15Jan 2026 by Post

Systems Biology and Intelligent Design: A Natural Fit

AmiGO, biological networks, biology, computers, coordination, Darwinian evolution, data networks, datasets, E. coli, Engineering, Gene Ontology, genomics, glycolysis, Intelligent Design, Introduction to Systems Biology, isoforms, Joel Bader, Junk DNA, living systems, long non-coding RNAs, metabolomics, molecular biology, Molecular Systems Biology, mRNA, mutations, optimal design, optimism, proteins, proteomics, reductionist biology, Rube Goldberg, Ruedi Aebersold, smartphones, Systems Biology, Technology, transcription network, transcriptomics, Uri Alon, Yuri Lazebnik
In December 2025, Molecular Systems Biology marked its 20th anniversary with a special editorial that reflects on the field’s development since 2005 (Bheda et al. 2025). Systems biology is an approach to studying living systems that assumes hierarchical, top-down design. The piece, authored by the journal’s editors and several contributors, shares personal perspectives on where the field stands today — and where it is headed. Ruedi Aebersold, the first contributor, states, “the first 20 years of MSB were grand; the next 20 years will be grander.”  I too am optimistic about the field’s future. My optimism comes specifically from how powerfully top-down design has succeeded in giving us the complex systems of the modern world. Top-down design prunes the vast search space of possibilities through an Read More › Source
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30Jul 2025 by Post

Recurring Design Logic in Attenuation Mechanisms

amino acids, Arginine, attenuation, biology, biosynthesis, blind processes, design logic, DNA, Engineering, enzymes, Evolution, genes, hairpin, histidine, homology, Intelligent Design, leader transcript, mRNA, operon regulation, operons, phenylalanines, prokaryotes, recurring design logic, regulation, Ribosome, RNA polymerase, transcription, translation, tryptophan, unguided processes
Despite the striking parallels between these systems in terms of the design logic, these attenuation systems are not evolutionarily related to one another. Source
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28Mar 2025 by Post

Nobelist Thomas Cech on “Junk RNA” 

biochemists, biology, Darwinism, DNA, Evolution, genetics, heuristic, Intelligent Design, Junk DNA, junk RNA, lncRNAs, long noncoding RNAs, mRNA, neo-Darwinian paradigm, Nobel Prize, predictions, proteins, RNA, scientific progress, The Catalyst, Thomas Cech, W. W. Norton
We can add this prominent biochemist to the ever-growing list of scientists who reject the “junk DNA” paradigm. Or, more pertinently, the junk RNA paradigm. Source
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27Mar 2020 by Post

More Hints of Order in the Genome

Abo1, Amir Bitran, ATP, biochemistry, Biozentrum, Caulobacter crescentus, central dogma, Chelsea R. Bulock, chromosomes, cohesin, cotranslational folding, Darwinian mechanism, DNA, E. coli, error catastrophe, genome, GGC, GGU, Intelligent Design, Junk DNA, Lego blocks, misfolding, mRNA, Nature Communications, Patricia Clark, PNAS, polymerase, polypeptides, Polδ, proofreader, proteins, RNA, South Korea, strand breaks, UNIST, University of Basel, University of Notre Dame, University of Seville, William Paley
Genomics has come a long way since the central dogma (the notion that DNA is the master controller that calls all the shots) and junk DNA (the expectation that much of the genome is non-functional). If scientists ditch those old dogmas and approach the genome expecting to find reasons for things, they often do. Synonymous Mutations To-may-to or to-mah-to? The British write flavour; the Americans write flavor, but generally each understands the other without too much difficulty. Genomes, too, have alternate ways of spelling things: GGU and GGC in messenger RNA both spell glycine. No big deal, thought geneticists; these “silent” mutations cause no change in the resulting protein. At the University of Notre Dame, however, biochemists are finding that the differences in spelling are not just background noise; they…
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