Abstract
In their manuscript1 entitled “No support for the adaptive hypothesis of lagging-strand encoding in bacterial genomes”, Liu and Zhang attempt to refute the findings of our 2018 Nature Communications paper2. Here, we demonstrate that multiple key claims made by Liu and Zhang are factually incorrect, and that their overall conclusions, including the title of their paper, are invalid. We show that multiple existing controls already preclude the null hypothesis proposed by Liu and Zhang. We also show that the authors falsely claim that we did not publish key data, when in fact, these data were presented in our manuscript. Similarly, we point out that the authors falsely claim that we made comparisons and logical arguments we never made. Furthermore, the authors claim that they reanalyzed our data when in fact they did not. Therefore, they could not, by definition, have identified errors in our data. Our reanalysis of the Liu and Zhang data reveals that the main problem is that the authors simply do not understand the meaning of the term “inversion”. This caused them to misjudge the limitations of both their own inversion detection technique and ours. In fact, we find that the Liu and Zhang method cannot, specifically, identify inversions. Lastly, we provide new empirical evidence demonstrating further that our method works properly as described in our original manuscript. We conclude that Liu and Zhang’s manuscript has no rational basis, and that our original hypothesis meets the criteria for acceptance based on their own standards.
Competing Interest Statement
The authors have declared no competing interest.