Week 7 HW

Part 1: IANNs

What advantages do IANNs have over traditional genetic circuits?

Traditional genetic circuits usually work like Boolean logic gates. They treat inputs and outputs as mostly ON or OFF.

IANNs are more flexible because they can handle graded, continuous biological signals. Instead of only asking whether an input exists, they can respond to the strength of each input and combine multiple inputs together.

IANNs can:

  • process noisy biological signals
  • weight different inputs differently
  • produce gradual output levels instead of only ON/OFF
  • recognize complex patterns of inputs
  • represent more complex behaviors than simple Boolean circuits

This makes them useful for biological systems where signals are rarely perfectly binary.

Useful application for an IANN

A useful application would be an engineered diagnostic cell that detects a disease-like state.

For example, the IANN could receive several inputs:

  • high inflammation signal
  • low oxygen level
  • cancer-associated microRNA
  • abnormal metabolic signal

The output could be a fluorescent protein or a therapeutic molecule.

Input/output behavior:

  • If only one weak disease signal is present, the output stays low.
  • If several disease signals are present, the output becomes medium.
  • If the full disease-like pattern is detected, the output becomes strong.
  • If the cell looks healthy, the output remains OFF.

This is useful because many diseases are not defined by one marker. They are defined by combinations of signals.

Limitations:

  • Biological circuits are noisy.
  • The response may be slow because transcription and translation take time.
  • Too many components can burden the cell.
  • The circuit may behave differently in different cell types.
  • It may mutate or become unstable over time.
  • It may be hard to tune the correct input weights.

Intracellular multilayer perceptron description

In a multilayer intracellular perceptron, the first layer receives DNA inputs and produces an intermediate molecular output. For example, layer 1 could produce the Csy4 endoribonuclease.

Csy4 then acts as the output of layer 1 and the regulatory input for layer 2. In layer 2, the fluorescent protein gene is transcribed into mRNA that contains a Csy4 recognition site. If enough Csy4 is produced, it cleaves the fluorescent protein mRNA and reduces fluorescence.

So the system works like this:

Input DNA signals → layer 1 gene expression → Csy4 production → regulation of fluorescent protein mRNA → final fluorescence output

The final output is the fluorescence level, which depends on how strongly the upstream inputs activate Csy4.

Part 2: Fungal Materials

Existing fungal materials and uses

Mycelium packaging

Mycelium can be grown through agricultural waste to make packaging materials.

Uses:

  • protective packaging
  • foam replacement
  • disposable molded products

Advantages:

  • biodegradable
  • lightweight
  • made from waste materials
  • lower environmental impact than plastic foam

Disadvantages:

  • less water-resistant
  • slower to produce
  • mechanical properties can vary
  • harder to standardize at large scale

Mycelium leather

Fungal mycelium can be processed into leather-like sheets.

Uses:

  • fashion
  • bags
  • shoes
  • furniture surfaces

Advantages:

  • animal-free
  • potentially more sustainable than animal leather
  • can be grown into sheets
  • texture and thickness can be tuned

Disadvantages:

  • may be less durable than traditional leather
  • often needs coating or finishing
  • water resistance can be limited
  • large-scale production is still developing

Mycelium insulation and building panels

Mycelium composites can be made into panels, bricks, acoustic tiles, or insulation.

Uses:

  • wall panels
  • acoustic panels
  • thermal insulation
  • temporary architecture

Advantages:

  • lightweight
  • biodegradable
  • good insulation potential
  • made from agricultural waste
  • can have good fire resistance

Disadvantages:

  • usually not strong enough for structural loads
  • sensitive to moisture
  • long-term durability is uncertain
  • building code approval can be difficult

What I might genetically engineer fungi to do

I would genetically engineer fungi to make responsive building materials.

For example, a mycelium wall panel could sense humidity, pollution, or damage and respond visibly or materially.

Possible input/output behavior:

  • Input: high humidity
    Output: produce water-resistant compounds

  • Input: pollutant or toxin
    Output: change color as a warning signal

  • Input: physical damage
    Output: produce binding polymers to help self-repair

This would make fungal materials more than passive materials. They could become living or bio-based interfaces that sense and respond to their environment.

Why use fungi instead of bacteria?

Fungi are useful for synthetic biology because they naturally form material structures. Their hyphae grow into dense networks, which can become sheets, foams, panels, or composites.

Advantages over bacteria:

  • fungi naturally make large physical networks
  • they can grow on cheap agricultural waste
  • they can secrete useful enzymes, pigments, and polymers
  • they are better suited for macroscopic materials
  • as eukaryotes, they can process more complex proteins than bacteria

However, fungi are often slower-growing and harder to genetically engineer than bacteria. Their growth can also be harder to control.