The Internet hourglass

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The Internet hourglass
IP
From Hari Balakrishnan
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The Internet hourglass
Everything on IP
IP
From Hari Balakrishnan
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ASes typically connect at all hubs.
Everything on IP
IP
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Applications
IP
Hardware
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The LEGO connector protocol
Robust Mesoscale
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The LEGO connector protocol

• The patented stud-tube connection is the heart
  of the LEGO system, and its most important
  protocol
• Ancillary protocols have been added over time, to
  create an elaborate protocol suite.
• The basic module is the brick, but additional
  modules have been added
• Higher level protocols and modules exist as well
• The bricks and stud-tube protocols make up a
  minimal LEGO (denote by LEGOmin)
• There are thousands of LEGO parts and complex
  sensors, actuators, and computer control systems

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Uncertainty
Robust Mesoscale
Robust
Uncertainty
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Robustness of the LEGOmin protocol and modules
Uncertainty
Robust Mesoscale
Uncertainty

• The snap connection allows for
• A huge variety of new and different toys to be
  built
• From a huge variety of different components
• Both toys and components can be rearranged and
  added in new ways
• There are associated fragilities as well

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Yet fragile
Systems

• Add or remove a tiny amount of material from
  either or both sides of a key interface.
• The system may completely fail, even though tiny
  amounts of material has changed, and the
  components are visually indistinguishable.
• Other parts of the bricks may be nicked or cut
  with minimal impact
• This robust, yet fragile feature of protocols is
  a candidate for a universal law
• What robustness/fragility properties do
  alternative protocols have?

Robust Mesoscale
Components
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The evolution of complexity
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Suppose you want to put a structure on wheels?
Easy Find Lego parts with wheels.
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Suppose you want to motorize a vehicle with
wheels?
Easy Add Lego motors,gears and battery.
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Suppose you want to motorize a vehicle with
wheels?
Easy Add Lego motors,gears and battery.
Additional protocols and modules.
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This cart/motor/gear configuration could be a
module that is reused in many toys.
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Q Suppose you wanted to change a Lego car that
had a motor and could move across the room, to a
Lego car that could also avoid obstacles as it
moved. What would happen to the cost and
complexity? A Both cost and complexity would
go up by orders of magnitude. Until recently,
this would have been essentially impossible. Now
it is doable, all parts are available from Lego,
but it is still very challenging.
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Sensors
Control
Vehicle
Sensors
Actuators
Control
Vehicle
Size ? Complexity
(Size of blocks reflects complexity of
components.)
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Sensors
Not only does the cost and complexity go up by
orders of magnitude, but new control protocols
(and subsidiary communications and computing
protocols) must be added.
Control
These additional protocols will greatly increase
the complexity, the robustness, and also the
fragility of both the Lego system and the toys
that are built using it.
If the assay is moving across an uncluttered
room, then most knockouts will be
nonnessential and have little or no phenotype.
However, some knockouts will have wild behavior.
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Complexity
protocols
structure
wheels
motor
controls
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Uncertainty
Robust Mesoscale
Robust
Uncertainty
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Yet fragile

• Catastrophic if it fails
• Difficult to change

Robust Mesoscale
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Yet fragile
Protocols allow for the creation of large complex
networks, with rare but catastrophic cascading
failures.
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Uncertainty

• Evolutionary selection
• Promotes evolvability of other levels
• Difficult to change

Robust Mesoscale
Uncertainty
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Principles

• Robust yet fragile (conservation of fragility)
• Complexity driven by regulatory networks
  sensors actuators
• Complexity/robustness spirals
• Protocols
• Facilitates robustness and evolvability
• Creates some fragility and brittleness

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Robustness of Lego

• There are many robustness features of Lego. All
  are facilitated by the snap/protocol/interface.
• Robustness of individual toys. Toys hold
  together despite bumping and movement.
• Robustness of a given Lego set. A huge variety
  of new toys can be made from the same Lego parts
  by re-using the components and connecting them in
  new ways.
• Robustness/evolvability of an individual Lego
  set. A huge variety of new components can be
  added to a Lego set.
• Evolvability of the Lego system. Entirely new
  capabilities can be added with new protocols,
  such as the control, communications, and
  computing interfaces of Mindstorm.

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Principles illustrated by Lego

• Robustness and evolvability are not incompatible
• There are many robustness features of Lego.
• Robustness of individual toys.
• Robustness of a given Lego set.
• Robustness/evolvability of an individual Lego
  set.
• Evolvability of the Lego system.
• Evolvability is robustness to large changes on
  long time scales.
• The evolvability and robustness of the LEGO
  system is facilitated by the LEGOmin protocol
  suite.
• The protocols and components are highly designed,
  highly structured, finely tuned. They produce
  specific forms of robustness, with the cost of
  fragility.

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Features of Modules

• Parts, components, ingredients, subsystems,
• Identifiable interface (protocol) to other
  modules
• Maintains identity when isolated or rearranged
• Facilitates simplified, reduced, or abstracted
  modeling
• Can be evolved somewhat independently
• Facilitates functional or variational description
  in addition to procedural
• May be largely in the eye of the beholder
• May have mixtures of features to varying degree

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Features of protocols

• Rules, recipes, architectures, etiquette,
• Rules or constraints on allowed interfaces and
  interconnections
• Facilitates modularity
• Facilitates independent evolvability of
  components and systems
• Simplifies modeling, abstraction, verification
• May be largely in the eye of the beholder
• Facilitates addition of new protocols and
  organization into protocol suites, which are
  collections of mutually supportive protocols
• Protocols are dual or orthogonal to modules

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Related terminology

• Components are subsystems with fewer identifiable
  features than modules. Modules is a stronger
  concept. Parts is the loosest notion, and
  implies the least.
• Architecture is a higher level concept than
  protocol, similar to a protocol suite.
• A motif is a recurrent pattern that suggests the
  existence of modules and protocols.
• Need to clarify these notions much better.
• Terms with overlapping and ambiguous meaning
• Protocol, architecture
• Module, component, part
• Law, constraint

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essential 230   nonessential 2373  
unknown 1804   total 4407
http//www.shigen.nig.ac.jp/ecoli/pec
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Essential
Nutrients, O2, T, ions,
Energy and materials flows
transport


Metabolism

• Autocatalysis (positive feedback in energy and
  materials)
• Oscillators for timing cell cycle and metabolism

Cell cycle
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Essential
Nutrients, O2, T, ions,
Energy and materials flows
transport


Metabolism

Cell cycle

• Protocols and modules of metabolism, cell cycle,
  and transport are built on top of biochemistry
• Constrained by laws of biochemistry and the
  lower level Trans and DNArep protocols
• A minimal protocol suite requires a few hundred
  genes (the genetic module part count) and a
  steady, nutrient rich environment

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Biological simplicity and complexity

• Biological simplicity is created by
• Universal Trans and DNArep protocols
• Highly conserved metabolism, cell cycle,
  transport protocols
• Minimal genome of a few hundred genes
• Refer to this protocol suite as BioMin
• BioMin protocols and modules become the low level
  modules and laws for biological complexity

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Biological simplicity and complexity

• Biological complexity?
• 1e3 to 1e5 genes gtgt BioMin
• Complex regulatory networks
• What are the protocols, modules, and laws, in
  addition to those in BioMin?
• BioMin protocols become laws underlying
  complexity
• What are the additional laws and constraints?
• What can engineering tell us about the nature of
  these laws?

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Other examples

• What follows is a collection of examples from
  biology, technology, and other sources
• Illustrate protocols, modules, laws
• Robust, yet fragile

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Taylor, Zhulin, Johnson
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• Variety of receptors
• Shared cytoplasmic domains and A-W complex
• CheY universal signal to motor
• Facilitates robustness and evolvability
• Robust chemotaxis with multiple ligands
• Can easily evolve new receptors

Ligands, Receptors
CheA-CheW
CheY-Motor
Attractants, Repellants
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Ligands, Receptors
CheA-CheW
CheY-Motor
Attractants, Repellants
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• Huge variety of receptors
• Large number of G-proteins grouped into similar
  groups
• Handful of primary targets
• Huge variety of downstream responses

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Robust Mesoscale
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Uncertainty
Robust Mesoscale
Robust
Uncertainty
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Biological common currencies

• Chemotaxis CheY
• Membrane potentials, ion channels
• Chemical energy ATP, NADH, glucose, acetyl coA,
  lipids
• Transcriptional regulation
• G-protein signaling
• .

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Energy currencies

• 110 V, 60 Hz AC
• Gasoline
• ATP, glucose, etc
• Proton motive force

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Consumers
Energy
Producers
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Consumers
Energy
Producers
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Various functionality
Digital
Analog substrate
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Applications
Operating System
Hardware
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Applications
Software Hardware
Modern Computing
Operating System
Hardware
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Applications
Software Hardware
Modern Computing
Operating System
Hardware
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Building complexity
High-level functionality

• Transparent to the user
• mostly for robustness
• easy to ignore from outside

Physical implementation
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Early computing.
Machine code
High-level functionality
Layers of rules and protocols
Logic
Transistors
Physical implementation
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User interface
Modern computation.
Applications
High-level functionality
Applications
Layers of rules and protocols
OS
Computer
Board
VLSI
Physical implementation
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User interface
VLSI design
Instructions
Applications
Logic
Applications
Topology
OS
Geometry
Computer
Timing
Board
Fabrication
VLSI
Silicon
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Designed versus generic
Instructions
Climate
Logic
Weather
Topology
Navier-Stokes
Geometry
Boltzmann dist
Keep only sets of measure zero.
Throw away sets of measure zero.
Timing
particle dynamics
Fabrication
Quantum mech.
Silicon
???
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Network protocols.
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The Internet hourglass
IP
From Hari Balakrishnan
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The Internet hourglass
Everything on IP
IP
From Hari Balakrishnan
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ASes typically connect at all hubs.
Everything on IP
IP
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Applications
IP
Hardware
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Applications
Robust Mesoscale
TCP/ IP
Robust, yet fragile
Hardware
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Network protocols.
HTTP
TCP
IP
Routers
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Network protocols.
HTTP
Transparent to the user
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Network protocols.
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Network protocols.
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Network protocols.
Transparent to the user
Danger It is easy to weave intriguing but
impossible notions about how this works.
It often requires great internal complexity to
create a robust, simple interface.
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Robust, yet fragile
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Consumers
Barter
Commodities
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Consumers
Barter
Commodities
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Consumers
Money
Investors
Commodities
Investments
Markets, Insitutions
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It is now possible to have a global financial
crisis which is completely independent of the
original motivation for money.
Consumers
Investors
Commodities
Investments
Markets, Insitutions
Money
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The hourglass
Garments
Dress
Shirt
Slacks
Lingerie
Coat
Scarf
Tie
Wool
Cotton
Nylon
Silk
Polyester
Rayon
Material technologies
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T-Shirt
Jacket
Shirt
Tie
Boxers
Shoes
Coat
Slacks
Socks
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T-Shirt
Jacket
Shirt
Tie
Boxers
Shoes
Coat
Slacks
Socks
Silk
Wool
Nylon
Rayon
Cotton
Polyester
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The hourglass
Garments
Dress
Shirt
Slacks
Lingerie
Coat
Scarf
Tie
Sewing
Cloth
It might not be obvious from simple observation
of this network that a sophisticated protocol was
involved.
Wool
Cotton
Nylon
Silk
Polyester
Rayon
Material technologies
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Uncertainty
Robust Mesoscale
Robust
Uncertainty
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Yet fragile
Difficult to change
Robust Mesoscale
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Yet fragile
Protocols allow for the creation of large complex
networks, with rare but catastrophic cascading
failures.
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Uncertainty

• Evolutionary selection
• Promotes evolvability of other levels
• Difficult to change

Robust Mesoscale
Uncertainty
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Protocols
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