Much confusion in genome-wide studies results from mistakenly interpreting correlation as causation. Zhao et al. observe a positive correlation between the codon bias index (CBI)—the extent to which a gene uses preferred synonymous codons—and the nuclear messenger RNA (mRNA) concentration among Neurospora crassa genes. This correlation could have originated from the processes of 1) high CBIs causing high mRNA levels, 2) high mRNA levels causing high CBIs, and/or 3) a third factor concordantly altering the CBI and mRNA level of a gene. Considering only process 1, Zhao et al. deduce that “codon usage broadly influences mRNA levels through transcription.” Below, we explain why processes 2 and 3 are likely, and why Zhao et al.’s conclusion is unwarranted.