 The problem with the first approach is that it is largely motivated by the assumption that the nucleotide sequence is what contains all the important information in the genome. But in fact it has become increasingly clear that this is not the case, especially as a result of the growing understanding of epigenetics. Epigenetics is the study of material modifications of the genome that affect what parts of the genome sequence are or are not transcribed into RNA, the first stage of the process by which the genome influences the containing organism. The two most well-studied classes of epigenetic modification are methylation, the attachment of a methyl group (-CH3) to one of the four nucleotides, cytosine, and various chemical modifications of the histone proteins, proteins that form the core structure of the chromosomes, and around which the DNA double helix is wrapped (Bickmore &amp; van Steensel 2013; Cutter &amp; Hayes 2015). The nucleotide sequence, then, provides the (extremely large) set of possible transcripts that the genome can produce, but the epigenetic state of the genome determines which transcripts are actually produced (Jones 2012). Both features of the genome (qua material object) must be specified, therefore, if we want to understand the biologically relevant behavior of the whole system.