And, to your explanation on human organs and ice....the entire Universe is within the Supreme Being. Shiva Lingam stands for the Purusha, the Supreme Creator. Ice Lingam indicates that God can take any form. Human Body is itself a wonderful creation. Scientists have been studying and have not been able to understand completely on how some of the parts like Brain, etc. work.
Worhsipping stones - Have you ever seen a Idol installation i.e., Pratishta? It is not just a stone. Vedic scholars recite the vedas, perform other rituals and place a Yantra underneath the idol. Basically, they create a image of the God to be worshipped since you cannot see the God directly. Also, we are free to pray to Him by looking towards the open sky.
