DNA-based device construction propounds an alternative, marginally less simplistic view of biological systems, asserted with equal assurance to the genetic program idea though clearly inconsistent with it. This method seeks to produce biochemical-genetic circuits that constitute “standard biological parts” or “BioBricks,”vi molecular Lego blocks that can be put together to build new life forms with desired properties.
The field’s Registry of Standard Biological Parts exemplifies the difficulties of implementing this program in the face of complexities of even the simplest living organisms. Whereas the Registry promises "a collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems,"vii presenters at a synthetic biology meeting in July 2010 concluded that, of the 13,413 items then listed in the Registry, 11,084 did not perform as advertised.viii
DNA-based device construction nonetheless capitalizes on and has contributed to the burgeoning field of systems biology, which works not only with genes, but also the physics and chemical dynamics of interacting gene products and cells on multiple spatial and temporal scales.ix Our best understanding of how these systems work comes from mathematical and computational models.
Even so, the results from these models seem to indicate that "partition[ing] of a network into small modules…could in some cases be misleading, as the behavior of these modules is affected to a large extent by the rest of the network in which they are embedded."x In fact, simple genetic networks with minuscule changes can give rise to qualitatively different or even opposite effects.xi Furthermore, many proteins change their structure and function depending on the context.xii
The major conceptual deficiency of synthetic biology, however, arises from its side-stepping of the evolutionary history of all present-day organisms (e.g., those that genome-driven cell engineering seeks to reprogram and DNA-based device construction hopes to embellish). This pertains even to much work in the scientifically most fundamental branch of the field, protocell creation, which seeks to construct the minimal units of life.
When the original, ancient protocells arose more than 3 billion years ago from nonliving components, they most likely contained no DNA, RNA, protein, or membrane-forming lipid (i.e., water-insoluble) molecules; different molecules provided the material substratum for ancient life.xiii,xiv Protocells made from modern biomolecules, however “basic” they may appear, provide little insight into life’s origins.
When it comes to the more practically and commercially driven branches of the field described in this article, there is little acknowledgment that genomes of present-day cells are overwritten and revised records of the billions of years of evolution since DNA became the primary genetic material. Fundamental cellular mechanisms are therefore impossible to decipher by simply reading (or writing) any modern organism’s DNA sequence.