Adaptive Reading Group
Table of Contents
Reading
April 9th
Axiomatization of Computability, Churches Thesis
axiomatizationofcomputabilitychurchesthesis.pdf
 Church's Thesis
 wiki:Lambda_calculus
 function of positive integers is such if it can be identified with the notion of a recursive function of positive integers (or of a lambdadefinable functions of positive integers)
some (like Post) thought that Church's definition of effectively calculable placed limits on the mathematical processes available to humans and was too quick in defining such a process when we should be continually trying to reevaluate and expand the process. > is a human nothing more than a Turing machine in terms of complexity? Stephan Wolfram would argue yes.
 partial function
 a function which is not defined for all inputs (i.e. division)
 Kolmogorov Machine
 an alternative to a turing machine with a type of connected graph for storage
Does Efficiency Sensing Unify Diffusion and Quorum Sensing
Does Efficiency Sensing Unify Diffusion and Quorum Sensing
straightforward and largely uninteresting simplification of existing theories
efficiency sensing measures the combination of (cell density, diffusion properties, and spatial distribution) and it is the combination of these three (basically how much can I saturate my surroundings) that really matters
intro
proposes efficiency sensing as a unification of diffusion sensing and quorum sensing. avoids problems of honesty and complex environments through growth of cells in microcolonies.
certain bacterial behaviors only happen on make sense at high cellular densities. the cells seem to signal/sense each other to make these determinations.
 bacteria secrete signaling molecules which disperse in the environment
 often these chemicals are autoinducers
 all responses to high levels of autoinducers tend to only make sense when carried out by many bacteria
 the use of autoinducers to both determine if enough bacteria are present to act, and to coordinate the action
 comeback to quorum sensing, basically the idea is that the only real information returned by autoinducers is their rate of diffusion (whether caused by nonporous surroundings, production by a quorum of other bacteria, or production by third parties)
 DS is simpler than QS because it doesn't rely on assumptions about social behavior
this paper will
 review QS and DS
 show that distribution is more important than density for autoinducers.
 propose efficiency sensing ES as a combination of QS and DS
 show that microcolonies default some problems of complexity and cheating
problems with QS
QS problems in situ

complexity problems
 spatial heterogeneities
 nonuniform environment
 biodiversity
 issues of crosstalk from other cells

cheating problems
 mutants that consume but do not produce public goods can outcompete normal individuals
 one possible answer to this is that when grown in microcolony (live near your children) the hereditary sharers would share mainly with their children
QS v.s. DS
there are some situations when the autoinducer is clearly used to sense a quorum (e.g. bioluminescence where the action take place internally, but only makes sense with many neighbors)
ES hypothesis
cells can only measure the combination of density, distribution, and autoinducer medium permeability
autoinducer concentration is a better predictor for effector concentration than it is for either diffusion or quorum
as cost saver
 easier to produce autoinducers than effectors
 low autoinducer production needed if its easily detected
 many different effectors may need to be produced
microcolonies avoid problems
growing in clumps
 promotes interclump diversity
 decreases likelihood of intraclump cheating
future work
more studies in situ rather than with bacterial dissolved in liquids
my thoughts
 if the system at large is arbitrary, and takes into account physical inconsistencies (i.e. the system could be a single cell in a box) then the QS and DS may be the same, namely a quorum is simply enough cell in the environment to create the required density of autoinducer.
 seems that QS and DS are setup as straw men
 its not fair to discriminate between spatial distribution and the cell density which QS purports to measure. If you draw your bounding box correctly then spatial distribution inconsistencies no longer matter
perhaps it would be better to give each cell its own density metric at some radius