On Evolution, Here Is What We Can Believe with High Confidence

adenine, biochemists, biology, E. coli, Evolution, First Rule of Adaptive Evolution, fitness, fossil record, gene, gene transcription, genes, genetics, genotype, homology, information, James Tour, lactose, Michael Behe, natural selection, promoter, random mutations, regulatory control, researchers, Rice University, S. cerevisiae, tryptophan, W303, When Can I Trust What Scientists Say? (series), yeast, YouTube videos
In a pair of YouTube videos, Rice University chemist James Tour and I reviewed more than ten recent studies of experimental evolution. Source
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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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Recurring Design Logic in Living Systems

attractants, Bacillus subtilis, bacteria, biological systems, biology, bioluminescence, chemotaxis, Complexity, Darwin's Black Box, E. coli, Evolution, genes, Intelligent Design, Jonathan McLatchie, Michael Behe, musicians, outer membrane, painters, poisons, proteins, Salmonella, signal transduction, sporulation, toxins
Architects, painters, musicians, and other creators apply recognizable patterns of thinking to their craft. Source
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Engineered Complexity in the Microbial World

adaptations, bacteria, biology, Carolyn Hovde, Conference on Engineering in Living Systems, Dustin Van Hofwegen, E. coli, engineered complexity, Engineering, Evolution, evolutionary leap, genetic mechanisms, ID The Future, innovation, Intelligent Design, Jonathan Witt, Journal of Bacteriology, microbes, Podcast, Scott Minnich, University of Idaho
On a classic episode of ID the Future, host Jonathan Witt speaks with molecular biologist and professor Dustin Van Hofwegen about his research into the engineered complexity in microbial life. The two sat down at the yearly Conference on Engineering in Living Systems to discuss the event, which brings together biologists and engineers to study how engineering principles can be applied to living things, as well as Hofwegen’s article in the Journal of Bacteriology, co-authored with Carolyn Hovde and Scott Minnich, based on research conducted at the University of Idaho.  Hofwegen shares his research on the famous decades-long E. coli evolution experiment conducted by Richard Lenski, which showed the sudden appearance of an ability to utilize citrate after many generations. However, Van Hofwegen’s own Read More › Source
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ORFanID: An Online Search Engine for Identifying Orfan Genes

bacteria, bioinformatics, C. elegans, D. melanogaster, Discovery Institute, DNA, E. coli, Evolution, evolutionary paradigm, fungi, gene classification, genes, genomes, genomics, genomics analysis, H. sapiens, Intelligent Design, nucleotide sequences, O. sativa, ORfan genes, plants, PLOS ONE, S. cerevisiae, search engine, taxonomic groups, Z. mays
The existence of such genes is surprising given the hypothesis of universal common descent. Source
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Hitting the Brakes on “Rapid Evolution”

Ann Gauger, Bijan Nemati, biochemical weapons, Culture, Darwinian evolution, Defense Intelligence Agency, DNA, E. coli, engineers, Eric Anderson, Evolution, extinction, Idaho, Intelligent Design, Iraq, Long Term Evolutionary Experiment, mutations, Richard Lenski, Scott Minnich, Why It Matters
Evolutionary biologist Richard Lenski hopes to demonstrate Darwinian evolution in action. But one humble scientist from Northern Idaho says not so fast! Source
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An Impressive Instance of Unguided Evolution? Not So Much

bacteria, biology, biophysicists, Cornelius Hunter, Darwin’s God, Dennis Venema, E. coli, Evolution, evolutionary theory, ID The Future, Intelligent Design, Michael Behe, mutations, natural selection, Podcast, protein-protein binding, Ray Bohlin, scientists, The Edge of Evolution, unguided evolution, vertebrate immune system
“There is a desire for the theory to be true in spite of the science," says Cornelius Hunter, "not because of the science.” Source
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Engineering and Evolution in the Microbial World

animals, Azusa Pacific University, bacteria, biology, Carolyn Hovde, Conference on Engineering in Living Systems, Dustin Van Hofwegen, E. coli, Evolution, ID The Future, Intelligent Design, Journal of Bacteriology, Long Term Evolution Experiment, Neo-Darwinism, plants, Podcast, Richard Lenski, Scott Minnich, University of Idaho
This year’s Conference on Engineering in Living Systems (CELS) is going on right now, exploring design principles at work in living things. Source
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Michael Behe on Why Lenski’s Experiments Show Devolution, Not Evolution

breaking things, citrate, Darwin Devolves, E. coli, Evolution, evolutionary biologists, evolutionary theory, flasks, genes, genetic information, ID The Future, Intelligent Design, Long Term Evolution Experiment, Michael Behe, Michigan State University, mutations, niche advantages, novelty, oxygen, Podcast
Biochemist Michael Behe reviews the well-known Long Term Evolution Experiment at Michigan State. Source
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From Darwinists, a Shift in Tone on Nanomachines

Adam Watkins, bacterial flagellum, BioEssays, biology, Bruce Alberts, Darwinian pathways, Darwinism, David Hume, Dubai, E. coli, Evolution, flagellar filaments, From Darwinists, Guide to Reading Jason Rosenhouse (series), Harvard University, Howard Berg, Intelligent Design, Jason Rosenhouse, magnetotactic bacteria, molehills, moles, mountains, nanomachines, National Academy of Sciences, Rube Goldberg device, Stone Age, Technology
The shift in tone from then to now is remarkable. What happened to the awe these systems used to inspire? Source
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