The most relevant part of the article: David Duvenaud, an assistant professor in the same department as Hinton at the University of Toronto, says deep learning has been somewhat like engineering before physics. “Someone writes a paper and says, ‘I made this bridge and it stood up!’ Another guy has a paper: ‘I made this bridge and it fell down—but then I added pillars, and then it stayed up.’ Then pillars are a hot ne…
Last I checked bridges came before Newtonian Mechanics and it seems strange to argue this wasn't a good thing. Admittedly paper writing wasn't the main mechanism of transmitting knowledge but it's fairly common for human engineering to come before the full theoretical foundations as opposed to after.
Bridge building is mostly well-understood engineering. When you study Static Mechanics [0] you learn all sorts of Physics equations, including Newtonian Mechanics, that completely describe the forces and motions of a structure based on measurable physical properties of the materials used and details about the shapes of those materials.
When you get into Fluid Dynamics, things are different. You start to encounter a bunch of things like Reynolds number [1], which is a dimensionless value related to turbulence that you just have to look up for the particular fluids and velocities you're working with. This number is pretty well defined, but there are a lot of others and their definitions and meanings aren't nearly as clear as F=ma. Back when I was in school, particle simulations for turbulent fluids was just beginning to be feasible, so to design something you plugged in dimensionless constants and didn't worry about the unpredictable fine-details. An example of this is the wind blowing through a bridge's structure, and water flowing around its base. The equations don't give you exact forces that the turbulent air and water will exert; they give you more of an average over time. A simulation, if you can do it, can show you things (like resonance) that the equations won't show you.
Then there was Strength of Materials. Here, the big thing was the Factor of Safety [2]. This is solidly in the rule-of-thumb engineering camp. This is where the engineer says "I think two 16" steel beams would be sufficient... so lets use three 20" beams just to be sure." This is still the way a lot of engineering design is done, because the real world is never precisely known, and the factor of safety will save you when something unexpected happens.
[0] https://en.wikipedia.org/wiki/Statics