In the field of biosemiotics in our time, Ferdinand de Saussure's theory of semiology has been dismissed for its glottocentric, anthropocentric, and dyadic characteristics and as such unsuitable for the said field. Such accusation is symptomatic of an extremely narrow view of Saussure, which ignores the efforts he made in tackling problems concerning the unification of biology (natural sciences) and semiotics (human sciences). A broader view of Saussure, emerging from the newly-discovered orangery manuscripts along with his thought-provoking course lectures, reveals that his epistemology is actually grounded in evolutionary differences and the concept of uniformitarianism. In order to demonstrate the value of his ideas, this paper proceeds through five sections. (1) To begin with, the understandings and misunderstandings of key terms are summarized while seeking to reconcile arbitrary and relatively arbitrary (analogical) modes of consciousness within the network of differences that Saussure proposes in his manuscripts. (2) My study points out how such a network blurs disciplinary or systematic boundaries between language and non-verbal systems and how it might serve as a framework for appreciating true analogies between natural sciences and the science of language. (3) The paradox of analogy, torn between the synchronic and diachronic schemes of time, is discussed. This unravels several strings that have made the functioning of analogy into such a delicate point in Saussure's theory of evolution. (4) The concept of état de langue is made comprehensive in relation to appropriations of Darwinian model and Neo-Darwinian ideas. Saussure's model of evolution explicates the phenomenon of symbiogenesis, which is non-linear, non-adaptive, non-restrictive as regards localities, yet claims certain truths about nature and culture. (5) Finally, my study draws attention to the implications of conceptualizing non-linear evolution within and across systems. There are indeed disparities between Saussure's epistemology and that of biosemiotics: nineteenth-century confused epistemology reoccurred within biosemiotics in its early phase.