BIOLOGY BY DESIGN

Intelligent Design in Cellular Systems

TRUTH CARRIERS EDUCATION SYSTEM
True Science Series - Adult/Teen Level

Psalm 139:14
"I will praise thee; for I am fearfully and wonderfully made: marvellous are thy works; and that my soul knoweth right well."

INTRODUCTION

Modern biology reveals something extraordinary: living cells are not simple "blobs of protoplasm" as once believed.

They are molecular factories of astounding complexity.

This workbook examines the molecular machines, genetic code, and irreducible systems that point unmistakably to intelligent design—using evidence from secular scientists themselves.

"The entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines." — Bruce Alberts, former President of the National Academy of Sciences

HOW TO USE THIS WORKBOOK

The Truth Carriers Learning Method — 6 Rs

This workbook uses the 6 Rs Learning Method for deep understanding and long-term retention:

1. RECEIVE
Read the teaching content about cellular design and molecular machines.
2. REFLECT
Complete fill-in-blanks, multiple choice, and discussion questions.
3. RECALL
Close the book and write key facts about each molecular machine from memory.
4. RECITE
Teach these concepts to someone else.
5. REVIEW
Use spaced repetition: Day 1, 3, 7, 21, 60.
6. RESPOND
Apply this knowledge. Share the evidence for design.

LESSON 1: THE MINIMUM REQUIREMENTS FOR LIFE

THE THRESHOLD OF COMPLEXITY

There exists a minimum level of complexity below which independent life is impossible. Even the simplest cells are far more complex than any machine humans have ever built.

The Simplest Known Organism

The smallest known self-replicating organism is Mycoplasma genitalium, a parasitic bacterium.

The 2016 Synthetic Minimal Cell

Scientists at the J. Craig Venter Institute built a "minimal" bacterial cell with genes (473).

Remarkably, they discovered that of these genes (149) had completely unknown functions—we still don't fully understand even the simplest cell.

Key Finding:
"Even the simplest cells are not fully understood. After decades of research, nearly one-third of essential genes have unknown functions."

The Cell Membrane

Every cell requires a plasma membrane (lipid bilayer) that:

Without a membrane, molecules would simply away (diffuse).

Romans 1:20
"For the invisible things of him from the creation of the world are clearly seen, being understood by the things that are made, even his eternal power and Godhead; so that they are without excuse."

Multiple Choice

1. The minimum number of essential genes for the simplest cell is approximately:

○ A) 50 genes
○ B) 150 genes
○ C) 380 genes
○ D) 1,000 genes

2. In the 2016 synthetic minimal cell, how many genes had unknown functions?

○ A) 0 - all functions were known
○ B) 149 genes
○ C) 10 genes
○ D) 473 genes

True or False

1. Early scientists believed cells were simple "blobs of protoplasm."
○ True ○ False — Correction:

2. A cell can function without a membrane.
○ True ○ False — Correction:

RECALL EXERCISE

Close this workbook. Write from memory: The minimum gene requirement. Why the 2016 experiment was significant. Four functions of the cell membrane.

TEACH-BACK CHALLENGE

Explain to someone why "simple cells" don't exist.

Person: Date:

SCRIPTURE MEMORY: Psalm 139:14

"I will praise thee; for I am fearfully and wonderfully made."

LESSON 2: ATP SYNTHASE - THE ROTARY MOTOR

THE MOLECULAR MACHINE

ATP synthase is a nanoscale rotary turbine that manufactures ATP—the universal energy currency of all living cells.

Structure of ATP Synthase

This molecular machine is embedded in cell membranes and consists of:

Astounding Performance

By comparison, the most efficient human-made motors achieve only 40-60% efficiency.

Scientific Quote:
"F₀F₁ ATP synthase is a ~100% efficient molecular machine for energy conversion in biology."

The Design Implication

ATP synthase operates like a turbine with:

Job 38:36
"Who hath put wisdom in the inward parts? or who hath given understanding to the heart?"

Multiple Choice

1. ATP synthase is best described as:

○ A) A simple chemical reaction
○ B) A rotary molecular motor
○ C) A random arrangement of proteins
○ D) A temporary structure

2. The efficiency of ATP synthase is:

○ A) About 10%
○ B) About 50%
○ C) Nearly 100%
○ D) Unknown

RECALL

Draw and label ATP synthase from memory. Include: rotor, stator, proton flow direction, ATP production.

APPLICATION

LESSON 3: THE BACTERIAL FLAGELLUM

THE OUTBOARD MOTOR

The bacterial flagellum is a rotary propulsion system with remarkable similarity to human-designed outboard motors.

Structure

The flagellum consists of 20-30 different proteins arranged as:

Approximately genes are required to build and operate the flagellum (40).

Performance

The Design Question:
"When we see a propeller attached to a motor with a driveshaft and bushings, we recognize intelligent design. Why should a molecular version be any different?"

The Critical Point

If any critical part is removed—the hook, rotor rings, or stators—the flagellum to function (fails/ceases).

A partial flagellum provides no advantage for (motility/swimming).

Colossians 1:16-17
"For by him were all things created, that are in heaven, and that are in earth... And he is before all things, and by him all things consist."

Multiple Choice

1. How many different proteins make up the bacterial flagellum?

○ A) 2-3
○ B) 5-10
○ C) 20-30
○ D) 100+

2. If the hook protein is removed from a flagellum:

○ A) It works slightly less efficiently
○ B) It completely fails to function
○ C) Another protein takes over
○ D) It works better

RECALL

List the 6 main components of the flagellum from memory. Explain why removal of any part causes failure.

TEACH-BACK CHALLENGE

Explain the bacterial flagellum to someone using the outboard motor analogy.

Person: Date:

LESSON 4: THE RIBOSOME AND DNA HELICASE

The Ribosome - Protein Factory

THE MOLECULAR 3D PRINTER

The ribosome reads genetic instructions and assembles proteins—like an automated factory assembly line.

Structure:

Function:

DNA Helicase - The Unwinding Engine

THE MOLECULAR UNZIPPER

DNA helicase unwinds the DNA double helix so it can be copied—rotating at speeds comparable to a jet turbine.

Function: Unwinds DNA at the replication fork

Speed: Approximately base pairs per second in E. coli (1,000)

Comparison: The rotational speed has been compared to a turbine (jet)

Bruce Alberts (former NAS President):
"We have always underestimated cells... The entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines."
Jeremiah 1:5
"Before I formed thee in the belly I knew thee."

True or False

1. The ribosome is a simple structure with only 2-3 parts.
○ True ○ False — Correction:

2. DNA helicase unwinds DNA at extremely high speeds.
○ True ○ False — Correction:

RECALL

Compare the ribosome to a factory. List 3 functions of the ribosome. Describe what DNA helicase does.

APPLICATION

LESSON 5: DNA - THE LANGUAGE OF LIFE

INFORMATION STORAGE

DNA is not merely a chemical—it is a language, a code, a set of instructions written in molecular form.

What is DNA?

DNA (Deoxyribonucleic Acid) is the molecular carrier of genetic information:

Human Genome Statistics

Carl Sagan (astronomer):
"A single cell contains information equivalent to 100 million pages of Encyclopedia Britannica."

The Genetic Code

DNA uses triplets called (codons) to specify amino acids:

Bill Gates (Microsoft founder):
"DNA is like a computer program but far, far more advanced than any software ever created."
Psalm 139:16
"Thine eyes did see my substance, yet being unperfect; and in thy book all my members were written, which in continuance were fashioned, when as yet there was none of them."

Multiple Choice

1. The human genome contains approximately:

○ A) 1 million base pairs
○ B) 3.2 billion base pairs
○ C) 100 base pairs
○ D) 50 billion base pairs

2. The genetic code uses codons that are:

○ A) 2 letters long
○ B) 3 letters long
○ C) 4 letters long
○ D) Variable length

RECALL

Write from memory: The 4 DNA bases. The number of possible codons. Bill Gates' quote about DNA.

TEACH-BACK CHALLENGE

Explain to someone how DNA is like computer code.

Person: Date:

LESSON 6: INFORMATION THEORY AND DNA

THE CENTRAL QUESTION

Can random, undirected processes create coded information? Information theory says no.

Two Key Properties of Functional Information

  1. Complex: Highly by chance (improbable)
  2. Specified: Matches an independent or goal (pattern)

Universal Experience

In our uniform experience, meaningful and languages always come from (codes; intelligence).

We never see complex, specified information arising from random processes.

Werner Gitt (information scientist):
"There is no known law of nature, no known process and no known sequence of events which can cause information to originate by itself in matter."

Key Observations

Error Correction Systems

DNA includes sophisticated error correction:

Result: Mutation rate of only 1 mistake per bases (10⁹ or 1 billion)

THE BOOTSTRAPPING PARADOX

You need repair enzymes to maintain accurate DNA. But you need accurate DNA to encode repair enzymes. Which came first?

Isaiah 46:10
"Declaring the end from the beginning, and from ancient times the things that are not yet done."

True or False

1. Random mutations can create new specified information.
○ True ○ False — Correction:

2. All codes whose origin we know came from an intelligent source.
○ True ○ False — Correction:

RECALL

Explain: The two properties of functional information. Werner Gitt's quote. The bootstrapping paradox.

APPLICATION

LESSON 7: THE ORIGIN OF THE GENETIC CODE

THE HONEST ADMISSION

Even leading secular scientists acknowledge the extraordinary difficulty of explaining the origin of the genetic code through natural processes.

Francis Crick's Admission

Francis Crick, co-discoverer of DNA's structure, made this remarkable statement:

Crick (Life Itself, 1981):
"An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears to be almost a , so many are the conditions which would have had to have been satisfied to get it going." (miracle)

The Chicken-and-Egg Problem

This fundamental paradox has no naturalistic solution:

This paradox was so perplexing that Crick even entertained " panspermia" (directed)—the idea that life was sent here by an advanced civilization.

Crick's Warning to Biologists

Crick (What Mad Pursuit, 1988):
"Biologists must constantly keep in mind that what they see was not , but rather evolved." (designed)

Why would he warn against this? Because biological structures look so much like designed machines that scientists need constant reminders to assume otherwise.

Hebrews 3:4
"For every house is builded by some man; but he that built all things is Elohim."

Multiple Choice

1. According to Francis Crick, the origin of life appears to be:

○ A) Simple and well-understood
○ B) Almost a miracle
○ C) Completely solved
○ D) Not worth studying

2. The chicken-and-egg problem refers to:

○ A) Poultry farming
○ B) DNA needing proteins and proteins needing DNA
○ C) Evolution of birds
○ D) Breakfast foods

RECALL

Write Francis Crick's 1981 admission from memory. Explain the chicken-and-egg problem.

TEACH-BACK CHALLENGE

Explain why even secular scientists admit the origin of life is a "miracle."

Person: Date:

LESSON 8: IRREDUCIBLE COMPLEXITY

DEFINITION

Irreducible Complexity (Michael Behe, 1996): "A single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning."

The Mousetrap Analogy

A standard mousetrap has five essential parts:

  1. Base (platform)
  2. Hammer (kill bar)
  3. Spring
  4. Catch (holds hammer)
  5. Hold-down bar

Remove piece and the trap fails completely (any/one).

There is no functional intermediate—no "half-mousetrap" that catches half a mouse.

The Implication for Evolution

Darwin wrote that his theory would "absolutely break down" if any complex organ could be shown that could not have been formed by , successive, modifications (numerous; slight).

Irreducibly complex systems cannot be built this way because stages would be non-functional (intermediate).

The Bacterial Flagellum Revisited

As we learned, the flagellum requires 40+ protein parts:

Michael Behe:
"A system which meets the criterion of irreducible complexity is resistant to gradual evolution by Darwinian means."
Genesis 1:21
"And Elohim created great whales, and every living creature that moveth... after their kind."

True or False

1. A mousetrap with only 3 of 5 parts still works partially.
○ True ○ False — Correction:

2. Irreducibly complex systems can be built by small, gradual steps.
○ True ○ False — Correction:

RECALL

Define irreducible complexity in your own words. Give the mousetrap example. Explain how this challenges evolution.

APPLICATION

LESSON 9: MORE IRREDUCIBLY COMPLEX SYSTEMS

Example 1: The Blood Clotting Cascade

A PRECISELY BALANCED SYSTEM

Blood clotting requires 12+ protein factors interacting in precise sequence.

Components include:

Evidence of Irreducibility:

People missing just one component suffer life-threatening bleeding:

Remove one part and the system fails (catastrophically).

Example 2: The Immune System

ADAPTIVE IMMUNITY

The immune system requires multiple interdependent components working together.

Requirements:

Key Point: If any crucial part is missing, the organism cannot mount specific responses (immune).

Richard Dawkins (The Blind Watchmaker):
"Biology is the study of complicated things that give the appearance of having been designed for a purpose."
Job 10:11
"Thou hast clothed me with skin and flesh, and hast fenced me with bones and sinews."

Multiple Choice

1. Hemophilia results from:

○ A) Having too many clotting factors
○ B) Missing one clotting factor
○ C) Having thick blood
○ D) Exercise deficiency

2. The complement system involves approximately how many proteins?

○ A) 2
○ B) 5
○ C) 20
○ D) 100

RECALL

Explain why hemophilia demonstrates irreducible complexity. List 4 components required for adaptive immunity.

LESSON 10: QUOTES FROM SECULAR SCIENTISTS

IN THEIR OWN WORDS

You don't have to take our word for it. Secular scientists themselves acknowledge the design-like nature of living systems.

On Cell Complexity

Michael Denton (geneticist):
"Although the tiniest bacterial cells are incredibly small... each is in effect a veritable micro-miniaturized factory containing thousands of exquisitely pieces of intricate molecular machinery... far more complicated than any machine built by and absolutely without parallel in the nonliving world." (designed; man)

On DNA as Information

Richard Dawkins:
"Biology is the study of complicated things that give the of having been designed for a ." (appearance; purpose)

On Origins

Stephen Meyer (philosopher of science):
"Systems with large amounts of specified complexity (especially codes and languages) invariably originate from an source – from a or personal agent." (intelligent; mind)

Discussion Questions

  1. Why do you think secular scientists acknowledge "design-like" features but reject an actual Designer?
  2. If biology "gives the appearance of design," what would actual design look like?
  3. How does Romans 1:20 relate to these scientific admissions?
Romans 1:20-22
"For the invisible things of him from the creation of the world are clearly seen, being understood by the things that are made, even his eternal power and Godhead; so that they are without excuse: Because that, when they knew Elohim, they glorified him not as Elohim, neither were thankful; but became vain in their imaginations... Professing themselves to be wise, they became fools."

RECALL

Write three scientist quotes from memory. Explain why each is significant.

TEACH-BACK CHALLENGE

Share these quotes with someone and discuss what they mean.

Person: Date:

APPLICATION

LESSON 11: APPLYING THE EVIDENCE

What We Have Learned

Review the key evidence for intelligent design:

  1. Minimum Complexity: Even the simplest cells require ~ essential genes (380)
  2. Molecular Machines: ATP synthase, flagellum, ribosome, helicase
  3. DNA Information: billion base pairs encoding life's instructions (3.2)
  4. Information Theory: Codes always come from (minds)
  5. The Origin Problem: DNA/protein paradox (chicken-and-egg)
  6. Irreducible Complexity: Systems that cannot be built gradually

Key Discussion Questions

  1. How is ATP synthase similar to a human-designed motor? How is it different (better)?

  2. If DNA is like computer code, what does that imply about its origin?

  3. Why is the chicken-and-egg problem so difficult for naturalistic origin theories?

  4. Can you think of any human-made system that is irreducibly complex?

Psalm 19:1
"The heavens declare the glory of El; and the firmament sheweth his handywork."

FINAL RECALL

Without looking back, list all 6 categories of evidence for design we covered.

TEACH-BACK CHALLENGE

Give a 5-minute summary of this workbook to someone.

Person: Date:

SPACED REVIEW TRACKER

Mark each box when you complete a review session:

LessonDay 1Day 3Day 7Day 21Day 60
1. Minimum Requirements
2. ATP Synthase
3. Bacterial Flagellum
4. Ribosome & Helicase
5. DNA Language
6. Information Theory
7. Origin of Code
8. Irreducible Complexity
9. More IC Systems
10. Scientist Quotes
11. Application

ANSWER KEY

Lesson 1: Minimum Requirements for Life

Lesson 2: ATP Synthase

Lesson 3: Bacterial Flagellum

Lesson 4: Ribosome and DNA Helicase

Lesson 5: DNA - Language of Life

Lesson 6: Information Theory

Lesson 7: Origin of the Genetic Code

Lesson 8: Irreducible Complexity

Lesson 9: Blood Clotting & Immune System

Lesson 10: Scientist Quotes

Lesson 11: Application

KEY SCRIPTURES SUMMARY

Psalm 139:14 - "I am fearfully and wonderfully made"

Romans 1:20 - "His invisible attributes... clearly perceived in the things made"

Colossians 1:16-17 - "By Him all things were created... in Him all things hold together"

Job 38-41 - Yahuah's questions about creation's complexity

Hebrews 3:4 - "Every house is builded by some man; but he that built all things is Elohim"

Isaiah 46:10 - "Declaring the end from the beginning"

Genesis 1:21 - "Elohim created... every living creature... after their kind"

Truth Carriers Education System

Biology by Design: Intelligent Design in Cellular Systems

Adult/Teen Level Workbook