System-Level Design Group

KU Institute for Information Sciences

NDIST'13 (Day 3)

Day three continues with interesting talks on biological systems.

Warren Hunt - Phylogeny

Rebuild trees by knowing the occurrence rate of subtrees. Specifically, know that a tree is constructed from subtrees and specify those occurrences.

Jacob Beal - Workflow talk

Discussed the concept of a biocompiler that translates “operators” to “motifs” which is pretty interesting.

Panel Session - Defenses, Biological and Computational

Can we learn from one another. Can we avoid repeated mistakes.

Howie Schrobe

  1. Near perfect components
  2. Core design formed in an era of scarcity
  3. Core design formed in isolated environment
  4. Evolutionary pressure from market - price performance
  5. Self-regulation and adaptation rarely considered - Runs open-loop
  6. No enterprise-wide survivability mechanisms
  1. Failable components
  2. Abundance of resources
  3. Evolution in ecosystem of predators and parasites
  4. Evolutionary pressure from ecosystem - survivability
  5. Self-regulation and adaptation are core mechanisms. Closed loop control.
  6. Diversity for population survival. Public-health systems in human society

Tom Knight - Biological Protection Mechanisms

Howie Shrobe (again)

At least 20-30% of the body’s resources are involved in constant surveillance and containment.

Part of the innate immune system engages the adaptive immune system

Adaptive immunity

  1. Hardware analog of immune system detects anomaly
  2. Software system analog of adaptive immune system is signaled
  3. System model is used to perform diagnosis
  4. System model is adapted with new attack-specific detector
  5. Adaptive immune system synthesizes plan to get around problem and patch to remove specific vulnerability

Workforce & Degradation is the Economic Trade-off

Processes of attacker and defender


  1. Recon
  2. Penetration
  3. Escalation
  4. Exploitation


  1. Detection
  2. Diagnosis
  3. Remediation
  4. Regeneration

Originally the subsystem that was exploited by the Car Shark system was isolated from the real-time control systems. But, to make diagnostics and only updating work, these were later bridged. Bingo!

Stuxnet attacked a system that was air-gapped.

Pat Lincoln -

Premises from 2000 are still valid

  1. We can not control the distribution of technology and information enabling the manipulation of biological systems
  2. Ineffective attempts to forbid access to basic biology manipulation incur high cost
    • Delayed gains
    • Missed opportunities
  3. Threats could arise form nature, nation states, loosely organized groups, and individual
  4. Threats could target any part of the living world relevant to human welfare

  5. Biosafety
    • What do you protect
      1. Humans
      2. Agriculture
      3. Ecology of niches
      4. Gaia
    • From what do you protect it
      1. Organisms from elsewhere and other times
      2. Unintended consequences of organisms and parts designed by humans
      3. Organisms and parts that are newly synthesized
  6. Biosecurity - Security against humans doing bad things with biotech.

  7. Mitigation of risks:

    1. Speed
    2. Cultural
    3. Legal
    4. Technical
      • Telomere-like generation counters 1
      • Alien-like overlapping code regions
      • Random parity-like signature checks
  1. Telomere limits replication to a specific number of generations