The positive(concentric) and negative(eccentric) portions of a rep, appear to have different effects on muscle growth. Understanding why one does it better than the other, could help us gear our workout routine for optimal muscle growth.

Studies on eccentric and cocentric rep training:

University of Alabama at Birmingham did a study on 10 male and female subjects, who did 8 heavy sets of squats per workout. One workout they did concentric, the other eccentric only contractions. They measured the amounts of IGF-1, IGFBP-4, and Androgen receptors in the muscle. The negative rep stimulated IGF-1 and lowered levels of IGFBP-4(which binds to IGF-1 to make it inactive) better than the concentric. The positive rep increased androgen receptor density (making it more responsive to testosterone) than the negative. From this study, we can see that eccentric reps induce growth more by IGF-1 and the positive mainly from testosterone.

Another study was done at UC Irvine by Ken Baldwin and other scientists, to find the chemical reactions behind eccentric contractions. They also found that they had a significant increase in IGF-1 over positive reps, but also in increasing MGF(mechano growth factor) and the lowering of Myostatin(an important chemical that regulates muscle growth).

Other effects of negative reps:

Besides the differences in hormonal and chemical actions, there is other reasons why eccentric portions of the rep
might be more effective than concentric. Eccentric contractions probably cause more muscle growth, due to the fact they cause more microtrauma on the muscle fibers. The positive portion of the rep causes very little muscle tearing damage compared to the negative portion.

Other possible benefits of negative parts of the rep, may be in the ability to stimulate hyperplasia muscle growth and muscle fascia stretching
.

Should we do eccentric only training then?:

One might conclude that it is best to do eccentric only training since it is more effective. However, eccentric only training is taxing on the system due to the increased muscle damage it causes.   It  would quickly lead to overtraining, without a subsequent drop in set volume. Doing half negative rep workouts, are also inconvenient and most bodybuilders prefer to be able to use the entire rep range. One alternative would be to modify your regular training routine instead, by lowering the volume slightly and emphasizing the negative portion of the reps more.   Negative emphasize training cannot be used indefinitely because your body will adapt (plateau) to it after a period of time, like with all training techniques.