Engineer Your Biology

Protocol

Engineer Your Biology

Medicine 3.0 is not reactive. It is predictive, proactive, and protocol-driven. This deck contains 42 habits derived from the cutting edge of geroscience, exercise physiology, and nutritional biochemistry.

Old Way
  • Wait for symptoms before acting
  • Treat organs in isolation
  • Rely on motivation
  • Accept age-related decline as inevitable
  • Exercise for aesthetics
  • Eat based on hunger and convenience
New Way
  • Intervene based on biomarkers and protocols
  • Optimize interconnected biological systems
  • Execute algorithms regardless of emotional state
  • Build physiologic reserve to buffer decay
  • Train for VO2 max and structural resilience
  • Time nutrition to circadian and metabolic signals

Does this sound familiar?

  • You get winded climbing stairs despite 'being active'
  • Your knees hurt when you squat below parallel
  • You crash at 3pm regardless of sleep quantity
  • You can't touch your toes or sit on the floor comfortably
  • Your grip fails before your muscles do
  • You eat well but still gain visceral fat
  • You sleep 8 hours but wake exhausted
"

The goal is not just to live longer, but to maintain the functional capacity of a 40-year-old well into the eighth and ninth decades of life.

The Longevity Engineer Protocol

Mechanism

The Five Core Systems

Click a system to explore its habits

Metabolic Engine

Metabolic Engine

Zone 2 training builds mitochondrial density. VO2 max intervals build cardiac output. Together they create the aerobic base that predicts mortality.

Structural Chassis

Structural Chassis

Joints, tendons, and grip strength. The Knees Over Toes philosophy, isometric loading, and the benchmarks that correlate with biological age.

Circadian Nutrition

Circadian Nutrition

Time-restricted eating, collagen pre-loading, sulforaphane optimization, and fasting protocols. Food as a signaling molecule.

Recovery Architecture

Recovery Architecture

Sleep hygiene, thermal stress (sauna + cold), and the 3-2-1 down-regulation rule. Recovery is where adaptation happens.

Neural Resilience

Neural Resilience

Autonomic control via physiological sighs, circadian light exposure, NSDR, and dual-task training to prevent cognitive-motor decline.

Getting Started

Step01

Week 1: Lay the Foundation

Start with the lowest-friction habits. Morning sunlight, floor sitting, the Talk Test. Build consistency before intensity.

Step02

Week 2: Activate the Metabolic Engine

Add your first Zone 2 sessions. Verify intensity with the Talk Test. Separate high and low intensity days.

Step03

Week 3: Reinforce the Chassis

Introduce backward sled pulls, ATG split squats, and grip work. These build the structural resilience that prevents injury.

Step04

Week 4: Optimize Recovery

Implement the 3-2-1 rule, cold exposure, and cyclic sighing. Recovery is not passive—it is engineered.

Step05

Month 2+: Progress to Growth & Mastery

Once foundations are solid, add VO2 max intervals, contrast therapy, and the fasting protocols.

A Day in Your Life

  • 06:00 — Wake & Light

    06:00

    Natural wake. 2-10 minutes of direct sunlight to set the circadian clock.

  • 06:30 — Structural Prep

    06:30

    10-minute mobility routine. Tibialis raises. Toe spacers on.

  • 07:00 — Fasted Deep Work

    07:00

    90 minutes of cognitive work. First calorie delayed until cortisol subsides.

  • 09:00 — Training Block

    09:00

    Zone 2 or Strength session. Collagen pre-loaded 30-60 minutes prior.

  • 11:00 — First Calorie

    11:00

    TRE window opens. High protein meal with sulforaphane-optimized sprouts.

  • 19:00 — Thermal Stress

    19:00

    Sauna + cold plunge. End on cold. Air dry.

  • 20:00 — Digital Sunset

    20:00

    Dim lights. No screens. Reading or audio only.

  • 21:30 — NSDR & Sighs

    21:30

    5 minutes of cyclic sighing or guided NSDR.

  • 22:00 — Sleep

    22:00

    Room at 65°F. Complete darkness. 7-8 hours.

Glossary

01

Zone 2

The aerobic intensity at which you can speak full sentences with effort. Corresponds to ~1.7-1.9 mmol/L blood lactate.

02

VO2 Max

Maximum oxygen uptake during intense exertion. The strongest single predictor of all-cause mortality.

03

TRE

Time-Restricted Eating. Consuming all calories within a consistent 8-10 hour window.

04

Autophagy

Cellular cleanup process activated by fasting. Degrades damaged proteins and organelles.

05

HRV

Heart Rate Variability. A measure of parasympathetic tone and recovery status.

06

Søberg Principle

End thermal contrast therapy on cold and air-dry to maximize brown fat activation.

07

Physiological Sigh

Double-inhale through nose, extended exhale through mouth. Fastest real-time stress override.

08

NSDR

Non-Sleep Deep Rest. A yoga nidra protocol that accelerates learning and reduces cortisol.

Mortality reduction (low → below avg fitness)

50%

Mortality reduction (elite VO2 max)

5x

Grip strength mortality risk increase

67%

Weekly cold exposure target

11min

Weekly sauna target

57min

VO2 max decline per decade after 30

10%

Progression

Habit Tiers

Tier 1

Foundation

Daily micro-habits: Talk Test, floor sitting, toe spacers, morning light, physiological sighs.

Tier 2

Growth

Moderate effort: Zone 2 sessions, ATG squats, TRE, cold plunges, dual-task drills.

Tier 3

Mastery

High-skill protocols: 4x4 intervals, contrast therapy, FMD, 2-minute dead hangs.

Tier 4Peak

Titan

Acute stress tests: VO2 max benchmarks, 36-hour fasts, dopamine resets. Use sparingly.

Myth

Common Myth

Longevity is about genetics and luck. You either have good genes or you don't.

Protocol Playbooks

Curated sequences of habits designed to be practiced together. Click a playbook to see its cards in the deck below.

Morning Spin-Up
5 cards

Morning Spin-Up

The first 90 minutes. Light exposure, hydration, mobility, and fasted focus.

View Morning Sunlight
Perform Tibialis Raises
Accumulate Floor Sitting Time

+2 more habits

Zone 2 Engine Day
5 cards

Zone 2 Engine Day

A complete aerobic base session with proper intensity calibration.

Apply the Talk Test
Track Your Resting Heart Rate
Execute a Zone 2 Session

+2 more habits

Structural Armor Session
7 cards

Structural Armor Session

Lower body resilience: knees, tendons, grip, and mobility.

Perform Tibialis Raises
Execute Backward Sled Pulls
Hold the Couch Stretch

+4 more habits

Evening Shutdown
8 cards

Evening Shutdown

The 3-2-1 countdown: food, work, screens. Then thermal stress and breath.

Close the Kitchen 3 Hours Before Bed
Set Your Room to 65°F for Sleep
Enforce a Digital Sunset

+5 more habits

Weekly VO2 Max Protocol
3 cards

Weekly VO2 Max Protocol

The 4x4 interval session for cardiac output and mortality reduction.

Complete the 4x4 VO2 Max Protocol
Separate High and Low Intensity Days
Test Your VO2 Max Benchmark

Quests

Challenges to accelerate your transformation. Click a quest to see its target cards.

Initiation

The Calibration Sequence

Implement seven core foundation protocols to stabilize circadian rhythms and metabolic baselines for optimal system calibration.

"The Protocol begins with calibration. We do not guess; we engineer the foundation of the human machine."

FOUNDATION tier streak for 7 days
7 cards
View Quest Cards
System Mastery

Architectural Integrity

Execute all architectural upgrades for the frame to ensure lifelong mobility, joint resilience, and peak structural integrity.

"A powerful engine is useless on a fragile chassis. Restore the human frame to its intended engineering specifications."

Complete Structural Chassis system
10 cards
View Quest Cards
Titan Trial

The Autophagy Reset

Abstain from all calories for 36 hours to trigger deep cellular repair and maximize metabolic flexibility.

"The system must occasionally clear its cache. Deprive the machine of fuel to force the ultimate cellular upgrade."

Complete TITAN tier
3 cards
View Quest Cards

The Full Deck

38 habits across 5 core systems

Systems:
Playbooks:
Apply the Talk Testfoundation

Apply the Talk Test

Verify Zone 2 intensity by speaking full sentences with slight effort.
⏱ 1m⚡ low
Metabolic Engine
Track Your Resting Heart Ratefoundation

Track Your Resting Heart Rate

Measure resting heart rate each morning before rising from bed.
⏱ 1m⚡ low
Metabolic Engine
Execute a Zone 2 Sessiongrowth

Execute a Zone 2 Session

Complete 45-60 minutes of continuous cardio at Talk Test intensity.
⏱ 60m⚡ moderate
Metabolic Engine
Separate High and Low Intensity Daysgrowth

Separate High and Low Intensity Days

Schedule Zone 2 and VO2 max sessions on different days to avoid interference.
⏱ N/A⚡ low
Metabolic Engine
Complete the 4x4 VO2 Max Protocolmastery

Complete the 4x4 VO2 Max Protocol

Perform four 4-minute intervals at 90-95% max heart rate with 3-minute recoveries.
⏱ 35m⚡ high
Metabolic Engine
Test Your VO2 Max Benchmarktitan

Test Your VO2 Max Benchmark

Perform a maximal effort test quarterly to measure cardiovascular capacity.
⏱ 20m⚡ very high
Metabolic Engine
Perform Tibialis Raisesfoundation

Perform Tibialis Raises

Complete 25 tibialis raises to strengthen the shin's shock absorber muscle.
⏱ 2m⚡ low
Structural Chassis
Accumulate Floor Sitting Timefoundation

Accumulate Floor Sitting Time

Sit on the floor instead of furniture to restore hip mobility passively.
⏱ 15m⚡ low
Structural Chassis
Wear Toe Spacers Dailyfoundation

Wear Toe Spacers Daily

Apply silicone toe spacers during sedentary time to restore natural toe splay.
⏱ 30m⚡ low
Structural Chassis
Execute Backward Sled Pullsgrowth

Execute Backward Sled Pulls

Walk backward against resistance for 5-10 minutes to bulletproof the knees.
⏱ 10m⚡ moderate
Structural Chassis
Hold the Couch Stretchgrowth

Hold the Couch Stretch

Open the anterior hip capsule with a 2-minute couch stretch per side.
⏱ 5m⚡ moderate
Structural Chassis
Perform ATG Split Squatsgrowth

Perform ATG Split Squats

Execute deep split squats with knee traveling past toes for full ROM strength.
⏱ 10m⚡ moderate
Structural Chassis
Complete the Farmer's Carry Standardmastery

Complete the Farmer's Carry Standard

Carry 100% bodyweight (split) for 1 minute to meet the grip strength benchmark.
⏱ 5m⚡ high
Structural Chassis
Hold a 2-Minute Dead Hangmastery

Hold a 2-Minute Dead Hang

Hang from a bar for 2 minutes to build grip endurance and shoulder stability.
⏱ 5m⚡ high
Structural Chassis
Apply Isometric Tendon Loadingmastery

Apply Isometric Tendon Loading

Hold 30-45 second isometrics for tendons requiring repair or maintenance.
⏱ 10m⚡ moderate
Structural Chassis
Pass the Sitting-Rising Testtitan

Pass the Sitting-Rising Test

Lower to floor sitting and rise without hand support to score 8+/10.
⏱ 2m⚡ moderate
Structural Chassis
Delay First Calorie by 90 Minutesfoundation

Delay First Calorie by 90 Minutes

Wait 60-90 minutes after waking before consuming any calories.
⏱ N/A⚡ low
Circadian Nutrition
Close the Kitchen 3 Hours Before Bedfoundation

Close the Kitchen 3 Hours Before Bed

Stop all food intake at least 3 hours before your target sleep time.
⏱ N/A⚡ low
Circadian Nutrition
Maintain a 10-Hour Eating Windowgrowth

Maintain a 10-Hour Eating Window

Consume all daily calories within a consistent 8-10 hour window.
⏱ N/A⚡ moderate
Circadian Nutrition
Pre-Load Collagen Before Traininggrowth

Pre-Load Collagen Before Training

Consume 15g collagen with 50mg Vitamin C 30-60 minutes before tendon loading.
⏱ 5m⚡ low
Circadian Nutrition
Prepare Sulforaphane-Optimized Sproutsgrowth

Prepare Sulforaphane-Optimized Sprouts

Heat broccoli sprouts to 70°C for 10 minutes to maximize sulforaphane yield.
⏱ 15m⚡ moderate
Circadian Nutrition
Execute a 5-Day Fasting Mimicking Dietmastery

Execute a 5-Day Fasting Mimicking Diet

Complete a 5-day FMD protocol with restricted calories to trigger autophagy.
⏱ 5d⚡ high
Circadian Nutrition
Complete a 36-Hour Water Fasttitan

Complete a 36-Hour Water Fast

Abstain from all calories for 36 hours to deepen autophagy activation.
⏱ 36h⚡ very high
Circadian Nutrition
Set Your Room to 65°F for Sleepfoundation

Set Your Room to 65°F for Sleep

Cool the bedroom to 65°F (18°C) to facilitate core temperature drop.
⏱ 1m⚡ low
Recovery Architecture
Enforce a Digital Sunsetfoundation

Enforce a Digital Sunset

Eliminate all screens 1 hour before bed to allow melatonin release.
⏱ N/A⚡ low
Recovery Architecture
Dim Lights to Red/Amber After Sunsetfoundation

Dim Lights to Red/Amber After Sunset

Switch to low-angle, warm lighting in the evening to support circadian rhythm.
⏱ 1m⚡ low
Recovery Architecture
Apply the 3-2-1 Down-Regulation Rulegrowth

Apply the 3-2-1 Down-Regulation Rule

Stop food at 3h, work at 2h, and screens at 1h before bed.
⏱ N/A⚡ moderate
Recovery Architecture
Execute a Cold Plunge Sessiongrowth

Execute a Cold Plunge Session

Immerse in cold water for 2-3 minutes, ending on cold to activate brown fat.
⏱ 5m⚡ moderate
Recovery Architecture
Accumulate Weekly Sauna Timegrowth

Accumulate Weekly Sauna Time

Complete 57+ minutes of sauna exposure per week across 2-4 sessions.
⏱ 20m⚡ moderate
Recovery Architecture
Execute Contrast Therapy Protocolmastery

Execute Contrast Therapy Protocol

Alternate sauna and cold plunge, always ending on cold for metabolic activation.
⏱ 30m⚡ high
Recovery Architecture
Complete a Sleep Audit Weektitan

Complete a Sleep Audit Week

Track sleep metrics for 7 days to identify patterns and optimize QQR.
⏱ 7d⚡ moderate
Recovery Architecture
Perform the Physiological Sighfoundation

Perform the Physiological Sigh

Execute a double-inhale followed by extended exhale to downregulate stress.
⏱ 30s⚡ low
Neural Resilience
View Morning Sunlightfoundation

View Morning Sunlight

Get 2-10 minutes of natural sunlight within 30 minutes of waking.
⏱ 10m⚡ low
Neural Resilience
Practice 5-Minute Cyclic Sighinggrowth

Practice 5-Minute Cyclic Sighing

Perform 5 minutes of physiological sighs to improve baseline HRV.
⏱ 5m⚡ low
Neural Resilience
Execute Dual-Task Walking Drillsgrowth

Execute Dual-Task Walking Drills

Walk while performing cognitive tasks to train brain-body integration.
⏱ 10m⚡ moderate
Neural Resilience
Complete NSDR Protocolmastery

Complete NSDR Protocol

Perform 10-20 minutes of Non-Sleep Deep Rest for neural restoration.
⏱ 20m⚡ low
Neural Resilience
Train Complex Dual-Task Challengesmastery

Train Complex Dual-Task Challenges

Balance on one leg while bouncing a ball and answering questions.
⏱ 10m⚡ moderate
Neural Resilience
Complete a 24-Hour Dopamine Fasttitan

Complete a 24-Hour Dopamine Fast

Abstain from all high-dopamine activities for 24 hours to reset baseline.
⏱ 24h⚡ very high
Neural Resilience

Sources & References

External reading that informed this stack.

8 links

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