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.


Design Challenge: Interview for Your Future Job

Design Challenge: Interview for Your Future Job

In this design challenge: interview for your future job we will be playing a game to discover what we as individuals find most interesting. By playing this game we should learn three things. We seek to discover who we are, what we like, where might we be able to do those things?

Start with Passions

Start by forming into your teams. Each team will work together for 15 minutes to create a summary of the things they know about themselves on a scrap of paper. Then they will collect those papers into a folder.

Pass the folder to the next team. That next team will take these pieces of paper and in 10 minutes compare them to careers provided that reflect some of the words in each description. Starting with the question “Who are we“, moving through “what we like“, and finishing with “where can we do those things?

Discussion: What Do We Mean By Passion?

What do we mean when we discuss passion? What do we mean when we discuss talent? Why do passion and talent matter?

Create More Meaning

Once the second team has organized the team prior into careers, pass the folder to the third team. The third team will be interviewing the original team and each other team the same. This should be done in five minute rounds.

The winner of the design challenge is the team that best captures the person described in the team dossier assigned to them. Is it possible to match a persons interests and impacts this way? What else should we factor in?


Design Challenge: Mastering Fear

Design Challenge: Mastering Fear

Design Challenge: Mastering Fear

In this design challenge: mastering fear we will be using simple tools or resources to create an 80 second hourglass or hourglass proxy. Why 80 seconds? This is the longest amount of time that any emotion can remain active in the body when focus is pulled from it.

The quote on the image above is a very famous quote from the book “Dune” written by Frank Herbert four years before I was born. What do we think it means? The idea is as old as legends, myths, and recorded history.

Let’s Talk About Fear

Let’s have a discussion about fear and panic and then we’ll get into the Design Challenge. How do we define fear? Why do we have fear?

The Challenge

Using just a few simple tools and objects, teams must research

  1. How emotions work
  2. How Hourglasses work
  3. How to create something that flows over 80 seconds

Each team will tackle one of these questions using a Raspberry Pi computer and monitor, a wifi signal and and a monitor. When the research is complete it should be documented on paper. When that step is complete we will begin building a fear hourglass.

What is an emotional Hourglass?

An emotional hourglass is a simple improvised hourglass made of simple tools and machines and substance that under pressure flows for 80 seconds. The hourglass DOES not have to be a device. It can also be done in code on a computer or as a poem. The only stipulation is that the process must take 80 seconds to complete one cycle.

Use The Design Cycle

We will be using the design cycle to design, build and test this design challenge. Each team will use the analyze and modify component of the design cycle to test another team’s solution set. Be brave, be adventurous and be clever!

The Design Cycle

Design Challenge: Prepare a Microscope Slide

Design Challenge: Prepare a Microscope Slide

Design Challenge: Prepare a Microscope Slide
Dry Prep Slide

In this design challenge: prepare a microscope slide we will determine what is on three different slides and learn to prepare our own slides. Students will be given 15 minutes to understand how a microscope works and how to prep and place a slide. Then using the microscope, they must determine what they are looking at.

The key to this Design Challenge is quickly learning how to properly use a microscope and slides. Students will also integrate lessons about light and energy in to this challenge. Lastly, they must integrate their lesson and learning to come up with a hypothesis of what they are seeing.

The Design Cycle

Using The Design Cycle

At Mezzacello I use the Design Cycle all the time. It’s the best way to teach and learn because it works like how children play. In this design challenge we will be playing with materials and light!

The most important part of the Design Cycle, in my opinion, is the analyze and modify section. this is where we see if it is actually going to work, and then we can either try to redesign or rebuild something to make it better. The design cycle helps us remember where we are so we have a better idea of where we want to go.

Safety Challenge

Since students are not 100% sure what they will be looking at on their slides, it is important that glove protocols be followed. Students should NOT touch slides with their bare fingers. Bare fingers leave oils on slides and can make it hard to see.

In addition there might be a bacteria that we do NOT want to touch directly. Glove protocol will be covered and enforced. It will be a fun experience for all and safe.

Materials

  • Gloves
  • Microscope slides
  • Microscope
  • Power source
  • Biomaterials
  • Q-Tips
  • Pipettes

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!


The First Chick of 2022

The First Chick of 2022

On Easter Sunday I thought I heard a tiny alarm going off in the dining room. It turned out it was the first chick of 2022 hatching in the incubator. That was a surprise!

I was sure I had another week. I had to run out to the livestock shed and collect all the materials I would need. Pine shavings, heat lamp, electrolyte solution, waterer, feeder, medicated feed, a box, and little dome that it could hide under.

Who knows how long until the rest of the eggs hatch. I have candled them all and they are full. Only time can tell.

Image Courtesy of backyardpoultry.iamcountryside.com

I will start up a new batch with the ducks. Problem is, I don’t know which eggs are the Saxony and which eggs are the Rouen. Life is an adventure, I guess.


The Long Tail of Life

The Long Tail of Life

The long tail of life
Eggs from the automated chicken coop. Not even the ducks can muddy them up!

These are eggs from the chicken coop at Mezzacello in winter. This is a shot os the true costs of life. Every molecule of every nutrient in this cache of eggs is an example of the long tail of life.

Lessons From History and Economics

In history, statistics and economics when we reference “the long tail” we are talking about the journey and the relevant facts of the topic at hand. Here, we are talking about the formation of Mezzacello, the systems, the automation, and the food streams and wastes put to use at Mezzacello. The long tail of Mezzacello starts in Downtown Columbus and eventually extends to every city on Earth, the Moon, and even Mars.

Why a long tail? Because every good farmer or strategist knows that every season starts the season before. At Mezzacello, every system, ecosystem, resource, automation, and decision is designed and leveraged to make the most out of it’s input and impact.

Mezzacello: Living in the Past, for the Future

That mission, leveraging the best of the past with the promise of the future is at the heart of our work and research. Ever step of the way we are:

  • Leveraging beauty and structure to improve neighborhoods
  • Pulling in resources and repurposing in place resources to create biomass
  • Creating renewable energy and water resources
  • Data and automation strategies to replicate and improve systems
  • Continuing our educational resources, camps and internships
  • Building relationships and partnerships with other farms and gardens
  • Leveraging databases, tools, and resources and tools to make all of this happen again

Like an egg there are many layers to this issue and its solutions. From the shell to the egg proteins, to the feed and water resources it took to raise it, to tomorrow’s chicken that will jumpstart the entire process again. These eggs are the future of food and the tech that will make food the ultimate tech for the world of tomorrow.

Now let’s crack these eggs open and see where it leads us next.


Fall Spa Day For The Ducks on the Farm

Fall Spa Day for the Ducks

The ducks of Mezzacello swimming in the pond enjoying life and being “rained on”

Today was an early fall spa day for the ducks at Mezzacello. It is more than just a treat it is a near necessity on an urban farm. This is because ducks are very delicate and ironically hardy creatures. They have very specific ecological and dietary needs. It stands to reason that if you can meet those two needs somewhat regularly, they will to thrive. It’s when you don’t meet them that things go awry.

It’s All About the Breed and the Niacin (AKA Vitamin B3)

The ducks I raise at Mezzacello are a very specific breed of duck. They are big and gentle and love eating bug pests. They have a lot of benefits and history as well. This breed was developed by a breeder in the early 20th Century. An Austrian Jew who lived in the Saxony region who crossed the Rouen Breed of duck with the Peking Breed of duck to create a new breed.

This new duck became known as the Saxony Breed of duck. But there is one problem and it’s a big one. The Saxony’s do not deal well without Niacin. All ducks need Niacin, but this cross between two ducks has amplified that fact. Therefore one has to be ready to solve this crisis. But first you have to understand the crisis.

In a perfect world, these ducks would live in the large pastures of the Saxony region. This is good, as they need constant access to ponds, waterplants and specific insects that are high in B3. On an urban farm, like where I live, there isn’t a lot of Niacin. So I have had to make adjustments. Like the aforementioned “Fall Spa Day”.

Winterizing the Saxony Ducks

During spring – early fall the ducks and the chickens can forage around the ecologies of Mezzacello for all of the bugs they can gobble up. It’s good for the farm, the insect population, and the ducks. Things go south in fall when the bugs go dormant. I cannot let the ducks live in the pond. It is actually against city code. So as a compromise I give them spa time. Time to swim and dive, and munch on all the lovely pond plants (which surprise! are high in niacin) and I even spray them with “rain” from the hose. They love it and it keeps them happy and healthy.

It’s also really good for the fish, the plants in the pond and for the biofilter attached to the pond. The aqueous wastes the ducks produce helps to manage the Ph of the water. This in turn is good for the plants. The ducks love to nibble on the leafs of the plants once again seeking that precious niacin, and the act of cutting actually helps the plant divide and grow. It’s a win win situation. I will let the ducks swim late into the fall. Then I will alter their diet.

Manufactured Niacin

Niacin molecule

As late fall progresses I alter the diets of all the poultry at Mezzacello. I add wheat germ to their feed, I add peas to their diet, and I feed them dehydrated mealworms – which they LOVE! All of these foods are high in niacin. This breed of duck is niacin deficient so as a result I really have to do this.

The fact of the matter is that with low niacin the birds slowly start to die. Their nervous system shuts down, they lose the ability to lay and their energy levels plummet. It is an easy fix, but you have to catch it early. So niacin spa days are an important part of the duck’s social calendar. And it makes for a great photo!


Lesson: Micro Hydroponics Systems

Lesson: Micro Hydroponics Systems

Building Micro Hydroponics Seedling Trays

This lesson: Micro hydroponics systems students will create rainwater hydroponics systems from to go containers and 3D printed bases. The hydroponic systems will be seeded by Eden’s Ghost, rabbit droppings, and ammonia. This provides the perfect liquid fertilizer.

Hydroponics is just a Greek word meaning water work. In hydroponics systems farmers let the water do the work of growing and sustaining the plants. Humans just provide nutrients in specific amounts to create a balanced ecology.

Materials

  • Take out container with a lid
  • A source of fresh water
  • A series of peat sponge plugs like this
  • A drill (requires adult supervision)
  • A 1/2″ drill bit
  • A sharpie marker
  • A carpet cutting knife (requires adult supervision)
  • A source of seeds
  • A source of fertilizer (see lesson: making the perfect fertilizer)
  • A tray or a set of trays to control water spillage

Instructions

  1. Give each student or team of students a take out container
  2. The size or shape of the take out container is not important as long as it is take out size and not too deep
  3. Have students draw “X” marks where they want to place the plugs
  4. Allow students to examine the plugs so they understand their scale, density and requirements

    • Each plug must have at least 4 cm of space around it
    • Ask the students to arrange their “X” to accommodate this

  5. Once their lids are marked, Drill their holes for them

    • This is best accomplished on a table, with a block of wood beneath it
    • Heating the tip of the drill bit works wonders on clean holes

  6. Allow the students to fill their container bottom with water
  7. Add the fertilizer in a 1:10 ratio

    • Cover ratios with your students if you must

  8. Replace the lid over the container
  9. Give students the seeds

    • The best seeds for this are kale, lettuce, turnips, and spinach

  10. Ask the kids to observe the plugs
  11. When the plug appears sufficiently damp, insert the seed into the hole in the top of the plug
  12. Ask students to carefully monitor the seeds over the first few days
  13. When germination begins, have students add just a 1/2 tsp of fertilizer a week

Teacher Note

It is wise to have a mockup ready and seeded so the students can see the sprouting of the plants. I will provide a few photos in this lesson plan just in case.

These systems are almost endlessly re-useable, so keep them or give them to the students. The roots in the plug will become fertilizer. Or the kids can clean the sponge with bleach and water. Users choice.


Lesson: Creating Perfect Fertlizer

Lesson: Creating Perfect Fertlizer

Creating fertilizer from algae in the Biofilter. This is just one type of fertlizer produced at Mezzacello.

This lesson: Creating perfect fertilizer from NHCOPS, eggshells, coffee grounds, and banana peels. Students will also explore pre-digestive compost runoff and worm tea. Comfrey tea, and fish effluent/algae fertilizer will also be synthesized. All are non-toxic but effective.

All fertilizers share one thing in common: They provide NHCOPS to all parts of a plant (see Lesson: NHCOPS and the Ladder of Life). Since all fertilizers share a common use, do they also provide the exact same benefits? Let’s explore that.

Periodic table of life
We most definitely recycle atoms and molecules!
Water Purification System that models 5 gallon and three gallon buckets.

Materials

  • A five gallon bucket
  • 3.5 Gallons of water (preferably rain water)
  • An air stone and an air stone pump
  • An extension cord rated for outdoor use
  • Maple syrup
  • Three cups of the following:

    • Worm casings (buy at Menards)
    • Chicken manure
    • Rabbit manure
    • Horse manure
    • Shredded leaves
    • shredded paper
    • Algae

  • A stirring stick (even a long twig branch will do)
  • A screen or large colander to collect solids

Instructions

  1. Set up the 5 gallon bucket, the air stone and air pump, the power strip in a safe space
  2. Fill the bucket with water
  3. Insert the air stone into the water and plug it in

    • One can have the air stone on before, but it is more dramatic if the students can see the bubbles

  4. Allow students to observe the bubbles
  5. Begin inserting the various manures and leaves, paper and algae

    • I like to call the shredded paper “human waste” and surprise the students that it’s paper

  6. Once everything has been dumped begin stirring the bucket to mix everything up
  7. Ask the students what they think is happening in the bucket
  8. Pull out the maple syrup
  9. Ask the kids what they think maple syrup is
  10. Ask the students if anyone has ever made bread

    • Do they know what yeast are?
    • Do they know what yeast eats?

  11. What do they think the maple syrup will do in the bucket?
  12. Add the syrup to the bucket – about 1/4 cup
  13. Wait 10 minutes and come back to observe the bucket

    • What do the students see on top of the bucket
    • There will be a beer like foam on top of the bucket
    • Allow the mixture to sit overnight

  14. When the next day arrives ask the students to smell the mixture
  15. It will smell like rain, ask them to hypothesize why [Petrichor]
  16. Strain the liquid and bottle it up, set the solids aside for compost starter
  17. Observe the fertilizer color, consistency, smell, and weight
  18. Ask your students to hypothesize why it weighs more than water and has that color if we took all the solids out
  19. Record their answers

Teacher Note

There is a lot of excellent chemistry, biology, math, physics, art, literature, and mechanics in this lesson. If possible power the unit with a solar array or batteries and discuss the role of energy in this system.

Nested Realities from the Organism to the energy that animates it.

In nature, what powers this transformation? Is it the sun? Yes? What role is the air stone playing in this system? This is the perfect time to tie the breakdown of molecular aspects with rust and oxidation.