After CCNY, Haines taught elementary school science at the Ethical Culture Fieldston School. He then became a laboratory assistant to Richard Block at the Boyce Thompson Institute where he studied the microorganism Ochromonas danica. When Block died in a plane crash, Haines took over his research projects. In 1964 he obtained his Doctor of Philosophy degree in chemistry from Rutgers University.
Haines became assistant professor of chemistry at City College in 1964 and full professor of chemistry in 1972, a position he held until retiring in 2007. In 1972 he co-founded the Sophie Davis School of Biomedical Education with University President Robert Marshak. This remarkable program took new undergraduates directly into medical school. It continues today as The CUNY School of Medicine. Haines taught biochemistry to undergraduates and served as director of biochemistry at the school from 1974 to 2006. Deeply committed to his students, he also taught remedial summer school and regularly counseled struggling students and their parents. On many occasions he was voted most popular professor.
Haines simultaneously conducted laboratory research and taught as professor of biochemistry in the doctoral program of biochemistry at the Graduate Center of the City University of New York. He has published extensively on the structure and function of living membranes, including on the function of cholesterol in blocking sodium leakage through membranes, and most recently on the function of cardiolipin in the mitochondrial membrane.
From 1994 to 2001, Haines chaired the [https://www.prdi.org/ Partnership for Responsible Drug Information], which organized lectures and conferences to educate the public about alternatives to the "War on Drugs."
Haines served as visiting professor at the Mitsubishi Institute in Japan, at the University of California at Berkeley, and in many other universities. On his retirement from CCNY, he became a visiting professor of biochemistry at the [http://www.sakmarlab.org/Overview/ Sakmar Laboratory at Rockefeller University].
In 2020, Haines was elected a Fellow of the American Association for the Advancement of Science "For initiating and setting up the CUNY Medical School at City College of New York to educate minority and disadvantaged students."