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The verbs essen and sein do not seem to conflict, but sometimes they do phonetically. This happens in the pronouns er/sie/es.
you eat you are
er/sie/es isst er/sie/es ist
he/she/it eats he/she/it is
As you can see, isst and ist sound the same! Also, in every day speech, the -t mutes sometimes. This only happens for ist, though! It is used much more, of course, and therefore everybody understands is just as much as ist in a sentence. An example:
Komm’ schon, Es ist doch nicht so schwer!
Come on, it isn’t that hard!
Now you might think: but iss is the imperative of essen! And you are right. But that imperative is not used as frequently as ist, and its place in a sentence is different – so there is no conflict here between the pronunciation of iss and ist.
Anyhow, let’s look at the origin! Why is it not er/sie/es esst? The secret is called e-i-Wechsel.
Both German and Latin come from the Indo-European family. In Latin, to be is esse. There were no personal pronouns in Latin. You could figure it out by the ending of the verb. With esse, that looks like this:
sum (I am)
es (you are – singular)
est (he/she/it is)
sumus (we are)
estis (you are – plural)
sunt (they are)
As you can see, est looks much like ist. From Indogermanic, the e transformed into an i in certain cases. A short e in the infinitive of a verb, such as essen, becomes an i in the du and er/sie/es conjugations. For a long e, this becomes an ie in those conjugations. Examples:
This also happened to the very irregular sein. est became ist, because it was a short e. Why this changed is not clear, but I assume it changed because ist became easier to pronounce and seemed more logical after the e-i-Wechsel.
PS: heed the two exceptions nehmen and geben. Even though both have a long e, they change. Nehmen becomes du nimmst and er/sie/es nimmt. Geben becomes du gibst and er/sie/es gibt.