What are the boundaries?

While they aren't separated, sometimes you have to make a choice of simplified models with certain boundaries because of limited computational power. See also the sequence about reductionism for more on that.

People also did this historically because some categories intuitively seemed more concrete than others. We're moving away from that because those categories have been explored thoroughly enough that we can see the links between them, and which new hybrid categories this points to.

But, yes, you're right, the frontier is moving, and cool stuff awaits beyond.

Would you say the boundaries are getting lower? With increasing specialization, it seems it gets harder to connect an ever greater number of disparate fields (with a couple of choice exceptions, as you note). Of course, in nature there is no boundary (eg., between chemistry and physics), but there are limits to what fits in a human brain.

The more we ignore the cognitive barriers we have placed upon the world, the greater our ability to problem solve. My own lab group (chemists and materials scientists) recently collaborated with microbiologists, civil engineers, and industrial engineers to produce a feed spacer which blocks biofouling in RO membranes using technology originally developed for use in medical devices using a catalytic process discovered by a nutritionist. It reduces biofouling by 3-5 logs, which is unprecedented, using a process that engineers never could have come up with had they remained focused on their own narrow field.

There is a reason that most universities are now encouraging collaboration between different departments.

It is useful to have specialized knowledge, of course, but we mustn't limit ourselves to our respective fields. Honestly, I think I would be against the creation of new fields of study at this point. Rather, people should be encouraged to work together with people of diverse backgrounds so we can apply what we have learned in one field to others.

As to the question, to pull a Rumsfeld, we have known unknowns and unknown unknowns. I could only guess at where the trend toward broad-based collaboration will lead us.

Molecular biology and physics are in the process of colliding.

Though of course, the changes that I'm blind to, I can't share with you.

A potential boundary is that between the seemingly objective and subjective. At the moment, science seems to be set on measuring things outside of the self. There is relatively little exploration of what one subjectively perceives. This facet of existence is almost completely ignored, even in psychology. I think in time this boundary will have to dissolve. There really is no good way of separating the outside world from the inside world.

Another one could be the artificial boundary between nature and nurture. It seems like the expression of all genes is mediated to some extend by the environment, therefore it is senseless to talk about any boundary between the two. I recently heard a metaphor that the debate between nature and nurture is akin to debating whether length of width is a better determinant of the area of a rectangle.