Information Processing in Living Systems

http://upload.wikimedia.org/wikipedia/commons/f/f3/Cavernous_hemangioma_t2.jpg

Does the brain compute?

http://www.cheniere.org/images/rife/rife20.jpg

Does the immune system compute?

Do ant colonies compute?

Do biological cells compute?

Need picture

http://www.cs.helsinki.fi/group/sysfys/images/01-kegg-metabolic_pathways.jpg

http://www.brooklyn.cuny.edu/bc/ahp/BioInfo/GR/GR.Operons.html

1. What plays the role of information in the system?

2. How is it read and written?

3. How is it processed?

4. How does this information acquire function, purpose, or meaning?

What does it mean to be a computing or information processing system?

Differences between computation in Turing machines and in living

systems

Example 1

Information processing in the immune System

Detection of Pathogens via Affinity Maturation

• Trillions of lymphocytes continually circulate in blood and tissues, with continual turnover of lymphocytes.

B-lymphocyte

http://www.miltenyibiotec.com/macs/products/human/b/911-51.htm

http://www.cs.unm.edu/~immsec/html-imm/BNDNG.JPG

• A lymphocyte’s surface is covered with identical receptors that bind to a range of molecular shapes with a range of affinities.

• Each individual lymphocyte is born with a set of unique receptors, due to random shuffling of variable gene libraries.

http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit5/humoral/clonal/images/u3fg8a.jpg

Continual random variation in receptors and individual receptor’s range of affinities:

Good coverage of huge space of possible pathogen shapes.

• Lymphocyte binds with antigen; range of possible affinities.

• Receptors can even self-adjust to make an existing bond stronger.

http://www.slic2.wsu.edu:82/hurlbert/micro101/images/101ThwithBcell16.gif

If number of strongly bound receptors exceeds a threshold, and lymphocyte gets “go-ahead” signal from helper T-cells with similarly bound receptors, then lymphocyte is “activated”.

http://www.slic2.wsu.edu:82/hurlbert/micro101/images/101ThwithBcell16.gif

• Activated lymphocytes secrete antibodies, which bind to pathogens, neutralize them, and mark them for destruction by other cells.

• Activated lymphocyte migrates to lymph node, and divides rapidly, producing large numbers of daughter lymphocytes with variation in receptor shapes.

• Daughters are subject to selection, depending on affinity for antigens. Best-matching new lymphocytes themselves produce the most offspring cells.

Clonal Selection

Immune Regulation

• How does the immune system avoid attacking the body's own molecules?

Not completely understood.

Conventional answer: Negative selection.

Other mechanisms:

Regulatory T-cells

B-cell competition for limited resources.

• How does the immune system up- or down-regulate its activity as a function of its success, or of harm it is causing to the body?

Not well understood.

General answer:

Cytokine signaling network.

– Immune system cells live in a sea of cytokines (secreted by other immune cells) , with concentrations varying in space and time.

– Decisions by cells are made (in part) by sampling local cytokine concentrations and change rates.

Example 2

Information processing in ant colonies

http://www.youtube.com/watch?v=-D-C5VJwbCI

Task allocation (Gordon, 2002):

• Workers in a colony divide themselves among a number of tasks: – foraging– nest maintenance– patrolling– refuse sorting– etc.

http://www.confluence.org/fi/all/n61e027/pic1.jpg

• The number of workers pursuing each kind of task adapts to changes in the environment.

• The number of workers pursuing each kind of task adapts to changes in the environment.

• E.g., if nest is disturbed, number of nest-maintenance workers will increase.

• The number of workers pursuing each kind of task adapts to changes in the environment.

• E.g., if nest is disturbed, number of nest-maintenance workers will increase.

• Or if food supply is large and high-quality, number of foragers will increase.

Question: – How does an individual ant decide which

task to adopt in response to nest-wide environmental conditions, even though no ant directs the decision of any other ant, and each ant interacts only with a small number of other ants?

Answer (Gordon, 2002):

Answer (Gordon, 2002):

Ants decide to switch tasks as a function of:

1. What they encounter in the environment

2. Their rate of interaction with ants performing different tasks.

Answer (Gordon, 2002):

Ants decide to switch tasks as a function of:

1. What they encounter in the environment

2. Their rate of interaction with ants performing different tasks.

An ant can tell what job another ant has been doing by sensing chemical residues on the other ant.

Example 3

Information processing in bacteria

http://www.youtube.com/watch?v=u077L2Uv6OQ

1. What plays the role of information in the system?

2. How is it read and written?

3. How is it processed?

4. How does information in the system acquire function, purpose, or meaning?

Information processing in Turing machines and living systems