Bad behavior (and therefore bad kamma?) due to physical ailments

"If his cyst was caused by past kamma, and if his bad behavior is caused by the presence of the cyst, then this implies that his present behavior is caused by his past kamma and he has no control of it. Is that true?"

He has control of his present behavior, but he doesn't have control due to ignorance. The bigger the ignorance, the less control of behavior he has.

It is not the cyst that is preventing him to have control of his behavior. It is ignorance. Let me put it this way so you can understand:

Suppose a child is born. Suppose this child, due to good kamma, can live a very long life. Suppose this child, due to bad kamma, is born with a cyst. Due to the cyst, he harms others. Suppose every time he harms another being, that being harms him back and causes him immense suffering. Suppose the child is harming others every time he sees a being, no matter what that being is. Suppose his parents take care of him and teach him how to get water, food and shelter. The child grows up into adulthood harming others and feeling immense suffering of his body due to others harming him in retribution to him harming others. The child harms others 10 years and feels immense suffering of his body due to his harming others. He harms others 20 years, 30 years, 40 years, 50 years ... all these years feeling immense suffering of his body due to him harming others. What do you think, would this child harm others more or less, after 50 years of harming others and feeling immense suffering of his body due to others harming him in retribution to him harming others? He would harm less. Why? Because he learned that by harming others he would feel immense suffering of his body, thus he decides not to harm others.

The story above is an extreme example, but this is exactly how beings get rid of ignorance. This same mechanism is at work all the time, be it in a subtle, non visible way (examples are diseases of the body and/or mind, or normal feelings of anger/sadness to disturbing/sad events), or an obvious, visible way (example is criminal behavior, having failed relationships in adulthood, compulsive lying, drug/alcohol/other addictions).

"If his bad behavior was caused by the presence of the cyst, then would Andrew be creating bad kamma (by attacking the girl) due to bad intention, or would he not be creating bad kamma (by attacking the girl), because it was due to the cyst and not due to his own intention?"

Andrew was creating kamma.

Was he creating bad kamma? Probably yes. How much bad kamma? We can't know for sure. It all depends why he acted upon his intentions to harm others.

Once the cyst was removed, he stopped harming others. Thus, he could see that he acted harmfully due to wrong views, thus, his bad kamma created while he was still having the cyst, has exhausted.

"What did the Buddha teach about the physical body (including brain) and its ailments or conditions, affecting the mind and kamma?"

He taught that from ignorance, there comes birth. From birth there comes diseases (ailments or conditions affecting the mind) and intention (kamma) and all the rest.

Please be aware that "birth" does not mean literal birth as we understand it. Also, "birth of being" does not mean literal being with a physical body as we understand it. It could be any birth, any being, any physical or non-physical body ... what is meant by birth, is merely a birth of self - the 5 aggregates. These 5 aggregates could be in any combination. The combination depends on ignorance.

"How do we avoid bad kamma, due to mind-influencing effects caused by physical conditioning?"

There are times when we can't avoid bad kamma, due to ignorance. In such times we have to experience this bad kamma through suffering in order to learn how to avoid it in the future. In this way we are eradicating ignorance and gaining wisdom. When ignorance is eradicated enough, complete liberation from suffering can be attained.

"How could Buddhist teachings help a person like Andrew (before his cyst was removed)?"

I think hardly. If he is not able to grasp the teachings, he would not follow the teachings. Sometimes there is nothing that can be done to liberate a being from suffering in his former life. It is not your fault, nor the fault of the being, nor anybody's fault.

The reasons for bad deeds by thoughts, speech and bodily actions are always either not-knowing, desire for pleasure (greed) or desire to avoid pain (aversion). So when ever such is the cause, there is "bad kamma "made", if done in harmful ways. If escaping from pain and gaining pleasure is made based on knowing, such is "good kamma". So in learning and teaching the means of the Eightfold path one could help. Outside of that, there is no real help.

In cases where one is incapable for such, just the reducing of touch which causes him/her pain, would be "helpful" if one is able to do so in rightouse ways.

[Note: This is a gift of Dhamma and not meant for commercial purpose or other low wordily gains by means of trade and exchange.]

If his cyst was caused by past kamma, and if his bad behavior is caused by the presence of the cyst, then this implies that his present behavior is caused by his past kamma and he has no control of it. Is that true?

Kamma is intention (AN 6.63). The cyst is not caused by past kamma because the boy never intended to have a cyst.

If his bad behavior was caused by the presence of the cyst, then would Andrew be creating bad kamma (by attacking the girl) due to bad intention, or would he not be creating bad kamma (by attacking the girl), because it was due to the cyst and not due to his own intention?

This question is not related to the core lokuttara (supramundane) Buddhist teachings because the core teachings explain ignorance is the creator of intention rather than a self (refer to SN 12.17). This question, about the kamma of a self ('satta') is defiled & mundane (MN 117; two sorts of view).

The pain & irritation caused by the cyst only creates bad kamma when the boy is attached to the kamma & takes the results of the kamma personally (becoming; AN 3.76).

If after the cyst is removed the boy's mind has no recollection of the kamma, it is not bad kamma. Or if the boy remembers the kamma & is completely remorseful, unable to believe he performed such an action & incapable of repeating the action in the future, the kamma is purified & finished.

What did the Buddha teach about the physical body (including brain) and its ailments or conditions, affecting the mind and kamma?

SN 22.59 is the 2nd sermon. Buddha taught each aggregate is subject to disease or illness (ābādhāya).

SN 12.2 & MN 9. The 2nd condition of dependent origination, affected/polluted by ignorance/ asava/ hindrances, is the kaya-sankhara (MN 44; in & out breathing), which in turn conditions the elements of the physical body (rupa). Thus, ignorance includes the anusaya/asava/hindrance (MN 9; AN 10.61) of ill-will (AN 7.11) and this causes the breathing (kaya-sankhara) to be agitated, which causes the nama-rupa (mind-body) to be agitated. Meditators that experience all-kaya (stage 3 in MN 118) understand how the unwholesome mind (nama-kaya) causes the breath-kaya and rupa-kaya to become agitated & stressed. Thus suttas such as SN 12.25 explain how kaya-sankhara (in & out breathing), affected by ignorance, cause kaya-cetana (bodily-intention).

D.O. -> ignorance/asava -> ignorant kaya-sankhara -> ignorant consciousness -> ignorant nama-rupa -> ignorant contact (avijjā­samphas­sa­jena) -> ignorant kamma

How do we avoid bad kamma, due to mind-influencing effects caused by physical conditioning?

For the boy, this was not possible, because his mind was too young, too immature & incapable of training. But for us, we can only be mindful that our mind, due to our body, is subject to irritation & short-temperedness (paṭighānusayo) due to painful feelings (vedana).

How could Buddhist teachings help a person like Andrew (before his cyst was removed)?

Very difficult to help Andrew to be aware & sensitive to how his actions might harm others & to be vigilant. If it was an adult who was once normal & had practised then the adult could be helped. But a boy without any prior training or moral sensitivity is difficult to help. It is like trying to help victims of child abuse, which is possible, but difficult. A 9 year old having a physical brain abnormality causing physical pain, pressure, oppression & thus anger in the brain is difficult to train.

In abhidhamma.-

There are 4 type of minds:

1. wholesome-root functional mind, good kamma.
2. unwholesome-root functional mind, bad kamma.
3. root's effect functional mind, kamma's fruit.
4. rootless functional mind, neither kamma nor fruit.

In one's life process:

1. human born just by wholesome kamma, but some organ, i.e. cyst, can arise by unwholesome kamma after born.
2. kamma has making body-sense for touching touch.

each mind's full process at body-sense:

3. contact of 3 dhātu: 1) touch arise & 2) body-sense arise & 3) 4th mind arise for to decide the kind of 3th mind, wholesome-effect/unwholesome-effect, that compatible with that touch (same time).
4. then 3rd mind knows that touch at body-sense, both are arose by kamma-cause.
5. then another 3rd minds know that touch by kamma-cause 2 times.
6. then touch is reached by 4th mind again for to decide the kind of 1st, 2nd, or 4th minds should arise to do new kamma in body.
7. then 7 times arising of 1st or 2nd mind and do new kamma.
8. then 2 times arising of 3rd minds.
9. then body vanished.
10. Above mind process, at body sense, can loop moreover trillion times per second, uncountable. There are more types of mind process than I show in this answer, this is just the example.

You can see that we receive fruit of old kamma and make new kamma in the same process and the same body.

His bad behavior is 1st, 2nd, and 4th mind. Just 3rd mind and a cyst organ are kamma's fruit.

So, the cyst organ is not a main cause of bad behavior. But previous bad behavior is the main cause of present bad behavior.

The cyst organ is just a fruit of the past bad behavior. It maybe one of side cause, but it is not the main cause. A human maybe feel very hurt and hard to decide to make arising of wholesome mind or unwholesome mind because of hurt at body-sense at 4th step but the decision is the 6th step. So, the 7th step is done by his decision in 6th step, not by kamma.

In the other hand: many example in tipitaka and commentary shown that there were many arahanta who were suffered at body-sense, but no one of arahanta have unwholesome-kamma, bad behavior.