The Central Dogma as a thesis of causal specificity

I present a reconstruction of F.H.C. Crick's two 1957 hypotheses 'Sequence Hypothesis' and 'Central Dogma' in terms of a contemporary philosophical theory of causation. Analyzing in particular the experimental evidence that Crick cited, I argue that these hypotheses can be understood as claims about the actual difference-making cause in protein synthesis. As these hypotheses are only true if restricted to certain nucleic acids in certain organisms, I then examine the concept of causal specificity and its potential to counter claims about causal parity of DNA and other cellular components. I first show that causal specificity is a special kind of invariance under interventions, namely invariance of generalizations that range over finite sets of discrete variables. Then, I show that this notion allows the articulation of a middle ground in the debate over causal parity.     

Improving Tree-Thinking One Learnable Skill at a Time

Representations are a critical way to communicate scientific knowledge. Systematists biologists are acknowledged as expert tree thinkers who can both read and build phylogenetic trees (e.g., cladograms) accurately. The purpose of this study was to identify the core skills essential to help college students overcome tree-thinking challenges. In this study, I used pre/posttests, interviews, weekly reflective journal entries, field notes from course observations, and student responses to coursework to learn how upper-level college biology students developed representational competence with phylogenetic trees. I identified essential core skills by investigating students’ tree-thinking progression over the course of the semester. Three major patterns emerged from the data: (1) students became better tree readers than tree builders by the end of the plant systematics course; (2) core skills are essential for students to develop tree-thinking competence; and (3) tree reading skills developed before tree building skills. By diagnosing challenges students face with tree-thinking, identifying core skills necessary to overcome these challenges, and developing a starting point for a context-based framework for representational competence, this study adds to our understanding of critical elements necessary for designing effective instructional interventions and improving student learning with phylogenetic trees.     

Genome semantics, in silico multicellular systems and the Central Dogma

Genomes with their complexity and size present what appears to be an impossible challenge. Scientists speak in terms of decades or even centuries before we will understand how genomes and their hosts the cell and the city of cells that make up the multicellular context function. We believe that there will be surprisingly quick progress made in our understanding of genomes. The key is to stop taking the Central Dogma as the only direction in which genome research can scale the semantics of genomes. Instead a top-down approach coupled with a bottom-up approach may snare the unwieldy beast and make sense of genomes. The method we propose is to take in silico biology seriously. By developing in silico models of genomes cells and multicellular systems, we position ourselves to develop a theory of meaning for artificial genomes. Then using that develop a natural semantics of genomes.     

Adult Hippocampal Neurogenesis in Mammals (and Humans): The Death of a Central Dogma in Neuroscience and its Replacement by a New Dogma

The review is a critical appraisal of the history and present status of the phenomenon of adult hippocampal neurogenesis (AHN) in the mammalian and human brain. Previous as well as most current studies of AHN have focused on highly inbred domestic mice and rats that are examined in rigorously controlled laboratory environments using psychology‐based behavioral tests. However, this approach cannot reveal the adaptive significance of AHN, a key unresolved question in the field. After the publication of several thousand articles in the field over the last 20 years, little progress has been made in our understanding of the biological utility of AHN in the real world. To accomplish this will require comparative studies employing a greater diversity of species and species‐specific behaviors that are investigated in a more naturalistic, evolutionary context. Although efforts along these lines are on the rise, they remain “voices in the wilderness.” This review is an attempt to hasten and increase those efforts.