Shapiro J A
J Biol Phys. 2002 Dec;28(4):745-64. doi: 10.1023/A:1021207310080.
Physicists question whether there are 'universals' in biology. One reason is that the prevailing theory of biological evolution postulates a random walk to each new adaptation. In the last 50 years, molecular genetics has revealed features of DNA sequence organization, protein structure and cellular processes of genetic change that suggest evolution by Natural Genetic Engineering. Genomes are hierarchically organized as systems assembled from DNA modules. Each genome is formatted and integrated by repetitive DNA sequence elements that do not code for proteins, much as a computer drive is formatted. These formatting elements constitute codons in multiple genetic codes for distinct functions such as transcription, replication, DNA compaction and genome distribution to daughter cells. Consequently, there is a computation-ready Genome System Architecture for each species. Whole-genome sequencing indicates that rearrangement of genetic modules plus duplication and reuse of existing genomic systems are fundamental events in evolution. Studies of genetic change show that cells possess mobile genetic elements and other natural genetic engineering activities to carry out the necessary DNA reorganizations. Natural genetic engineering functions are sensitive to biological inputs and their non-random operations help explain how novel genome system architectures can arise in evolution.
物理学家质疑生物学中是否存在“普遍性”。一个原因是，主流的生物进化理论假定每次新的适应性进化都是一次随机过程。在过去的50年里，分子遗传学揭示了DNA序列组织、蛋白质结构以及基因变化的细胞过程的特征，这些特征表明存在自然基因工程进化。基因组作为由DNA模块组装而成的系统，呈层次结构组织。每个基因组都由不编码蛋白质的重复DNA序列元件进行格式化和整合，这很像计算机驱动器被格式化一样。这些格式化元件在多种遗传密码中构成密码子，用于不同的功能，如转录、复制、DNA压缩以及基因组向子细胞的分配。因此，每个物种都有一个具备计算能力的基因组系统架构。全基因组测序表明，遗传模块的重排以及现有基因组系统的复制和再利用是进化中的基本事件。对基因变化的研究表明，细胞拥有可移动的遗传元件和其他自然基因工程活动，以进行必要的DNA重组。自然基因工程功能对生物输入敏感，其非随机操作有助于解释新的基因组系统架构在进化中是如何产生的。
