New inorganic aromatic ion
Excerpt:
Aromatic molecules are a staple of organic chemistry.
This comment was removed by the site staff for violation of the comments guidelines :
“… when a molecule that looks perfectly reasonable does not exist, the reason may be as simple as nobody has yet found a way to make it.”The same claim explains all biodiversity. Although no one has found a way to re-create existing differences in morphological and behavioral phenotypes, theorists think it is reasonable to claim that they evolved.For example, this report attests to the theory that the bacterial flagellum re-evolved in 4 days. Evolutionary Rewiring The flagellum was not created but it “re-evolved”
Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed “the blind watchmaker.” To some extent, it just happens.”
The relevance of my comment comes from the physicist Richard Feynman. See:
Protein Design. What I cannot create, I do not understand.
A designed ion channel. The ability to reproduce a biological activity in a designed membrane protein, reported by Joh et al., is an essential step in establishing that the underlying principle is understood, as stated succinctly in Richard Feynman’s well-known dictum of the title
…most amino acid chains do not have a folded structure. This may seem counterintuitive, because the chains we typically encounter are those of natural proteins, and most of these are folded. However, screens of polypeptide libraries have shown that fewer than one in a billion exemplars is folded. Second, for the few chains that fold, the free energy of folding is equivalent to just a few hydrogen bonds. Most folded proteins are thus energetically quite close to the unfolded state—a fact illustrated by the disruption that heat shocks of just a few degrees above normal growth temperature can cause. Because structure is a prerequisite for chemical activity, protein engineering is still caught up in this problem.
Excerpt:
The study of Joh et al. convincingly breaks several barriers in protein engineering: taking protein design from the solvent into the membrane, aiming for dynamic properties rather than for stability, and achieving an advanced biomimetic function from first principles, without recourse to screening or directed evolution.
De novo design of a transmembrane Zn2+-transporting four-helix bundle
Conclusion:
Our design strategy combined the strengths of traditional computational design techniques with biophysically motivated conformational ensemble–based reasoning. Although Rocker’s activity falls short of natural transporters, it remains significant that function was achieved without high-throughput screening or directed evolution—and bodes well for future investigations in which computational design is combined with these powerful experimental methods.
My comment:
Evolutionary theorists do not seem to understand that protein folding is biophysically constrained by nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to cell type differentiation via the physiology of nutrient-energy dependent reproduction in all genera. In the context of de novo design, the light-induced de novo creation of amino acids is linked from photosynthesis to RNA-mediated amino acid substitutions and the de novo creation of all other cell types that are designed to ecologically adapt to ecological variation. The only way to avoid discussion of creation compared to evolution is to eliminate any comment that attests to creation but allow any that appear to link mutations to evolution. I think the Science X network made their intentions perfectly clear.
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