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Published in Phillip A. Laplante, Dictionary of Computer Science, Engineering, and Technology, 2017
artificial life the attempt to understand the emergence of life by re-creating possible life-forms as simulation programs on computers and studying their behaviors. In other words, rather than using a descriptive approach as in biological disciplines, a synthetic approach is adopted to understand those aspects of the life phenomenon that are independent of the media in which it is implemented. According to Langten, the artificial life approach allows us to understand not only the current existing lifeforms (“life-as-we-know-it”), but also other lifeforms which are feasible but not yet created in nature (“life-as it-could-be”). Evolutionary computation is usually adopted to simulate the evolutionary aspect of life emergence. Examples of artificial life programs include Tierra, Swarm, and Boids.
How to Untangle Complex Systems?
Published in Pier Luigi Gentili, Untangling Complex Systems, 2018
The research line called “Artificial life” refers to the theoretical studies and the experimental implementation of artificial systems that mimic living beings. Its birth is normally attributed to Chris Langton, who used the term as a title for the “interdisciplinary workshop on the synthesis and simulation of living systems,” organized in September 1987, in Los Alamos, New Mexico (Langton 1990). Although life has been studied for a long time, its fundamental principles are still hidden (Schwille 2017). In fact, there is not a universally accepted definition of life, and we do not know if the project of producing artificial life is feasible yet. This state of affairs means that the first level of the analysis of life, the computational level (refer to Figure 13.5), is incomplete. We can have an idea of the complexity of life if we compare a BIS with a von Neumann computer. A peculiarity of BIS is the lack of crisp boundaries between memory, processor, input and output components (Brent and Bruck 2006), and between software and hardware. The hardware of BIS is made of macromolecules, such as DNA, RNA, proteins, and simple molecules and ions. But DNA is also the software (Ji 1999). The DNA code uses the four nucleotides (adenine, cytosine, guanine, thymine) as letters; the genes as words; the conformations of chromatin as sentences. As we learned in Chapter 12, a BIS is more comparable to a Neural Information System. In fact, in a cell there are sensory proteins that collect information; such information is processed within the signaling network; the output of the computation triggers the genetic network; the latter has the power of affecting both the metabolic and the signaling network. Systems Biology investigates the characteristic networks of a cell and their interactions (Klipp et al. 2016). The best way to check our degree of comprehension of life is to develop Systems Chemistry (Ashkenasy et al. 2017) and try to implement a so-called protocell (Luisi 2006). A protocell is a system that should mimic the first unicellular organism supposed to be the ancestor of all forms of life on Earth, called LUCA that is the acronym of Last Universal Common Ancestor (Weiss et al. 2016). This system should have the properties we consider fundamental for life. The first is teleonomy, which is the quality of having the purposes of surviving and reproducing. The second is the ability to use matter and energy to encode information and exploit it to accomplish its objectives. The third is a boundary that separates these information-based processes from the environment. The fourth is a metabolic network to self-sustain the system. The fifth is adaptability to an ever-changing surrounding. The sixth is the possibility of reproduction, hence birth and death. So far, no one has succeeded to obtain life from scratch. Perhaps, the easiest way for implementing artificial biological systems is through “Synthetic Biology.” Synthetic biologists take parts of natural biological systems (“bio-bricks”) and use them to build artificial biological systems. Their activity is essential not only for understanding the phenomenon of life, but also for biomedical application, and production of chemicals and fuels (Stephanopoulos 2012).
Design of artificial cells: artificial biochemical systems, their thermodynamics and kinetics properties
Published in Egyptian Journal of Basic and Applied Sciences, 2022
Adamu Yunusa Ugya, Lin Pohan, Qifeng Wang, Kamel Meguellati
The top-down construction of ‘minimal cells’ is carried out by decreasing the genome of living cells. A primitive living organism does not require a high number of genes to be alive. Venter and colleagues discovered 517 genes in the parasitic bacterium Mycoplasma genitalium in 1995 [19]. An artificial infectious poliovirus was created by a top-bottom approach in 2002. With this method, the full-length poliovirus DNA (cDNA) is synthesized de novo and later transcribed into highly infectious viral RNA with the help of T7 RNA polymerase. Then, the transcription and replication of viral RNA took place in the cytoplasmic extract of uninfected cells, producing poliovirus with identical physiological and pathological properties compared to natural virus [20]. In 2004, minimal-gene sets were redefined for cell viability by Gil et al. [21]. Recently, a computer-based genome sequencing named Mycoplasma mycoides JCVI-syn1.0 was designed by Venter et al. on two strains of M. mycoides subspecies capri GM12 [22]. The expected phenotypic properties of M. mycoides, which can self-replicate, were seen in the resulting new cells. These types of cells are called ‘synthetic cells’ The developed synthetic DNA was integrated and accepted by the newly designed semi-synthetic artificial cell. Although the construction of large DNA sequences was enabled by synthetic biology, the creation of more complex artificial life still requires a long process to manipulate, modify, and develop them.