I am an Assistant Professor at a University, and I joined it three years ago. My employer submitted my I-140 under EB1-OR in December of last year. 

We received an RFE asking us to show three years experience in research and teaching. Will the three years be counted as of the current date? Can I use my PhD time counting towards the three year experience? Thanks in advance!

You can use your PhD research towards the three years experience, if it contributed towards your outstanding accomplishments in the field. You can give an effective RFE reply by showing your Ph.D. work as outstanding, such as how many papers you were published during your Ph.D study and the citation number.