#+TITLE: Adaptive Reading Group
#+OPTIONS: toc:2 num:nil ^:nil

* Reading
** April 9th
- jthsmithGA.pdf
- decisionmaking.pdf

** Axiomatization of Computability, Churches Thesis
   :CUSTOM_ID: axiom-of-comp

- Church's Thesis
- wiki:Lambda_calculus

- effectively calculable :: function of positive integers is such if
     it can be identified with the notion of a recursive function of
     positive integers (or of a lambda-definable functions of positive

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 re-evaluate 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
   :CUSTOM_ID: 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

- bacteria secrete signaling molecules which disperse in the
- often these chemicals are /autoinducers/
- all responses to high levels of autoinducers tend to only make sense
  when carried out by many bacteria
- quorum sensing /QS/ :: the use of autoinducers to both determine if
     enough bacteria are present to act, and to coordinate the action
- diffusion sensing /DS/ :: comeback to quorum sensing, basically the
     idea is that the only real information returned by autoinducers
     is their rate of diffusion (whether caused by non-porous
     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
- propose *efficiency sensing* ES as a combination of QS and DS
- show that microcolonies default some problems of complexity and

*** problems with QS
QS problems /in situ/

- complexity problems
  - spatial heterogeneities :: non-uniform environment
  - biodiversity :: issues of cross-talk from other cells
- cheating problems
  - mutants that consume but do not produce /public goods/ can
    out-compete 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. bio-luminescence 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 inter-clump diversity
- decreases likelihood of intra-clump 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
  #+begin_src ditaa :file data/distribution-vs-density.png :cmdline -r :cache :exports results
    |                                                                 |
    |    +------------------------+                                   |
    |    |                        |                                   |
    |    |                        |                    +              |
    |    |   +      +             |                                   |
    |    |                 +      |                                   |
    |    |                        |                                   |
    |    |        +               |                                   |
    |    |      +    +            |                                   |
    |    |                        |                                   |
    |    | yes quorum here  cF78  |                                   |
    |    +------------------------+                            +      |
    |                                                                 |
    |                                       +                         |
    |                                                                 |
    |                                                                 |
    |                +                                                |
    |                                                                 |
    |                                                                 |
    | no quorum here      +                              c1AB         |

  perhaps it would be better to give each cell its own density metric
  at some radius