The inquiry into the essence of organisms has long been a thriving topic in biology and philosophy. Hypothesises are commonly employed in biological research to understand lives. These hypothesises can be grouped into two categories: ① the machine hypothesis, likening the components and organizational structure of organisms to the operation of machines, and ② the autopoietic hypothesis, likening organisms to complex systems with purposeful and unique attributes. Both play an epistemic role in various fields of biology, serving as theoretical hypotheses, heuristic tools, and means of scientific communication. The machine hypothesis, for instance, has been influential in areas such as molecular biology and systems biology, where organisms are viewed as intricate machines made up of interacting components. The autopoietic hypothesis, on the other hand, has been more prominent in theoretical biology and philosophy of biology, highlighting the self-organizing and self-producing nature of living systems. The development of synthetic biology, which aims to redesigning and constructing biological systems from scratch, has challenged the traditional dichotomy between natural and artificial entities. Both the machine and autopoietic hypothesises are reflected in the advancement of synthetic biology, as researchers attempt to engineer living systems using principles and methods adapted from various disciplines, including engineering, computer science, and materials science. While the hypothesises serve epistemic purposes, their usage also raises some controversies, particularly in the context of synthetic biology. The conflation of ontology and epistemology, where hypothesises are mistaken for literal descriptions of reality, can lead to ethical concerns. For example, the machine hypothesis may suggest that organisms are merely complicated machines to be manipulated, potentially diminishing their intrinsic value and ethical status. This article examines the origin and clarification of these two hypothesises, their applications in synthetic biology, and addresses the potential confusions and ethical implications arising from their usage. It advocates for a cautious approach to the usage of the epistemological hypothesis, considering both its epistemic impact and ethical consequence. As synthetic biology continues to advance, it is crucial to maintain a critical and nuanced understanding of hypothesises employed, recognizing their heuristic value while also acknowledging their limitations and potential pitfalls. The discussion of hypothesises for organism origins in the context of synthetic biology highlights the importance of interdisciplinary collaboration and dialogue between scientists, philosophers, and ethicists. By examining the philosophical and ethical issues of hypothesises, we can better navigate the complex and rapidly evolving landscape of synthetic biology, ensuring that our scientific endeavors are guided by a deep appreciation for the intricate and multifaceted nature of lives.