The article makes a big point of saying that the Eureqa is able to calculate F=ma or put differently: There is some quantity called force that is proportional to the instantaneous change in the instantaneous change of position of the pendulum. The Eureqa machine is capable of using calculus as a given. What made this task so hard for Newton was he had to create the calculus of instantaneous change. The problem that Eureqa solved is much more like that which a first year physics student solves (only, it did it with a much more impressive dataset) in that, thanks to Sir Isaac Newton, we have all the rules of calculus and mathematics to assist us.
It takes a lot of work to analyze exactly how two proteins will bind together, or produce substances that alter the other in some way. But, just having a large system of differential equations can be just as useful as determining in what orientation two domains of two proteins interact and with what affinity. Supposedly that's the budding new field of biology, I had a conversation with my boss a few months ago about it!