I’m not a scientist or a theologian. But it can definitely be a big paradigm shift to go from thinking God created everything and is actively controlling it all to realizing we have free will, and so do other animals. There are different ways to think of God being in our lives. How many times have you just chosen to do something, went to some place, did something, and just came across someone to share the gospel with? I think the Holy Spirit interacts with us but does not interfere with our free will.
I’m not sure why the gender thing is more of a battle than any of the other things as far as naturalism goes. For me I was unsure for a while because I never heard any convincing arguments. It was all just “ trust them and feelings “ and it just meant very little to me. I need evidence to come to a conclusion or rather I need it to really defend a position or change my mind.
In a nutshell this is what evidence convinced me about gender.
So we all basically start off as essentially females in the womb and several weeks later , somewhere under 2 months I believe, the Y chromosome is activated in the males and they begin developing testosterone. Up until then, morphologically we are all female. Then our genes begin to develop us into male or female. But at the same time we can’t just go off of genitalia because there are intersex people whose anatomy just is unclear, to the point even medical doctors are not always certain. I believe intersex people are mentioned in the Bible as eunuchs.
New American Standard Bible
12 For there are eunuchs who were born that way from their mother’s womb; and there are eunuchs who were made eunuchs by people; and there are also eunuchs who made themselves eunuchs for the sake of the kingdom of heaven. The one who is able to accept this, let him accept it.”
So it’s mostly clear what it means by eunuchs who were made that way or who made themselves that way. That’s men , or maybe even people in general, who have had some kind of surgery don’t to their privates. But it mentions those born that way and so logically it means someone born with non traditional genitalia. Which sounds like intersex. Jesus accepted them and so did the apostles. So if a mutation can occur to cause ambiguous anatomy then perhaps we can just go with chromosome which are typically XX for females and XY for men. But the issue is that we also have XXY , XXXY and maybe a few others. But then we could argue well if there is a Y then they must be make regardless of how many X there are but the issue with that is there are women who can naturally get pregnant and give birth who have XXXY chromosomes. So that means we have males and females with Y chromosomes and we have males and females with ambiguous biological sex.
This is further complicated by the fact that our body has around 24,000 genes, or at least protein coding genes and I’m not sure how many transcribing genes we and we have nucleotide bases of DNA: adenine (A), cytosine (C), guanine (G) and thymine (T) that makes up 60 something codons. I’m not sure how many ACGTs we have in our body but they say each person has several billion of them. There is a lot we still don’t know but I am guessing with billions in play, some errors can definitely affect us in ways that we may not know yet about gender other than the typical things you hear.