Not sure I can really explain the rule but I'll give it a shot.
The "being" is not a gerund but a participle - ie it's not functioning as a noun in this case.
"the first/earliest [of which] being the heating of clay"
a) it is assumed the reader will understand that "the first/earliest" refers back to the "chemical changes" earlier in the main clause of the sentence. Therefore "the first/earliest" is the subject of the dependent clause above.
b) We need a non-finite verb in this phrase because it's a dependent clause. If it were a main clause, using for example 'the first/earliest are(or were) the heating of clay' then you would need either a conjunction or a semi-colon in order to join the clauses and make the sentence grammatical. Hence the participle.
c) It has to be in present tense because of the verb "have" in the main clause, which sets the sentence in the present (one reason why I hesitate to use 'were' in the example in b)
d) more than that, if one used the finite verb "are" in the present tense above, even linking with a conjunction etc as in (b), the sentence would imply that these earliest methods are continuing in the present. This is in fact the case, but there's a very subtle difference in meaning where using "being" allows the interpetation of the sentence as having more to do with the earlier era referred to in the first half of the sentence to be a little smoother I guess. I'm sorry; I know I'm not explaining this well, but it's all I can really come up with for it.
Suffice it to say that the sentence is completely correct and this is actually a fairly common construction, especially in written formal English. It's less used in common speech, though I do use it myself,
being somewhat pedantic.
