Reply to My Critics: A Response to Reviews of Darwin's Black Box: The Biochemical Challenge to Evolution

In Darwin's Black Box: The BiochemicalChallenge to Evolution I argued thatpurposeful intelligent design, rather thanDarwinian natural selection, better explainssome aspects of the complexity that modernscience has discovered at the molecularfoundation of life. In the five years since itspublication the book has been widely discussedand has received considerable criticism. Here Irespond to what I deem to be the mostfundamental objections. In the first part ofthe article I address empirical criticismsbased on experimental studies alleging eitherthat biochemical systems I discussed are notirreducibly complex or that similar systemshave been demonstrated to be able to evolve byDarwinian processes. In the remainder of thearticle I address methodological concerns,including whether a claim of intelligent designis falsifiable and whether intelligent designis a permissible scientific conclusion.     

Editorial: Attention to finer-details: Progression from bulk to single-cell studies

This editorial is focused on the special issue titled as emerging field of single-cell technologies leading to comprehensive understandinh of biology.     

Introduction to the symposium: responses of organisms to climate change: a synthetic approach to the role of thermal adaptation

On a global scale, changing climates are affecting ecological systems across multiple levels of biological organization. Moreover, climates are changing at rates unprecedented in recent geological history. Thus, one of the most pressing concerns of the modern era is to understand the biological responses to climate such that society can both adapt and implement measures that attempt to offset the negative impacts of a rapidly changing climate. One crucial question, to understand organismal responses to climate, is whether the ability of organisms to adapt can keep pace with quickly changing environments. To address this question, a syntheses of knowledge from a broad set of biological disciplines will be needed that integrates information from the fields of ecology, behavior, physiology, genetics, and evolution. This symposium assembled a diverse group of scientists from these subdisciplines to present their perspectives regarding the ability of organisms to adapt to changing climates. Specifically, the goals of this symposia were to (1) highlight what each discipline brings to a discussion of organismal responses to climate, (2) to initiate and foster a discussion to break barriers in the transfer of knowledge across disciplines, and (3) to synthesize an approach to address ongoing issues concerning biological responses to climate.     

Reprint of: gene susceptibility to oxidative damage: from single nucleotide polymorphisms to function

Oxidative damage to DNA can cause mutations, and mutations can lead to cancer. DNA repair of oxidative damage should therefore play a pivotal role in defending humans against cancer. This is exemplified by the increased risk of colorectal cancer of patients with germ-line mutations of the oxidative damage DNA glycosylase MUTYH. In contrast to germ-line mutations in DNA repair genes, which cause a strong deficiency in DNA repair activity in all cell types, the role of single nucleotide polymorphisms (SNPs) in sporadic cancer is unclear also because deficiencies in DNA repair, if any, are expected to be much milder. Further slowing down progress are the paucity of accurate and reproducible functional assays and poor epidemiological design of many studies. This review will focus on the most common and widely studied SNPs of oxidative DNA damage repair proteins trying to bridge the information available on biochemical and structural features of the repair proteins with the functional effects of these variants and their potential impact on the pathogenesis of disease.