Some words have two opposite meanings. Why?

Fans of ancient history may have thrilled to the news in the New York Times that a mystery was solved: “A Long-Lost Branch of the Nile Helped in Building Egypt’s Pyramids.” A new study, the subheading said, “confirms a long-held theory that builders used the river to transport the heavy blocks that comprise the ancient wonders.” But usage grumps may have scowled. Indeed, the line was soon changed: in the revised version, the wise old theory was “that builders used the river to transport the heavy blocks that make up the ancient wonders.”