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I am currently in a biomedical research PhD program. In my program, we have students from a wide range of background - biology (obviously), engineering, psychology, chemistry, etc.
I think your GPAs should be okay, especially since you've been working in a path lab and have a publication. Doesn't matter that the research/publication was in ecology/behavioral biology.
The only thing that may be of concern is lack of physics. You didn't take ANY physics in undergrad? A lot of programs require at least 2 semesters of physics, but I'm not sure how hard of a requirement that is.
It won't matter which you put first and which you put second. They will see both. I think education is usually listed as most recent to least recent. You could opt to just leave both GPAs off. I wouldn't include the undergrad GPA and omit the grad GPA, though.
If I were you, I would have the counselor address it in his or her letter, but I would ask him or her to not specify the disorder and just say that you were facing health challenges your freshman and sophomore years that are now being successfully managed. Unfortunately, depression and other mental illnesses are often viewed negatively by college admissions.
When my mother was alive, I loved Mother's Day! I loved picking our the perfect card and the perfect gift and planning something to make her feel special! Every Mother's Day she'd thank my sister and me for making her a mother and we would just laugh. I do not have children of my own yet (unless fur babies count), and although I adore my mother-in-law and am more than happy to celebrate her, Mother's Day is still difficult for me. I usually get a little down on Mother's Day, but am grateful to have had so many wonderful memories with my mom before she passed. She was my best friend and I like to believe she's still with me every day. Looking forward to one day when Mother's Day is a happier day for me.
I am so sorry to hear about your father's cancer diagnosis. I too struggled with having a parent battling cancer while I was in undergrad (my mom), who unfortunately passed away my senior year. Short of talking to the dean, I'm not sure what else you can do in this situation. It may be possible though to talk to each individual professor and see if they would be willing to allow you to make up some of the points you lost in another way.
Please feel free to reach out to me if you need support from someone who has gone through something similar. One last thing - spend as much time with your dad as you can. Get his voice on tape. Wishing you strength and peace.