For me it ends up being a slightly different debate. It's not instinct versus science. It's nature versus science--or at least, my understanding of nature versus science.
I knew I could have a homebirth because my physiology supports it--I am a mammal and that's what we do. You don't see cows hooked up to IVs, or fetal monitors unless it's a Hathor the Cow Goddess cartoon. (I know some women have problems--I'm not starting a debate here. My point is that we are natural beings with all of the equipment, if it's supported right, to birth naturally.)
I knew I would breastfeed because my mom did and all of the women preceding her. I was no different than all of the other women in the world through all of history--I have breasts, so I will breastfeed.
My son was born with a foreskin, so we would not lop it off.
My kids did not have an aluminum/mercury/attenuated cells deficiency, so I felt no need to inject them with those ingredients.
In my thinking, the default is nature and what that means. Does it mean processed food and antibiotics at every sniffle, or does it mean real whole food and letting a fever burn off a bug?
I think true science begins with accurate observation to see what is and why. Next come hypotheses and experiments that help describe and suggest limits. Vaccine research doesn't seem to do any of this. Or, not much. The science doesn't try to understand nature and yet we are natural beings, despite the plastic, pollution and toxins that surround us.
When my kids were little, a woman in a playgroup with me said that she had read an article in a parenting mag (not Mothering...) where the author had suggested that there's not enough medicating of ADD or ADHD. They thought many more kids should be drugged up.
My thinking was nature based--how is this generation different than any other generation--how could their chemistry be wired wrong? My answer was that it couldn't be different except to the extent that maybe it had been messed with.
Perhaps routine ultrasound, invasive prenatal testing, invasive medical procedures during birth, formula, vaccines, CIO, and all of the other western medical approaches to pregnancy and birth and infancy do have a negative effect on brain function or digestion or metabolism or every other system in a newborn.
Maybe these things add up. A stressed out baby has different brain waves and breathing and body temperature than a baby at peace. That is science. That is also nature.
A formula fed baby has a different gut flora than a breastfed baby--also nature and science.
I also think people get stuck into thinking that they are healthy because of western 21st century medicine. The medical community can identify when things are going wrong, but I don't think they are much good at fixing it. Or they identify symptoms, treat them, and ignore the underlying cause. That's not all that scientific to me.
My kids are healthy. Again, I don't want to debate, but, they have none of the health issues that so many of the kids in our homeschooling group have. These other kids have been vaccinated and get drugged up when sick. Solids were introduced at an early age. Fevers were always treated with drugs. They have food allergies, skin conditions, asthma. They get colds easily and often.
These other parents have bought into an allopathic or conventional medical approach to health and their kids are the sicker for it. I don't think true science supports what they have done. Nature certainly doesn't.
I guess my instinct tells me to follow nature and try to understand that. If science seems to explain that well, then I accept it.