The short answer is “we don’t know what is going on in that 3% that causes different expressions of shared genetic traits”
But here’s a more fun one:
Humans are more than 60 percent identical to bananas. Many of the “housekeeping” genes that are necessary for basic cellular function, such as for replicating DNA, controlling the cell cycle, and helping cells divide are shared between many plants (including bananas) and animals.
Basically at the micro scale a lot of biological processes are the same or very similar in very different species and thus the DNA that provides the instructions for these processes are similar. Small micro changes to processes and structures can result in very large differences.
Another way of looking at it is: 2 water molecules contain 4 hydrogen atoms and 2 oxygen atoms and take the form of an incombustible liquid; however 2 diatomic hydrogen molecules and one diatomic oxygen molecule take the form of a highly flammable gas despite having the same subcomponents.
There’s also a lot of “junk” DNA that is inactive and doesn’t really control anything but still gets copied and passed on during reproduction.
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