to the theory, the Platonic abstraction of causation, and demand larger, longer, more expensive studies to find the elusive truth?
One can quibble about the terminology we're using relative to professional philosophy, but this to us shows that even modern science, that sneers so readily at metaphysics, is very metaphysical at its core. Vested interests, beliefs, hunger for simple or tractable theories, unstated appeal to satisfying theories in other sciences, and so on, as well as occasionally supportive evidence, all lead us to generalize from instances to theory by forcing the theory on the instances.
In this sense, as we often say, rather than siding with those who complain about its lack of dramatic results, that GWAS have not been a failure. They've been over-done for many unjustified reasons, and will be over-done even more in the future, but these studies have shown that some of our deeply wished-for ideas about nature, our abstractions, our Platonic ideas, simply aren't that way. But we don't want to hear that message, and certainly not to be accused of delving in metaphysics. So we cling to the theory even in the face of clear evidence that it's inaccurate at best--or we reinvent the theory so that we water down our criterion for calling effects 'major'.
Is this the Zen of genomics: when No means Yes?
There are some relevant issues here that make the story less clear than we've stated. They have to do with the real, or metaphysical, nature of 'emergence' or 'interactions', and we'll comment on that next time.