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DS9: "By Inferno's Light":

[Internment centre]

(Ikat'ika stops Worf as he crawls to a post.)

IKAT'IKA: Enough, Klingon. You have proven your worth.

MARTOK: Worf, you heard him. Enough.

WORF: I will not yield.

DEYOS: What are you waiting for? End this.

IKAT'IKA: It's over.

WORF: It is not over.

DEYOS: You heard him.

(Worf cannot stand, and Ikat'ika is breathing hard.)

IKAT'IKA: I yield.

DEYOS: You what?

IKAT'IKA: I yield. I cannot defeat this Klingon. All I can do is kill him, and that no longer holds my interest.

DEYOS: Shoot them both.

DS9 "Hippocratic Oath":

ARAK'TARAL: You caught him. I shouldn't have doubted you. Should we kill them ourselves or let the others?

GORAN'AGAR: I will do the killing.

(He shoots Arak'Taral.)

GORAN'AGAR: Take your ship and go.

BASHIR: Goran'Agar, if you stay here, they'll kill you.

GORAN'AGAR: Unless I kill them first. It would be better for them to die quickly in battle, than slowly as the drug runs out.

BASHIR: You don't have to do this. Even if we can't save their lives, there's no need to sacrifice yourself.

DS9 "To The Death":

OMET'IKLAN: That's as it should be. After all, I'm the First.

SISKO: As far as I'm concerned, on this mission, I'm the First.

(They lock eyes, and neither blinks.)

OMET'IKLAN: Until the traitors are found and terminated. After that, we shall see. Am I dismissed?

SISKO: For the time being.

{Later in the episode}

(Omet'iklan vapourises Weyoun.)

OMET'IKLAN: That was for questioning our loyalty. I think there's been enough killing for one day.

VIRAK'KARA: The Vorta will have no further use of this. (the white)

OMET'IKLAN: My men and I will remain here. There are still disloyal Jem'Hadar on this planet. They must be hunted down and eliminated.

SISKO: Good luck.

OMET'IKLAN: You fought well. But the next time we meet, we'll be enemies.

SISKO: I'll keep that in mind.

From these episodes we see a recurring theme from a few Jem'hadar. Once these Jem'hadar usually ones in power positions, that are a little older and more seasoned, get a chance to meet outsiders they show compassion, empathy, mercy, and a sense of fairness that's supposed to be bred out of them.

Is this pattern I'm seeing real? And if so where does it come from since they are genetically engineered? Is it so few and far between that it could be chalked up to being a genetic mutation of some sort?

Writers notes on the Jem'hadar are more then welcome.

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    I don't think a random mutation in one single generation could result in something as complex as empathy, if empathy was in fact removed from their genetic makeup. I would say that the above examples clearly show that it was suppressed and not removed. They also clearly show that it was able to resurface at times. I kinda think the answer is contained within the question. Would you mind clarifying why you find it confusing? – Misha R Jun 20 '15 at 6:30
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    It does seem to be the older more experienced officers who develops a sense of "warrior's honor". The younger ones just kill on command. Could be that as they grow older they start to think for themselves more. Probably part of the reason for their short lifespans. – Boelabaal Jun 20 '15 at 6:59
  • @MishaRosnach They are genetically engineered, not altered. I don't think they removed empathy, I think they engineered them exactly how they wanted them. – JMFB Jun 20 '15 at 7:59
  • @Boelabaal I agree, it's what I was thinking. Anything published that states this? – JMFB Jun 20 '15 at 7:59
  • Dupe of scifi.stackexchange.com/questions/80681/…? – Valorum Jun 20 '15 at 8:51
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The pattern about older Jem'Hadar showing some forms of mercy might be on the money. Consider the following excerpt from the Memory Beta page on the Jem'Hadar:

Without white the Jem'Hadar circulatory system would break down resulting in their eventual deaths. However, there were rare anomalies allowing some Jem'Hadar to produce the enzyme internally. The Jem'Hadar Taran'atar and Goran'agar both had this ability. Starfleet autopsies of Jem'Hadar found that it was a trait in some older Jem'Hadar, ten years or more, to begin to develop the means to naturally produce the enzyme in small quantities. (DS9 episode: "Hippocratic Oath"; DS9 - Avatar novel: Book Two)

(emphasis mine)

Now, you do point out that these are typically older Jem'Hadar who show this leniency; my expectation would be that if there is the possibility for these Jem'hadar to produce the enzyme they need naturally, they may begin to re-evaluate their lives slightly; no longer being dependent on the Founders, something they are taught from birth, would be considerably ground-breaking for them. Consequently, in those more seasoned Jem'Hadar, they may begin to question some of their beliefs. Just speculation, but it does seem to fit.

I doubt this would be a genetic change, but perhaps a biological one or psychological. I cover the psychological change in the above paragraph. Biologically, though, there may be a slight difference in the structure of the enzyme they produce naturally compared to Ketracil White, meaning there could be changes to their neurochemistry, establishing this tinge of empathy and mercy.

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    Good explanation. I wouldn't even call this a weakness, necessarily. Either the Founders don't care, because living ten years is beyond the Jem'Hadar's design specification; or it's deliberate, in that older Jam'Hadar "go soft" and are out-competed (and killed) by their younger and more competitive compatriots, thereby constantly renewing the Jem'Hadar command structures without requiring micromanagement. The final alternative is that perhaps you simply can't prevent a truly sapient being from eventually developing empathy, regardless of your abilities where genetic engineering is concerned. – Wolfie Inu Oct 20 '15 at 5:19

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