Thanks for a great question. I'd almost have to go ine-by-line to address all of your thoughts, but that would end up being close to a book. Instead I'll address some general ideas and a few specific lines, and hopefully that will engender conversation.

There is a vast difference between "pre-programming" and the limitations of biology. Any biological organism or mechanism is, by nature, only capable within its biological capacity. Therefore it's a misnomer, as well as a misunderstanding, to claim that biology has been "pre-programmed" with intentional flaws to create problems. God is not wholly responsible for suffering. Instead, the inherent limitations of non-divine beings (rooted in biology and governed by the processes of mutation and selection). God is uncreated, and therefore anything that is created is non-God and subject to the pros and cons, strengths and weaknesses, benefits and harms of biological reality.

> to act in a certain way.

To act in a certain way, yes, but to act without the possibility of deleterious mutation, no. Part and parcel of the process of mutation and selection necessarily involves deleterious mutation and the process of being selected [i]against[/i]. Without this dynamism in nature, the process of thinking itself would be impossible, and evolution itself would be impossible. Thinking can involve the brain creating new pathways. Bodies repair themselves (for instance, the heart after a heart attack) by creating new blood flows. Human cells continually exercise autophagy to refine the organism, but these processes are only possible in a dynamic environment where the negative and the positive develop side-by-side.

> These systems produce mental disorders, cognitive problems, and emotional malfunctions. We are preprogrammed to suffer, and God did the programming.

It's correct that these systems on occasion create mental disorders, cognitive problems, and emotional malfunctions, but that does't require that they were pre-programmed to do that. Instead, they were preprogrammed to succeed (biology is astoundingly set up to produce effective life, as we see all around us) with the necessary possibility of negative mutation. That negative possibility is what makes the systems work, so it's wrong, in my opinion, to regard these as not only unnecessary but then also morally malevolent on the part of the Creator.

> We are preprogrammed to suffer, and God did the programming.

I don't think this is fair to say. Suffering happens by nature of the interaction of life forms on Earth and by virtue of the necessary non-divinity of life, but it's incorrect to claim that God programmed it that way. It's very possible, by the reasoning of some philosophers, that we are in the best of all possible worlds, and God is to be credited for that, not blamed. That discussion is a much longer one.

> Think of mood disorders.

Mood disorders, as we know, can be just as much a function of nurture as nature. Our environments, particularly relational environments, create far more mods disorders than our genetics. Mom and Dad, Uncle Phil, and our adolescent peers are far more responsible for mood disorders than genetic propensity, though genes can provide a predisposition for their development.

> There's also environmental conditions which fashions our neural system.

Yes, but then I would assume you would not blame God when you blame environmental conditions.

> Down syndrome, cystic fibrosis, They were programmed by God to suffer and die.

There's no reason, biblically, to think that God programs genetic disorders. Such disorders are the result of deleterious genetic mutation, not the direct action of God.

> Some of these replicating molecules became viruses

Yes, and again we know that viruses are part of the "pros and cons" picture of the viability of biological life. There are ways in which viruses are responsible for a certain amount of health and stability in the ecosystems that allow life. They also mutate to harm. Such is the nature of dynamism, and a dynamic system is to be preferred to a static one. Though there are certainly down sides to dynamism, we are far better off in a dynamic environment than a static one.

> How is God good if he is responsible for how our neural networks evolved?

Therefore God is good for superintending our neural networks. As of the present time, we humans know [i]nothing[/i] as complex and marvelous and capable as the human brain. It's a functional miracle of biology and consciousness.

> Whatever your response to this may be, how do you know that you had any choice to think that at all?

You speak as if the mysteries of consciousness are well known and that they are known to be biological. This is not the case. Consciousness is still one of the great mysteries of the universe: where it came from, how it works, and what is its nature. It's premature to conclude that choice is an illusion. Now, for instance, someone like Annika Harris speculates that consciousness is a fundamental reality of the universe. To be fair, she also thinks that free will is non-existent, but I find her position to be somewhat self-contradicting. That's a longer discussion also. In my humble opinion, free will is necessary for true rational thought, for science to be real, and for essential human qualities like love and justice to be authentic. That's what makes me think free will is essential to human life and is a reality.

> It was all the result of natural processes

The purely materialistic view of life is self-defeating. In a book called [u]Understanding Scientific Theories of Origins[/u], the authors write, [quote]"A reductionist materialist might object that intelligence is ultimately the product of the same basic physical processes that produce everything else in the universe. That is, intelligence is reducible to brain functions, which in turn are reducible to the processes chemists and physicists study. But this objection will not do, because we then would have no grounds for trusting intelligence. If intelligence is the product of physical and chemical processes that don’t aim at truth, cannot understand, and are incapable of making judgments, then reason is unreliable. Physical processes don’t lead us to meaning, judgments, values, and logic (entities that do not exist in the subatomic, chemical, biological, or molecular phenomena). This reductionist-materialist objection is self-defeating."[/quote]

> So we don't choose what we think ... How is God good if he gives us the illusion of free will?


You can't know this. It may just be a false premise on which you are basing your conclusion.

> How does the existence of suffering from biological sources align with how God presents himself in the bible (abounding in steadfast love; giving Israel a choice)?

As I have briefly outlined (and, as I said, one could write a book in response to your very good questions), suffering was not necessarily preprogrammed in by God, and free choice may very well be not only real but necessary. Therefore God would very easily be good and not malevolent, which is the biblical picture.

It is difficult to believe that God is good because it becomes evident that God is solely responsible for suffering. A common rebuttal to the problem of evil involves God giving humans autonomy. I'm not talking about human malevolence here, however, but about illness/disease and our apparent lack of free will, which is the worst suffering.

Illness and Disease

If God was the great intelligence who orchestrated all these events, then he guided the first replication of molecules, and some of these molecules evolved to become nucleotides, they grouped together and became instruction manuals for our bodies, and proteins instructs molecules to act in a certain way. Proteins made neurotransmitters and these formed electro-chemical connections. We don't choose how our neurons group together to become systems, and we have no choice in how these systems affect our cognition, our emotions, and our behavior. These systems produce mental disorders, cognitive problems, and emotional malfunctions. We are preprogrammed to suffer, and God did the programming.

Consider the people many of us would consider "wicked" or "evil". Many of them are psychopaths and theists would consider their antisocial and violent behaviors to be "sinful". In the Christian framework, sin separates us from God, but this population has no choice but to "sin". They're preprogrammed not only to have empathy deficits and to be dishonest, but they're programmed with the inability to make emotional connections with others and feel the gnawing unending frustration of boredom/understimulation (for anyone with dopamine deficits, you have a taste of what this feels like). So not only are they preprogrammed to sin, they're preprogrammed to feel empty. That's suffering. Others are preprogrammed to be tormented by imaging things that aren't there, have fragmented thinking, and feel disconnected from reality. That's suffering. That's just one example of genetic disorder.

Think of mood disorders. There's also environmental conditions which fashions our neural system. Heightened stressors in our environment inevitably caused our malleable neural system to become anxious or depressed whether we're in danger or not. Now we have panic attacks, meltdowns.

Others are programmed to have a physical disorder. Take your pick on any video on this channel and you'll question God's goodness. Down syndrome, cystic fibrosis, They were programmed by God to suffer and die.

Some of these replicating molecules became viruses. Through natural selection, these molecules began to hijack cells to harm the body. There's no need to elaborate on the pain involved in viral infection. If God conducts or at least supervises evolutionary events.

2. Free will

How is God good if he is responsible for how our neural networks evolved? It's not just a psychopaths problem. We're preprogrammed to be malevolent. Think of it, all the trillions of neurons working together responding to stimuli, and the results are our thoughts and actions. We don't choose what we think, our thoughts just come out of nowhere. We respond without thinking, we exhibit tics and quirks which are out of our control. Whatever your response to this may be, how do you know that you had any choice to think that at all? Did you have any choice but to type a response? It was all the result of natural processes. So we don't choose what we think, therefore we don't choose how we act, so we engage with God the way we do and consciously watch our bodies perform without our control. Trapped in a VR system and forced to experience a horror movie. Why would a good God subject us to such torture? We're cognizant of the fact that we have no control. How is God good if he gives us the illusion of free will?

How does the existence of suffering from biological sources align with how God presents himself in the bible (abounding in steadfast love; giving Israel a choice)? If we don't have free will, this doesn't just put Gods goodness into question, it challenges the whole theistic framework itself!