The Fall from Grace: A Tale Beyond the Garden

Plebius Seenothingus Maximus Walnut

Here are the results of a peer reviewed scientific article I posted above. ALE is a highly effective means for obtaining target strains with specific phenotypes that make them more productive or tolerant to adverse environments relevant to industrial applications. Adaptive evolution has a wide range of applications in microbial breeding for metabolic pathway activation, substrate utilization, optimization of microbial growth phenotypes, and overaccumulation of target metabolites. Due to the development of massively parallel microbial culture techniques, high-throughput sequencing, bioinformatics, and genome editing technologies, adaptive evolution has become a powerful breeding tool, which also provides an important research basis for genomic analysis, mechanistic studies, and rational metabolic engineering. However, ALE technology still has many problems to overcome. For example, the evolutionary process is often time-consuming and labor-intensive, which is an important reason limiting the widespread use of this technology. ALE technology should be closely integrated with rational metabolic engineering to maximize its role in rapidly improving strain phenotypes. Compared to rational metabolic engineering, which introduces exogenous genes directly or knocks out the original genes, ALE cannot significantly reshape metabolism in a short period of time, but if a rationally engineered strain is used as the initial strain for evolution, it can significantly shorten the evolutionary process, especially for the acquisition of complex phenotypes, where the combination of metabolic engineering and ALE is more effective. In addition, the genetic stability of the constructed industrial strains is also an important issue, which will cause serious losses in the process of fermentation scale-up. Fully understanding ALE and combining it with systems biology approaches can provide insights into strain stability, leading to a reduction of deleterious mutations and an increase of production stability, facilitating the transfer of the strain to industrial-scale applications. Notably, the growth-coupled ALE design is an excellent choice to address this issue (Czajka et al. 2017; Czajka et al. 2020).

Furthermore, although the accumulation of mutations during evolution can be analyzed by technologies such as genome and transcriptome sequencing, the random nature of mutations results in a complex and often intractable evolutionary mechanism, which makes it difficult and time-consuming to identify the relevant beneficial mutations for reverse engineering. With the widespread use of ALE, mutation analysis and elucidation of evolutionary mechanisms has become increasingly important, and the investigation of genotype-phenotype relationships has become an important area of research. Although reverse metabolic engineering has made great progress, its scope still limited, and the interpretation of genotype-phenotype associations in ALE studies still lacks standardization. To solve this problem, more multi-omics techniques should be used in future studies to fully integrate genomic, transcriptomic, proteomic, metabolomics, and fluxomic information and thereby increase the available data for the identification of phenotype-genotype associations at the systems biology level. ALE technology has been used to systematically resolve the evolutionary mechanisms at the levels of microbial metabolism and gene regulation (Henson et al. 2018). In conclusion, ALE technology facilitates the selection of industrial production strains, and the development of related technologies has led to its rapid application as an important tool for industrial microbial breeding strategies.

The authors of that study claim to have observed microscopic evolution in a lab which is what you challenged me to produce. You called me a liar. Are you now insinuating that they and the scientific journal that published the article are lying too?

I have presented references to voluminous evidence from multiple scientific sources and disciplines that support evolution of the human species by natural selection. And I have barely scratched the surface. But, it’s not like I supposed I would change your mind. You showed yourself to be a committed dogmatist from our first discussion.

Studies comparing human and chimpanzee DNA have consistently shown a high degree of sequence identity, often stated as 98.8%. This means that a significant portion of the DNA building blocks (nucleotides) are identical in both species. Coincidence? I don’t think so. If you weren’t committed to a dogma which sees evolution as an anathema, that fact alone might persuade you.

You have presented zero evidence to support whatever your theory is, claiming a lack of funds to begin to investigate it scientifically. The preponderance of evidence overwhelm ingly supports the modern evolutionary theory. Your quibbling at the margins is unpersuasive to me. I don’t think any amount of evidence could change your dogmatic mind. Maybe some who think that they have to negate science in order to hold to their faith might agree with you.

Ironically, the rhetorical style you now take offense at is me responding in kind to your own style. You can dish it out including cursing me to hell or outer darkness etc. but you can’t take it. Anyway, we’re just chatting. It’s all in good fun. I recognize you are a child of God. Ciao