I am sitting here making sure that my first year courses are all set for September and just read a reply from the chemistry advisor (Paul) saying that if I want to take chemical biology second year, I need to take MATH 1A03 instead of 1LS3. However, the course calendar says I don't necessarily have to take MATH 1A03. Do you really need to take MATH 1A03 to do well in Chemical Biology?

No.
I took math 1LS3 last year and still got into chem bio.
HOWEVER, the admissions requirements for programs do change from time to time.
And the only place that I can see you needing to know math very well would be kinetics.

The requirements to get into chembio are here: http://registrar.mcmaster.ca /CALEN...nt/pg1553.html

I also got into chembio after only taking 1LS3, so unless they change the requirements, it shouldn't be a problem.

However, they used to require 1A03+1AA3, and it's possible that they'll go back to that if they decided that we were really lacking in math skills. Many chembio kids took 1AA3 and/or 1B03 as electives anyways, though. I'm not sure why you were told they require 1A03...maybe email them back and ask why the course calendar says something different?
Within the physical science departments (chem/chembio, physics/astronomy, medical physics) there's a huge bias against the 'life sci' versions of physical sci courses...such as math 1LS3 and physics 1L03. They'll always encourage you to take math 1A03 and physics 1B03, but unless they're changing things, it shouldn't be a requirement. Your best bet is to email back for clarification

He probably advised you to take Math 1A03 because of the physics requirement, I cannot remember if it's either Physics 1B03 or L03 that's needed, but for 1B03, math 1A03 would be a lot more help.

Everybody seems to be saying that (Math 1A03 helps with Physics) but ...apart from knowing how to integrate a polynomial, I don't really remember why it was so useful.

It helped me with uncertainties. There's always at least one uncertainty question per midterm and one of them, differentials saved my butt. There was another question which had to do with integration but it was more graphical.

eeevil uncertainties although you don't technically learn multivariable/partial derivatives until the end of 1AA3, knowing the basics will definitely help you/let you figure it out yourself.

It also helps you to understand where all of the equations come from, and their relationship to each other (since some equations are the derivative or integral of another), and understanding these relationships helps you out a lot with the theoretical questions. Some theoretical questions required you to take the derivative or integral of something else, too.