Two more lines of research that we're no longer working on:
3. When did eukaryote sexual reproduction begin? During the first 10 years that I was working on competence, I fully intended to switch to studying the origins of meiosis in eukaryotes. The plan, and the reasons I set it aside, are explained in this post from last summer. (Fortunately John Logsdon has taken up the torch.)
As the first steps in this project Joel Dacks, then a M.Sc. student in my lab, and I published two papers on the phylogeny of early-diverging eukaryotes. These results have been since confirmed by more detailed analyses, although the deep phylogeny of eukaryotes is still rather obscure.
4. Quorum sensing and/or diffusion sensing: Most bacteria secrete small more-or-less inert molecules into their micro-environments and monitor the external concentrations of these molecules.When this autoinducer-secretion was first discovered it was proposed to be a means of cell-cell communication, evolved to enable bacteria to monitor the cell density of the population they are living in and to respond with appropriate changes in gene expression. This "quorum sensing" explanation quickly became dogma, despite having serious theoretical/evolutionary problems. In retrospect, this acceptance was partly because there were no alternative explanations for the evolution of autoinducer secretion and sensing, and partly because the idea that bacteria are secretly talking to each other is very appealing.
In 2002 I published an opinion piece (in Trends in Microbiology) proposing a much simpler explanation, that the secreted molecules serve as inexpensive sensors of the diffusional properties of each cell's microenvironment, and thus allow cells to secrete expensive effector molecules (such as degradative enzymes) only when they and their products will not be lost by diffusion. This ‘diffusion sensing’ hypothesis was welcomed by evolutionary biologists but largely ignored by the many researchers actively investigating quorum sensing. My lab initially tried to develop experimental systems to demonstrate that isolated cells use secreted autoinducers for gene regulation, but gave up because of the technical problems of monitoring gene expression at the scale of single isolated cells.
However the paper now gets regular citations in reviews of quorum sensing, and several other research groups have produced evidence validating the importance of diffusion in autoinducer regulation. The latest is a study of Pseudomonas cells on leaves (Dulla and Lindow PNAS 2007), which found that diffusion and other physical factors in cells' microenvironments are major determinants of this regulation. They pointed out that my proposal "has received little attention despite the extensive study of QS in many species", and even quoted approvingly my sentences about what research is needed.
How can you trust non-gardeners?
12 hours ago in The Phytophactor