So, it's a question of 'unfair advantage', not cheating--and would be so even if she had known of her unusual state before the race in Berlin that caused such an uproar. Apparently Ms Semenya runs faster than other fast women because she makes more testosterone. But what's 'unfair' about it?
"This is a medical issue and not a doping issue where she was deliberately cheating," IAAF [International Association of Athletics Federations] spokesman Nick Davies was quoted as saying.
"These tests do not suggest any suspicion of deliberate misconduct but seek to assess the possibility of a potential medical condition which would give Semenya an unfair advantage over her competitors. There is no automatic disqualification of results in a case like this."
The question assumes that all women have an equal chance of becoming world-class runners. But, world-class athletes are an elite group, presumably not only because of how hard they train, but, at least in part because of the genetic make-up of their muscles and how they work. Even Ms Semenya's competitors run faster than women with shorter legs, or heavier builds, or muscles that don't fire as quickly, or due to less efficient oxygen usage, and their advantages are not considered to be unfair. Ms Semenya just happens to be the elite of the elite.
Copy number variation, in which we each have different numbers of copies of parts of our genome, occurs in all of us. Some CNVs are associated with disease, or traits like the sensitivity of our sense of smell. But most CNVs are of no as-yet known function. But suppose someone comes along who has, say, 3 rather than 2 copies of the erythropoietin gene, that helps make red blood cells (that handle oxygen and hence relate to endurance). Is that natural CNV any different, in terms of 'unfair advantage', than Epo doping, which is currently very much against the rules of sport?
Certainly as the relevant genotypes become known, there will be designer babies and they will be at a metabolic advantage over the normal population, for whatever reason. They will be so not because of doping but because of their inherited genotype. Of course, modifying the genotype for in vitro fertilization could be viewed as a kind of gene doping if it's designed to alter the future individual in some relevant direction, but in fact the intelligently designed would be functionally no different from someone who has the same genotype just by luck of the draw.
Much may have to do with the degree to which different genotypes actually improve performance, relative to the modifiable factors that currently affect who stands on the Olympic podium while their national anthem is played. If genotypic effects seem to be minimal relative to diet, weight training, skill training, practice, and wearing the best Adidas shoes, then there will be no big issues. After all, we are all genetically different already.
If it turns out that genotype can make a difference, naturally or because training can be tailored to the competitor's genotype, then we may reach a decision point. We could create new genotype-based competition subdivisions, much as there are weight classes in wrestling, or sex classes in most sports. Or, we could just decide that each athlete plays the cards dealt, and some have an advantage. Only those lucky ones will show up at the Olympics.
What counts as fair and what as cheating is culture-laden, potentially contentious, and not always an easy call. But whatever the definition, we can be sure that lots of people will try to use it to their advantage, and they will still be the ones breaking the tape.