Field notes · Guides · Essays

Notes on biology,
written plainly

25 field notes from cultures we actually run — the successes and the 2 a.m. crashes alike.

How to Start a Home Spirulina Culture

What you need, live culture vs powder, warmth, light and alkalinity — the honest first steps.

Spirulina

Harvesting Fresh Spirulina

When to harvest, simple screening methods, storage, freshness economics.

Spirulina

Reading Your Culture: Color, Density, Smell

A no-lab guide to reading Spirulina health: blue-green color cues, spoon-depth density tests, smell diagnostics and the cheap measurements worth taking daily.

Spirulina

Keeping a Home Spirulina Culture Warm Through Winter

Heaters, insulation and placement strategy for keeping Spirulina in its 30–37°C comfort band through cold months — warmth before anything else.

Spirulina

Zarrouk Medium and Nutrients

The chemistry that feeds Arthrospira: bicarbonate as carbon source and shield.

Photobioreactors

Light, Temperature and Mixing

The three physical levers — and why more of any one stops helping early.

Photobioreactors

Alkalinity as a Control Variable

In Spirulina culture, pH is not a knob — it is the readout of the carbon budget. Why alkalinity is the real control variable, and what that means for automation.

Photobioreactors

Dissolved Oxygen as a Stress Signal

Afternoon oxygen plateaus explained: supersaturation, self-poisoning of photosynthesis, and how a twin treats DO as a state variable rather than a footnote.

Photobioreactors

Six Culture Signals: What a Reactor Senses

pH, temperature, wall irradiance, OD750, dissolved oxygen, conductivity — six channels each telling a different biological story about one culture.

Photobioreactors

Spirulina Is a Cyanobacterium

What Arthrospira actually is, and why the taxonomy matters for growers.

Microalgae

Troubleshooting Contamination

Grazers, competitors, and using high pH as passive biosecurity.

Troubleshooting

pH and Carbon Problems

Rising pH is carbon fixation's fingerprint — until it becomes starvation.

Troubleshooting

AI Optimization in Photobioreactors

Bounded proposals checked by hard limits and a physics twin — never direct control.

AI + Biology

Digital Twins for Cultivation

State variables, counterfactuals, simulation-first control of living systems.

AI + Biology

A Digital Twin Built on Droop and Steele

The physics inside an algae digital twin: Droop quota kinetics, Steele's photoinhibition limb, Beer–Lambert self-shading and oxygen inhibition as state variables.

AI + Biology

Control Loop Architecture for Living Systems

Sense → twin → propose → verify → act. The layered loop architecture that lets software participate in biology without ever owning the pumps.

AI + Biology

Bounded Autonomy: Keeping AI Proposals Safe

Hard-limit validators, counterfactual simulation and firmware clamps: three independent layers that let an AI propose while never risking the culture.

AI + Biology

How Algaephyte Keeps Your Culture Safe

Plain-language walkthrough of the two-check safety system plus physical backstops — and why doing nothing is usually the safe action.

AI + Biology

What Is Algaephyte? (Plain Language)

No-jargon tour of an AI-tended photobioreactor: what it senses, how it decides, why every proposal passes gates, and what the human still owns.

AI + Biology

Edge AI for Biological Systems

Why vision inference belongs on-device at ~2 W: latency, privacy of your lab bench, and the reliability story cloud loops cannot tell.

AI + Biology

Vision-Based Contamination Detection, Honestly

What a microscope camera can and cannot classify: healthy helix vs fragment vs not-spirulina — flags that hold pumps, never ones that open them.

AI + Biology

Computer-Vision Contamination Detection Across Two Kingdoms

The shared visual vocabulary problem: why mushroom mycelium and algae culture both defeat naive accuracy claims, and what honest flagging looks like.

AI + Biology

A Federated Learning Network for Algae Reactors

Sharing fitted twin parameters instead of images or traces: MQTT topics, bounds-checking, last-will obituaries and vandal-resistant averaging.

AI + Biology

AI-Controlled Mushroom Cultivation

Inside Mycophyte: microclimate control, twin-guided decisions and bounded autonomy applied to fruiting chambers instead of photobioreactors.

Mycology

Computer Vision for Mushroom Cultivation

Pins, canopy and anomalies: what on-device detection honestly adds to a fruiting chamber, and why flags beat verdicts.

Mycology

Algae Living (playable)

Start as one cell; end operating the reactor. A game model of this whole page.

Interactive