If you look at the DNA, as a huge integrated molecular composite configuration, there is a logic for stem cell differentiation. The DNA does not exist as free DNA, but rather the DNA is either hydrated by water and/or it is packed with protein to various degrees. Theoretically, the simplest way to tune-in any differentiation of the DNA is by changing the global potential around the DNA, so an integrated equilibrium configuration differentiates.
If we compare totally unpacked DNA, to fully packed DNA; packed chromosomes, these are the two extremes configurations. The first defines the highest entropy, while the second defines the lowest entropy. The packing creates order and minimizes freedom and entropy. All genetic differentiations are in the middle and define intermediate integrated entropy, based on packing/unpacking ratios.
Embryonic stem cells would be expected to be closer to the lower end of the entropy spectrum. This higher level of DNA order, in light of the second law; entropy has to increase, creates a natural push to unfold and define other configurations.
When the DNA packs, the DNA winds around packing protein. While reversal of packing requires enzymes. The first direction is spontaneous, while the second direction requires extra machinery, because it is an uphill battle. Moving to higher DNA entropy has to be done deliberately. The other way, occurs spontaneously because packing lowers the DNA energy. This is done by design.
This works on the same principle seen in water and oil. If we combine water and oil, they will spontaneously separate into two layers. This lowers the system entropy.This is possible because it also lowers system energy/enthalpy cause by surface tension. To go the other way, or increase system entropy, we need to add energy. In the case of water and oil, this is done with agitation. While with the DNA, enzymes play the role of agitators to make gene bubbles. Like water and oil, if we stop the enzymes or agitation, the DNA will spontaneously repack (merge into fewer layers).
Acids are kosmotropic or add order to the water. This helps to add order to the DNA, back to fewer layers; stem cells.