NeoDarwinian Review

"In terms of junk DNA, we don’t use that term anymore because I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome, as if we knew enough to say it wasn’t functional. … Most of the genome that we used to think was there for spacer turns out to be doing stuff.” - Francis Collins, head of the (failed) Human Genome Project, promoter of Junk DNA  The concept of "junk DNA" has undergone a dramatic transformation in recent decades. Initially, vast stretches of the genome that did not code for proteins were dismissed as non-functional remnants of evolution. This included ultraconserved elements (UCEs), which are sequences of DNA that are virtually identical across distantly related species, suggesting strong evolutionary pressure to preserve them. The assumption that these elements were merely "junk" highlights a historical neo-Darwinian bias in molecular biology that focused primarily on protein-coding...

Ultraconserved elements (UCEs) are stretches of DNA that show extraordinary similarity across species separated by vast evolutionary distances. These sequences are virtually identical, with no insertions, deletions, or substitutions, even between species as diverse as humans and chickens. This remarkable conservation suggests that UCEs play critical roles in biological function, making their alteration highly detrimental. However, a puzzling question arises: why is the number of UCEs so low compared to the staggering diversity of animal life? The Nature and Significance of Ultraconserved Elements UCEs were first identified in the human genome by comparing it to the mouse and rat genomes. These initial studies revealed hundreds of these elements, each over 200 base pairs long, that were 100% identical across the three species. Subsequent research expanded the scope, finding UCEs in a wide range of vertebrates, including birds, fish, and reptiles. The fact that UCEs have rema...

The recent publication , "The Cambrian of the Grand Canyon: Refinement of a Classic Stratigraphic Model," challenges long-held assumptions about the Cambrian Period and the "Cambrian explosion." This period, roughly 541 to 485 million years ago, witnessed an unprecedented diversification of life forms, often explained by neo-Darwinian evolutionary theory. However, the new research findings present a more nuanced picture, raising questions about the adequacy of gradualistic explanations and highlighting the potential role of epigenetic mechanisms in driving rapid evolutionary change. Challenging Neo-Darwinism Neo-Darwinism posits that evolution proceeds through the gradual accumulation of small, random genetic mutations that are selected for by environmental pressures. This model struggles to explain the abrupt appearance and rapid diversification of complex life forms during the Cambrian explosion. The Grand Canyon research further complicates this p...

The existence and evolution of ultraconserved elements (UCEs) present a fascinating challenge to traditional neo-Darwinian evolutionary theory, particularly when considering the debate surrounding non-coding DNA. Neo-Darwinism posits that evolution primarily occurs through the gradual accumulation of random mutations in protein-coding genes, followed by natural selection for beneficial traits. However, UCEs, which are long stretches of non-coding DNA that are nearly identical across distantly related species defies this explanation. The Challenge of Ultraconserved Elements UCEs are enigmatic for several reasons: Extreme Conservation: Their sequence identity across species separated by hundreds of millions of years of evolution is extraordinary. This level of conservation suggests an incredibly strong selective pressure against any changes, implying a critical function. Non-coding Nature: They reside in non-coding regions of the genome, traditionally considered "junk ...