Do the noble Qur’anic verses, "He found it setting in a spring of dark mud" contradict modern science, and is the soul created or is it from the command of Allah, like "Ruh Allah" (the Spirit of Allah) mentioned in the Qur’an?

The soul, by consensus among Muslims, is a created entity. Its attribution to Allah in verses like, "Then We breathed into him of Our Spirit," is an attribution of honor and veneration, similar to the attribution of the Kaaba as "the House of Allah." And His, the Almighty's, saying: "Say, 'The Ruh (spirit) is from the command of my Lord,'" means "that which is commanded," and there is nothing in it to indicate that the soul is uncreated.