Lesson: Molecular Machines in Nature

Lesson: Molecular Machines in Nature

The array of super-tiny atomic-scale molecular machines in the world is truly mind-boggling!

In this Lesson: Molecular Machines in Nature we will be discussing how nature uses all six of the simple machines and some really cool molecules to do work right within the cell! This happens in plants, insects, animals, and even in bacteria and in viruses. All it takes is to reframe the idea of what you call a machine or motor.

Chlorophyl: The Original Green Solar Panel

Did you know that around 3.5-3.8 billion years ago chlorophyll evolved in ancient organisms called Archaeans (ancient bacteria). It was the beginning of the great period of oxygenation on our planet. Chlorophyll played a big part of that.

Cyanobacteria and later plants, have oxygen as the waste product of photosynthesis. Thus slowly Earth became oxygenized. This Great Oxygenation Event wiped out most of the anaerobic organisms including the purple bacteria. So plants are green because chlorophyll is more suited for a star that shines in blue or a red light (UV and Infrared).

How exactly is it that chlorophyll is a molecular machine? I’m glad you asked! It has to do with that ring at the top of the molecule (see below).

Chlorophyll Molecular Motor

There are five atoms in that central ring. Magnesium (element 12) and Nitrogen (element 7). The magnesium is ionized and just two of the Nitrogens are ionized.

As the magnesium reacts, it spins being attracted and repulsed by the positive and negative Nitrogens. This transforms photons into electrons and those electrons travel down that long tail creating O2, Sugars, and water.

It’s remarkable to think every day we eat tiny little green electric motors and solar panels and that is how we get our power. When animals eat plants, and we eat animals or insects, we still get that power. We are living batteries and power plants powered by plants!

DNA: Take It Apart and Reassemble It – FAST!

Most people know what DNA (DeoxyriboNucleic Acid) is. But two things that you might NOT know is that:

  1. DNA and its family – Genes, Nucleotides, Chromosomes, and Messenger RNA (RiboNucleic Acid) only code for proteins.
  2. DNA must be built, unbuilt and a new copy made in every cell in every living thing on this planet and that is done by a series of machines that physically manipulate the DNA polymer molecule.

To accomplish this amazing feat of bioengineering DNA uses DNA transcription machines to unzip the double helix DNA, then create two versions of the same DNA and then put it all back together again. Transcription motors do this so fast they are almost as fast as jet engines! The spin and unlock the DNA and then they have to ACCURATELY put that DNA back together again every time.

This screenshot is used courtesy of Veritaseum.

Question: What do you think would happen if the DNA got put together again and even one base pair nucleotide was wrong?

The tiny spinning and reassembling molecular machines are incredibly efficient. In fact, they RARELY get the reassembly process wrong. That’s because the way DNA works is very much like a form of LEGOS. The nucleotides will only click with a certain nucleotide and none others.

Here’s an interesting question: Is DNA a sugar, a plastic, or an acid?

  • DNA does have a sugar backbone in its double helix
  • DNA technically is a polymer (a long chain of carbon-bonded molecules) just like plastic
  • DNA has an acidic Ph as the nucleotides (ladder rungs) are made of amino acids

Sugars are everywhere. Just like carbon, we need the molecular shape of sugars to support and sustain life, and carbon is an excellent building tool. So yes, DNA does have a sugar aspect to it.

DNA is a polymer, so it is plastic. But is DNA a plastic are are all plastic polymers — but not all polymers are plastic. Remember a polymer is simply a long chain of carbon atoms.

Why do you think DNA is acidic? Is there something about ions and energy that might be built into DNA? Why does DNA only code for proteins and not more specific traits?

When we reframe this idea as a LEGO block issue, it becomes much easier to understand how and why the transcription molecular motor works so very well. It doesn’t change the fact that that it is extraordinarily complex, but it does make it easier, right?

Dynein Motor: We’re Walking, We’re Talking

Would you believe that in your body right now, in every cell of every living organism there is an army of walking machines called Dynein Motors? They are tiny machines that carry proteins around inside the cell on highways called microtubules. They are the most amazing molecular motors in my opinion.

Watch DNA Transcription and Dynein Motors in Action!

Of course, these amazing motors are not “alive” in the real sense of that word. They are molecular machines that react to the microtubule highways in the cell and they place one “foot” in front of the other and move around the cell.

If we were to look at a Dynein Motor could we determine which of the six simple machines it uses to move? Let’s have a look.

How many simple machines do you see?

Notes for an Educator:

The goal of this lesson is to introduce biotech, bioengineering, and biochemistry students to the idea that nature uses engineering principles, biological truths and physics and chemistry to bring atoms and molecules to life. It is an important idea that seemingly miraculous and complicated things can be understood by breaking them down into pieces and then reframing the whole.

It would be an interesting activity to do this with an animal and a simple molecule model. Even proteins can make more sense when they are viewed as machines. This is also useful for building team cohesion.

If we can see the smaller parts of a group, we can better understand how we can all come together on common ground. Intolerance or arguments become pieces of data. We need to name them and then reframe them in a positive light.


BioEngineering Lesson Plans

BioEngineering Lesson Plans

Lesson: Pressure and Temperature in a Dome
Building a Biodome over ice

Welcome to the Mezzacello 2024 BioEngineering Lesson Plans page. Here you will find the suggested lessons, activities, design challenges, plans and resources for running the BioEngineering summer camp at Mezzacello. If you would like to sort through other lessons, simply click here.

Day One:

Introduction to Mezzacello and BioEngineering

  1. LESSON: Farm Systems – Layout and Systems of the farm and safety protocols
  2. ACTIVITY: Nature, Engineering, and Problem Solving
  3. Design Challenge: Duct Tape Trivia
  4. Design Challenge: Build a Gate

  1. LESSON: Team Building – Types of Engineers
  2. ACTIVITY: Leadership Roulette
  3. Design Challenge: Team Identity
  4. Design Challenge: STEM Identity

  1. LESSON: Layers of Reality – A fun way to introduce the STEM in #UrbanAgTech by creating a model for the way the world works through art and lecture.
  2. LESSON: Molecular Machines in Nature
  3. Design Challenge: Build an Atom

Day Two

Webs of Life and Pressure

  1. LESSON: Webs of Life – a quick review of where in our world we interact with Atoms and why.
  2. ACTIVITY: Three Systems to Understand Mezzacello

  3. Design Challenge: Water and Air Pressure
  4. Design Challenge: Phases of Matter

  1. LESSON: Under Pressure – How pressure is everywhere and seemingly nowhere and why
  2. ACTIVITY: Building a Water Evaporation System in the Biodome
  3. Design Challenge: Build a Chicken Feeder and Waterer
  4. Design Challenge: Build a simple dome for growing plants and sterilizing water

Day Three:

Biomimicry and Pattern, Process, and Structure

  1. LESSON: The Circle of Life – a crash course into Applied STEM and Math integration in Ag and in STEM.
  2. ACTIVITY: Break a complex problem into simple machines – explore the six simple machines at Mezzacello.
  3. Design Challenge: Explore all aspects of pressure (physical, electrical, emotional, social)
  4. Design Challenge: Identify a Reframe of a Simple Problem
  5. Design Challenge: Make a mechanical origami bird and bird launcher

  1. LESSON: As Above; So Below – a reminder that life is sophisticated and deeper than we want to acknowledge, but is essentially Yin and Yang with a boundary layer.
  2. ACTIVITY: Fear, Anxiety, Failure, and Confidence emotional pressure
  3. Design Challenge: Air, Water, Earth, Fire– the way energy propagates across our experience

Day Four

Careers and Why Engineering Matters on a Farm

  1. LESSON: Career Crossover – Allows students to reflect on what they have observed and how it impacts their curiosity and their future.
  2. ACTIVITY: Being an Engineer: Three problems to solve
  3. Design Challenge: Team Algorithm
  4. Design Challenge: Interview for Your Future Job

  1. LESSON: Public Speaking 101
  2. ACTIVITY: Discuss and whiteboard with your team what your video will be
  3. Design Challenge: Assign Random Roles
  4. Design Challenge: Create a Bio dome
  5. Design Challenge: Create a Biome
  6. Design Challenge: Create an ecology in a box

Day Five

Presentation Day

  • Finish Your Product Development
  • Prep for Presentation and finalize scripts
  • Shoot your team’s video
  • Present your Final Presentation

Project BioEngineering Arts and Crafts

Project BioEngineering Arts and Crafts

Project BioEngineering Arts and Crafts
Exploring crystals with found objects.

These are some of the proposed Project BioEngineering Arts and Crafts projects for the 2023 Summer Camps. Some projects are subject to change.

  1. Make foil, copper, and vinyl mazes

    • a simple maze made out the camper’s name that lights up with a circuit and a small battery.

  2. Make a grass weaving tool

    • A simple loom made of popsicle sticks and a simple weft and shuttle system for weaving fabric.

  3. Make a rabbit maze

    • Using milk crates and hoops build a rabbit maze that will keep rabbits engaged and searching for a carrot.

  4. Make chicken washing soap

    • Make soap in a bag made of woven pieces to better wash chickens and rabbits. Welding with thread.

  5. Make a LEGO mold

    • Using a large lego mold, create plaster bricks that can be used to make a foundation. An alternate will be a sugar, salt, and fat mold with seeds to feed birds.

  6. Make a 3D printed pinecone bird feeder

    • Using 3D printed pine cones, lotus cages, and magnolia seeds to create peanut butter and seed feeders.

  7. Make a chicken swing

    • Make a simple swing from rope or rubber twine and a stick to allow chickens to swing.

  8. Make a chicken tractor

  9. Make a 3D Paper Mache treasure map

    • Make a flat topographic map of Mezzacello and take turns hiding a treasure. Then create fun clues that can be integrated into the map.

  10. Make a sugar window charm

    • Make an isomalt or sugar window charm with popsicle sticks, or pipecleaners that is rigid enough to stand on its own.

  11. Make glass bees

    • Make a bee from glass stones, onion skins, twigs, and hot glue that will stand on its own.

  12. Make a woven bird house

    • Make a bird house from a 3D printed base shape that is decorated with objects and pieces that birds can actually use to build a house.

  13. Make a biodynamic keychain

    • Make a dynamic tensor shape with dowel rods, play dough, and rubber bands.

  14. Make a fingerprint art charm

    • Make a clean finger print that can be projected to twice its size and retraced into a piece of art.

  15. Make seed bombs

    • Make flour, water, and salt play dough embedded with wildflower seeds inside.

  16. Make Hoberman fences

    • Make a dynamic expanding fence with popsicle sticks and brass brads that will stretch across a space and remain stable.

  17. Make a model seed

    • Make a seed model from felt, foam, paper, and confetti.

  18. Make ultrasonic sand art

    • Using an ultrasonic plate with a paper plate attached, add sand and attenuate the ultrasonic frequency to make a geometry. Then spray the sand into a locked position.


Lesson: The Circle Of Life

Lesson: The Circle Of Life

Exploded View of the helical heart

Welcome to the lesson: The Circle of Life. This lesson is about the most misunderstood component of life: The role of Math and Science in everyday life. The circle of life is far more complex than it at first appears.

For example, did you know the human heart is a circular muscle? The heart is not just the neuro-muscular, electrochemical “blood pumping organ”. It is a wrapped circle, often called a Gordian Knot.

In this lesson we explore the human heart as a metaphor for a deeper understanding of nature itself. We all think we know what something “does” we understand it. There are deeper truths exposed when we examine the structure, purpose, and function and form to determine why nature evolves systems.

Not a Pump; Not a Machine; A Spiral Wave

When we reframe the what, why, how, when, where of any heart we are able to see nature and her precious sacred geometry in action. You like many people, probably imagine the heart as a very complex structure of rooms, like this:

The traditional understanding of the heart as a series of chambers

This system is accurate, but it’s proposed function is out of line with the way nature and the reality of life itself evolves and creates things. It is useful metaphor, but it requires a human way of thinking of things that is often not supportable by fact. What’s missing in this conception of the heart is the role of the SPIRAL.

Would it surprise you that the heart is a spiral? Further would it surprise you to learn that all blood vessels – arteries, veins and capillaries use ridges to cause blood flow to spiral? or that the very shape of the blood cell, flat, with rounded edges and a depressed middle area is optimized to spiral through the spiral of the blood stream?

Panta Rhei (Everything Spirals)

It is not always intuitive, but nature does love the spiral, and it appears everywhere in nature. Another misunderstood fact is that nature builds complexity from smaller forms, and the most common and dynamic form is a spiral – usually one of five or a combination of spiral forms:

  1. Phi – a transcendental number represented by the ratio 1:1.618 [The golden spiral]
  2. Pi – a transcendental number represented by the ratio 1:3.14 [What is Pi?]
  3. e – a transcendental number represented by the number 2.71828 [Exponential Growth]
  4. Fractals: [Link]
  5. Euler’s Identity: e^i π + 1 = 0

Euler’s Identity

Electromagnetic Waves

Transcendental Numbers

Why do transcendentals exist? We do not know, we only know they do – across time and cultures. Where we fail in our science is when we try to ignore them in the general application of science and technology.

Tell me right now, three places you see spirals in nature. I will challenge you to follow that to infinity.

Jim Bruner

We can find transcendentals in every field, INCLUDING math. Disease, sociology, psychology, materials science, astronomy, engineering, biology, civic design, aerodynamics, energy, field theory, forever. So what does all of this have to do with the heart?

Lesson Challenge: Make a Heart

The heart is a circle of life that is also defined as a knot; a gordian knot to be precise. A knot that wraps through and around itself and using electrical impulses and the structure of the knot to push, contract, propel and flatten it pulses so that the pressure of the BODY propels the heart, NOT the other way around.

Let’s explore where we see the five transcendental ideas above in the heart.

Materials

  • Computer
  • Wifi
  • Display
  • Speakers
  • Whiteboard
  • Ropes

Instructions

  1. Using the Links on this page start a discussion about how one thing can be reframed as another.
  2. For instance, the heart is not an empty organ, it is a muscle that has topography.
  3. Discuss topography and mathematics in general.
  4. Math is a language that nature uses to help us make sense of the way reality assembles itself.
  5. When you have introduced the Transcendentals and watched the videos begin building a heart.
  6. Have each team of students work with the thick rope.
  7. Challenge them to fasten it into a Gordian Knot that wraps into itself.
  8. Have them explain how the system brings in and expels the energy wave.
  9. Give them 10 Minutes to better understand this feature of maths, topology, and anatomy.
  10. Ask them to use one of the transcendental numbers to support their claim.

Learning Integration

Rarely in nature are things always as they appear. Larger ideas can always be broken down into smaller ideas that will generally relate back to discreet mathematical concepts. Review a simple object and ask students to break into the SIX simple Machines:

The Six Simple Machines

  1. Lever
  2. Fulcrum
  3. Pulley
  4. Screw
  5. Inclined Plane
  6. Wheel and Axle

Give them 10 minutes to do this exercise.

This integration of mechanics and Math is useful in problem solving and in identifying both problems and their solutions. This also gives students agency to recognize, reframe and react to problems on their own!


Lesson: As Above So Below

Lesson: As Above So Below

The Role of Pattern, Structure, and Process in the World

This Lesson: As Above So Below is intended to allow young urban farmers the ability to understand why soil health, water and ground conditions, bio system ecology, and atmosphere are in balance. This lesson will rely heavily on the Lesson: The Nested Levels of Reality to make relationships between atoms, molecules, compounds, cells, organs, organism, and ecosystem. Students will create drawings or dioramas of the complete ecosystem of their choice.

This project REQUIRES reflection and teamwork. It also works best if the students can craft a demonstration about why nature needs these systems in balance. The system should also identify what life lives in each level and how it benefits that organism and at least two others.

Pattern

This is how things are similar but quite different. Let’s discuss tree limbs and tree roots, or skeletal structures between animals, or patterns of Phi that we see in the natural world.

Process

This is how things work. Think of feathers for example. They look completely different from fur or hair, but in reality they are just fur and fingernails arranged in new patterns.

Structure

This is how things are arranged. Think of atoms and molecules for example. They seem so small, but they arrange themselves in endless new and predictable new structures.


An alternate strategy would be to split the camp into three teams and have each “team” provide data and insight to each other group. This cross pollination of ideas and knowledge will also have the useful benefit of building collaboration and teamwork.

Language and art are just as important as science and math in this exercise. Take advantage of the surprising mystery of the Yin Yang (below, surface, surrounded by atmosphere) model of ecologies to ask your learners where the great split between above, surface really begins.

Materials:

  • 10 Gallon Aquarium
  • Craft supplies (felt, yarn, stamps, ink)
  • Pipe Cleaners
  • Foam blocks
  • Craft Paper
  • Markers
  • Plexiglass sheet
  • Glue
  • Tape

Instructions

  • Decide whether each team is building a diorama, a drawing, or a plexiglass maquette
  • Conduct a brief bio blitz of three areas of the Urban Farm
  • Give students time to conduct then blitz and make observations of what they believe they see
  • Review their notes and ideas and get ready to design and build
  • Distribute materials to each group
  • Allow them to build their product
  • Allow them to test and modify their creations
  • After an appropriate amount of time, organize the camp and allow groups to present

Lesson Integration

This is a useful way to address scale, proportion, chemistry, materials, pathology, energy, conductance/resistance, phase changes, materials science, anatomy, health, ratios, and structural analysis.


Lesson: Solar Water Purifier

Lesson: Solar Water Purifier

A finished solar evaporator unit
The Schematics to build a solar water Evaporator.

In this Lesson: Solar Water Purifier we will create a system that mimics the Earth’s atmosphere and specifically the Troposphere to turn waste water into drinkable water. This sealed wooden box with a glass lid and a ceramic tray is angled so that when the evaporated water hits the glass, it rolls towards a drip edge and into a tray and then out into a sealed collection bottle.

Why Does This Work?

Remember water is a simple molecule with two covalently bonded hydrogen atoms and one oxygen atom. It is easy to transfer water from a solid, to a liquid, to a gas. All we need is pressure (AKA heat).

As the sun heats the interior of the box, the pressure increases and the water turns to vapor on the inside of the glass. Water is magnetic, so it wants to clump together. This makes raindrops on the inside of the glass that stick to the glass and roll down towards gravitational center of the planet.

Super Useful for Two Reasons

The water and pressure INSIDE the solar evaporator is higher than the outside pressure, so the water condenses quickly due to the glass surface being cooler. On our planet, it is actually the COLD vacuum of space that causes our atmosphere to cool and condense like this. So at night, the condenser is working until the interior cools down again.

Water vapor condensing on a spider web as dew.

This is exactly why we see morning dew and fog. The warm water is a vapor in the atmosphere and when touches the colder spider web or tree and plant leaves, it condenses back into water. This is called condensation and you can see it on your cold glass on a very hot day.

The other benefit to using a solar evaporator of solar condenser is that any impurities stay in the tray. Only PURE molecular H2O is transferred into vapor. This way the water we collect is very pure and drinkable.

Earth atmosphere layers infographic. Thank you Wikipedia!

Now, we still have some impurities (not a lot) but an even bigger issue is that this type of water is FILLED with ions. We need to add some minerals to it to make it drinkable. In nature our planet and atmosphere do that, but in this water we just need to add a bit of calcium and magnesium (salts).

Now Let’s Build a Solar Evaporator!

Materials

  • A wooden box (I use wine boxes)
  • A piece of glass the size of the box
  • some wood to serve as a glass edge frame
  • Silicon caulk
  • Wood Glue or small Screws
  • Ceramic, glass or metal pan that will fit inside the wine box
  • Piece of tin foil to make drip edge and line the box
  • 1/2″ PVC tubing
  • 1/2″ PVC tubing cut in half
  • 1/2″ PVC bulkhead assembly
  • 1/2″ PVC elbow
  • 1/2″ to 3/4″ male screw end adaptor
  • Small garden hose with a female end
  • Screw adjustable legs for adjusting the hight of the high end of the box
  • Jigsaw Power Tool
  • Powered drill and 1/8″ drill bit
  • Screwdriver or drill screw attachment
  • Electricity connection

Instructions

  1. First clean the wine box. Most small wine boxes are 11×14″ so buy a frame that is also 11×14 and that takes care of fitting your glass properly.
  2. Use the wine separators to make your glass edge shim. I use wood glue to hold the wood shims to the outside of the box, but you can screw it on mechanically as well, your choice. Just make sure you seal any holes!
  3. Add the screw adjustors to the bottom of the wine box so you can create an angle of the box towards the water collection drip edge.
  4. Line the inside of the wine box with foil. You want photons to reflect around and increase pressure!
  5. Line the top edge of the wine box (inside the glass shims) with silicon caulk and let that set. This will be the seal for the evaporator.
  6. Create an “L” shaped drip edge at the end of the evaporator glass that will be in line with the PVC water catchment and the bulkhead out of the box. This will direct water into your collection tray.
  7. install the bulkhead into the side of the wine box’s lowest point. Follow instructions on the bulkhead assembly package.
  8. Fit the drip catch PVC into the inside face of the bulkhead (below the drip edge) and then add a 1/2″ PVC connector to the elbow, one below the elbow into the male 1/2″ to 3/4″ screw connector and attach the hose.
  9. Place the pan for dirty water in the wine box and seal the glass on top. Use tape or string to keep the glass tight against the silicon caulk to provide just a bit more sealing.
  10. Place your solar evaporator with dirty water into the sun and wait!