I finally understand how to think about my question in a way that I can put into my own words. I will address the last part of my OP, which said,
There is also work done by the object on you, but the issue is, that other object didn't have any potential energy. So how can the other object do work on you, without transferring any energy to you? What is the right way to think about this situation?
The issue stemmed from confusing how work is treated in an intro mechanics course vs how work is treated in a thermodynamics course. See the linked posts at the end of this post. Also, we should point out that for extended bodies there is a difference between body forces and contact forces. I will focus only on contact forces in this discussion (so no gravity or electromagnetism).
Work
As pointed out in this post and this post, there is a difference between "work due to a particular force" and the "center of mass work"/"net work"/"pseudowork."
When you are dealing with work due to a particular contact force $F$ on a body/system, you must always track the position at which the force is applied when calculating $dW_{F} = F\, dx$. This is how work is calculated in thermodynamics, and if $F$ is the force done by an outside system or environment on the system you are interested in, then $W_{F}$ is the energy transfer into the system due to the force $F$.
Summing all such work gives you the energy transfer into the system due to all the contact forces acting on the system. When we add energy transfer due to heat, if any exists, we obtain the equation for the first law of thermodynamics.
Now there is another form of work, commonly called net work, which is invoked in the study of Newtonian mechanics. It is known that when you sum all forces $F_{i}$ acting on a body/system, the center of mass obeys $\sum_{i} F_{i} = MA$ ($M$ being total mass and $A$ being the acceleration of the center of mass) even if the forces are not applied at the center of mass. Now the work-energy theorem then states that if we define $dW_{\text{net}} = F_{\text{net}}\, dX$ (where $F_{\text{net}} = \sum_{i} F_{i}$ and $X$ is the center of mass position), then the change in the translational kinetic energy associated with the motion of the center of mass is $\Delta KE = W_{\text{net}}$. Note this theorem, as I stated it, discounts kinetic energy associated with internal motion and it discounts any mention of potential energy.
Remarkably, the two forms of work I pointed out are different, and you don't run into any contradiction if you track all forces carefully enough.
Original Scenario
Now how does all this apply to the original question? Going back to the original scenario, let us take system $1$ ($S_{1}$ for short) to be the person jumping off and let us take system $2$ ($S_{2}$ for short) to be the other object.
Alternatively, we can imagine that we have two blocks with a spring in the middle (the specifics of what mechanism is used to push objects apart or the force law is not important), and we can take $S_{1}$ to be the system consisting of one block plus the spring attached to it and $S_{2}$ to be the system consisting of the other block. Note that in the analysis, we will not need to consider the spring as its own system! Other posts that say the spring or whatever pushes things apart has to be its own system are misleading!
Choose a coordinate system so that (the center of mass of) $S_{1}$ moves in the $+$ direction along some axis and (the center of mass of) $S_{2}$ moves in the $-$ direction along the same axis when the two are pushed apart.
Assume $S_{1}$ and $S_{2}$ are pushed apart and end up with final velocities $v_{f}$ and $-v_{f}$ along some axis. When $S_{1}$ and $S_{2}$ are pushed apart, the potential/chemical energy of $S_{1}$ is converted to the kinetic energies of $S_{1}$ and $S_{2}$.
When the two systems are being pushed apart, the following two things are true:
- Since $S_{1}$ is expanding (either because the person is jumping off in one scenario or the spring is expanding in the other scenario), the contact point is moving in the direction of $S_{2}$ with overall velocity.
- The center of mass of $S_{1}$ is moving away from $S_{2}$.
Statement (1) concerns the point at which the forces act, so thermodynamic work is relevant. Statement (2) concerns the center of mass, so the center of mass work is relevant.
We have $F_{\text{by 1 on 2}} = -F$ and $F_{\text{by 2 on 1}} = +F$. When considering thermodynamic work, we look at the contact point, whose displacement is $-\Delta x < 0$, and find the following:
- $W_{F_{\text{by 1 on 2}}} = -F\cdot -\Delta x > 0$, and
- $W_{F_{\text{by 2 on 1}}} = +F\cdot -\Delta x < 0$.
The fact that $W_{F_{\text{by 1 on 2}}}$ is positive means that $S_{2}$ is gaining overall energy, and the fact that $W_{F_{\text{by 2 on 1}}}$ is negative means that $S_{1}$ is losing overall energy. This makes perfect sense, because $S_{1}$ is losing potential energy to $S_{2}$ (and the remaining energy that stays with $S_{1}$ is converted to kinetic energy).
When considering the center of mass work, we look at the center of masses. The CoM of $S_{1}$ is displaced by $+\Delta x > 0$ and the CoM of $S_{2}$ is displaced by $-\Delta x < 0$. We find the following:
- $W_{F_{\text{net on 1}}} = +F\cdot +\Delta x > 0$, and
- $W_{F_{\text{net on 2}}} = -F\cdot -\Delta x > 0$.
The net work for each system is positive. This is exactly what is expected by the work-energy theorem: both objects gain kinetic energy and accordingly the center of mass work for both is positive.
Summary
Returning back to
There is also work done by the object on you, but the issue is, that other object didn't have any potential energy. So how can the other object do work on you, without transferring any energy to you? What is the right way to think about this situation?
We have to clarify what we mean by work.
If by "work" we mean "work due to a contact force," then in the OP scenario, the person jumping off is doing positive work on the other object, and the object is doing negative work on the person, because you must track the point at which the force is applied. Accordingly, the person's total energy decreases and the total energy of the object increases.
If by "work" we mean "net work"/"center of mass work"/"pseudowork", then in the OP scenario there is positive work done on both the person and the object. Accordingly both have an increase in kinetic energy. This of course says nothing about how the total energy is transferred, because the work-energy theorem only deals with changes in kinetic energy only. Thus, there is no issue or contradiction.
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