Context, context, context, my friend. Surely you're a deeper thinker than that. The context for the referenced passages makes it quite clear that Jesus and the other quoted persons are taking literally about another child of Mary.
John 2:12: "After this He went down to Capernaum, He, and His Mother, and His Brethren, and His disciples: and they continued there not many days." Disciples and brethren are mentioned separately here.
John 7:3-5 "For neither did his brethren believe in him." One of the stories that Catholics never hear, because they don't read the Bible cover to cover (only the parts the priests point them to), is that Jesus' biological brother James did not believe in him as Savior until his resurrection; after which James because the leader of the church of Jerusalem and died because he professed the truth of Christ. A lovely story which makes much sense.
Mark 6:3 "Is not this the carpenter, the Son of Mary, the Brother of James, and Joses, and of Juda, and Simon? and are not his sisters here with us?" Mentioning his mother, brothers and sisters surely has nothing to do with the general notion of a disciple being a brother.
There are at least another 8 similar passages where the context is clear. Jesus' mother Mary had other children.
And, lest you still be skeptical, try Mt 1:25:
And [Joseph] knew [Mary] not until she had brought forth her firstborn Son: and he called His name, Jesus!" Joseph didn't "know Mary" (in the Biblical sense) until after Jesus' birth.
Sorry, my friend, perhaps you need to do some delving into the Good Book personally. Good luck to you --
Did it ever occur to you that Joseph was older and may have had other children by a previous wife?
Thus these borthers and sisters could have been step-brothers or half sisters.