Question: 1. The philosophy seems to promote man killing if he can reason it, but sometimes the reason is not really substantiated. What is to stop someone justifying themselves wiping out a species for a bad reason?

2. Some people do not have morals. What is to stop them creating a mass disease or such if they logically believe that they have to?

Answer: There is a short answer for both your questions: law enforcement agencies.
Objectivism is an individualist philosophy, but it does not hold that each person should be allowed to do anything that that person deems reasonable. In politics, Objectivism holds that no person should be allowed to initiate the use of force against any other. The determination of whether any given use of force is consonant with this principle is made by law courts and enforced by agencies like the police. In a society constituted along Objectivist lines, then, the right to life, liberty, and property of every individual would be rigorously protected, so long as the bulk of people in the culture, and especially the intellectuals, continue to uphold the basic philosophical outlook this presumes.
In your first question you are concerned about someone wiping out an entire species. This would be prevented by the enforcement of property rights. Since it would be highly unlikely for a person to own the entire population of a species, one would be prevented from killing the animals that one did not own. The law enforcement agency charged with protecting rights would stop or punish this individual if he attempted to kill the property of another individual. In those rare cases where one individual does own all the individuals of a species, then they would be permitted to kill them. The best protection under these circumstances is for concerned individuals to purchase some of the members of that particular species before the irrational individual does. This prevents that person from gaining full ownership of the species.
Objectivism would question the probability of this ever occurring. The resources, time, and effort needed to accomplish such an action would be great, and what is the gain for wiping out a species? The level of irrationality required for such an occurrence would be rare and self-limiting. That is, a person of such irrationality would be unlikely to be effective or successful precisely because of his irrationality. So while this could logically occur, the likelihood is slim.
In your second question, you are concerned about mass murder. This too would be prevented and punished by law enforcement agencies that protect rights. In the same way that the police, in cases of simple murder, protect people, the police also protect against mass murderers.

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