Energy and Information Drive the Cycles

It’s not easy to think about levels of organization as real things. It’s much easier to think of ourselves as real and everything else as a thing, but in fact we are only one cog in the wheel of life — from the life of a cell that perhaps makes up part of your body to the interacting behaviors of organisms, from plants to animals to fungi and other organisms that all interact to spread the food of life throughout the ecosystem.

What would it feel like to be an ecosystem? Or a cell? We can’t know things like that; the only thing we can know is what it feels like to have a brain. They don’t. But we do have the advantage that we can use the brain to figure out what we should do or should not do if we want to stay alive. One thing we should do is to think about our relationships with the other parts of the creation. If we believe in God, then it is a certainty that these other parts of the creation were put here so that we could survive and thrive; if we don’t believe in God, these other parts of the creation are still necessary for our survival. If we want to survive, then, the God question is not nearly as important as the responsibility question. If we only think about what we want today, we have now enough power to throw the ecosystem off balance forever. That’s what the scientists mean by the “tipping point.”

We talk about the tipping point as though we could see it or measure it. We can not. If you were a scientist, you might say: “We don’t want to do that experiment.” It’s no different from experimenting with human lives. Why on this living earth would we want to “wait and see what happens” before we do what we know is necessary to our survival into the future of life on earth?

So let’s try to think about levels of organizations again, and how they relate to the flow of energy and the cycling of materials through the ecosystem, and the flow of information through space and time. Because those are the three requirements for survival of any living thing. Materials recycle, energy flows throughout, information directs all the processes through time.

Let’s begin with the materials that cycle through the whole, because that is relatively easy to imagine. Materials are made of atoms. Atoms are the basic units of elements, or you could say the basic units of matter. Elements are the building blocks of matter. Molecules are made of atoms. Your desk is made of atoms and molecules. If your desk is wood, it’s made of organic molecules. If your desk is metal, it’s made of inorganic atoms and molecules . The difference is the organic molecules are carbon based and were made by trees.

Wood is mostly cellulose. Cellulose is a carbohydrate that was made by a tree using energy from sunlight to bond together carbon, hydrogen and oxygen atoms in a particularly strong configuration. If you burn up your desk, that sun energy is released as heat, the carbon atoms combine with oxygen from the atmosphere to make carbon dioxide, and the hydrogen atoms combine with oxygen from the atmosphere to make water (or actually steam at this temperature).

We do not eat wood because we can’t digest wood. That is, our bodies do not have the necessary enzymes to break apart the molecules of cellulose. If you eat sawdust, for example, it will come out pretty much as it went in. But if you eat a potato that is made of other kinds of carbohydrates, it gets all broken up in your gut into glucose molecules, and then the glucose molecules are transferred from the gut into your blood and they are pumped around your whole body so that every cell in your body has some glucose to burn. Just like you burned your desk, except the cells are able to burn the glucose ever so slowly and capture the energy to do the work of staying alive. The work of staying alive is mostly making other kinds of molecules. All of that is controlled and directed by your genes. Humans don’t have genes that will direct the digestion of sawdust. Quite a few different kinds of organisms do. They can digest sawdust and recapture the energy that is in wood and use it as food to stay alive.

Why do we not have the enzymes to digest sawdust? Enzymes are proteins. For every different kind of protein produced in a living body there is a genetic code. The human genome (all the genes) is not set up for us to eat wood. However, there are genes in fungi, for example, that do make enzymes for digesting sawdust. In the entire ecosystem, there are genes that permit every function that is required for the flow of energy through the ecosystem. This is necessary for keeping the entire ecosystem alive.

Think what happens if you cut off the flow of blood to one part of your body so it can not receive the glucose or the oxygen it needs. That same sort of thing happens if we prevent one part of the ecosystem from getting the organic molecules (food) that it needs to stay alive.

So, basically, food is organic molecules that are burned inside the body. Most of the energy is then used to do the work of staying alive. All of the functions of staying alive are directed by the genes

Notice, this has nothing to do with burning trees or burning gasoline, and this is one of the very important things the media do not want to tell you about. We are talking about using organic molecules to stay alive, not to drive cars. Burning the organic molecules inside our cells and breathing out the carbon dioxide and urinating the water. Not putting them in a big pile and destroying them. Either way, the result is carbon dioxide and water into the atmosphere, and the energy is gone away as heat.

Global warming.

When the ecosystem is in balance, then the carbon dioxide and water would be breathed in by the plants and used to make more organic molecules, under the direction of the plant genes, so all the related cycles of life could be repeated, over and over again, directed by all the genomes of all the organisms.

Similarly, all the other kinds of atoms and molecules that we need to be alive are recycled by the ecosystem. We don’t need to describe every different kind of cycle, because that information is available on the internet. The important point is that all the animals and plants and other organisms are involved in this kind of recycling. Different kinds of organisms have different tasks in the various cycles. They all work together to keep the cycles of materials balanced so that nobody ends up poisoned and nobody ends up deficient in some kind of atom or molecule that is needed for life to stay alive. The energy to do all this work comes from the sun and is not recycled. (Contrary to what you may have heard in the media.) It is changed into heat. The genetic information that directs all these millions of processes and keeps them in balance is not recycled. It is carried forward by sexual and asexual reproduction from one generation to another, changing a bit over time in response to changes in the conditions of the whole of life (we will describe this next post). Materials recycle; energy flows through and is lost; information, if lost, is forever gone.

This sort of thing does not happen on the moon. It does not happen on Mars. It does not happen on the sun. Because none of those places are alive. It will not happen on the earth if we throw it so far beyond the tipping point that it can no longer recover its balance.

Photosynthesis

Note added on 10/11/11-We are getting a lot of hits on this site. Just want to say the book that this post came from, the Bare Bones Ecology Energy Handbook, is available as a free download on the right side of the blog.

You can easily find books that describe all the hundreds of chemical reactions that are required for the two overall processes of photosynthesis and cellular respiration that support life in our earth ecosystem, for example Lehninger Principles of Biochemistry by David E. Nelson. Biochemistry is the chemistry of living things that focuses on organic molecules and their interactions in cells. It’s not so easy to find an explanation, as we have developed, of the importance of the flow of energy that supports the emergent property of life at all its levels within the earth ecosystem.

The overview, of course, you have heard in almost every post of this internet project. For life to exist in The Creation as we know it today, it requires many things, but we are talking about energy and. And it requires that the energy be available to every living part of the ecosystem. We have used the term “flows through,” because the energy comes into the system as light, a higher form of energy, and leaves as heat, a lower form that can not recycle back to light.

The energy that can be used to sustain life is distributed throughout the system is in the organic molecules that we use as food, (and in the case of humans also fuel and raw materials run our economy.

Molecules are atoms that are joined together by energy bonds. Organic molecules are very large molecules, such as proteins, carbohydrates, lipids (fats and oils) and nucleic acids, that are made inside living cells, including all of our cells. Organic molecules make up most of the structures of our bodies and also direct most of the functions, such as thinking, moving, breathing, all the things we do to stay alive. The energy bonds of molecules are the energy that is used to sustain life; therefore we have referred to this kind of energy as organic energy, as a type of energy, because there are quite a few different sorts of energy bonds.

Plants and photosynthetic bacteria, and also phtosynthetic one-celled eukaryotic organisms (protista), can do photosynthesis because the cells contain chlorphyll to absorb most of the energy from light, and then they can use that energy to make organic molecules in a process called carbon fixation. None of these processes is just one biochemical reaction. Each consists of a series of dozens or hundreds of chemical reactions. To cause these chemical reactions to happen at the right time in the right place, the cells contain a set of enzymes that are required to direct specific chemical reactions. An enzyme is a protein that functions as a catalyst. A catalyst is a anything that causes a reaction to happen but is not used up in the reaction.

A chemical reaction is a change that happens among atoms or molecules. Each kind of atom or molecule is unique; therefore the ways in which they can or can not fit together depend their unique characteristics. That is a subject for chemistry and biochemistry. We generalizing about chemical reactions.

Enzymes direct most reactions. Because the enzyme is not an integral part of the reaction, it is not permanently changed during the reaction. Therefore it can be used again to cause another of the same kind of reaction. Enzymes are specific to reactions. Each reaction requires it’s own kind of enzyme. By controlling the enzymes, the cell can control the reactions. We will discuss that fact later when we cover the second major requirement of life.

Photosynthesis is a multistep biochemical process that includes the absorption of energy, as described in the previous post, and carbon fixation. Carbon fixation is the uphill process of taking carbon dioxide from the air and using it, along with water and energy, to make glucose, as diagrammed below.

The overall process of photosynthesis and carbon fixation involves a complicated pathway consisting of many small steps during which small changes are made as energy is transferred under the direction of multiple enzymes. In eukaryotic cells, one kind of specialized organelle, the chloroplast, is responsible for organizing the overall process of photosynthesis. Organelles are composed of membranes (lipids) that contain all the necessary enzymes (proteins), organized in the best way to cause these complicated reactions to occur. The glucose product is then made available to the entire cell, and all the cells of the body of the plant (because plants also have circulatory systems). The oxygen product is released into the atmosphere. We need the oxygen to breath and we need organic molecules for our food/energy.

Glucose is a carbohydrate. The plant makes other carbohydrates from glucose. It also can make lipids and it can add nitrogen and other kinds of atoms to make proteins and nucleic acids and other organic molecules that it needs to survive.

The organic energy is then distributed throughout the ecosystem by animals eating plants, other animals, cells, tissues and dead organic matter. By eating, animals (that would include us) obtain the glucose and other organic molecules that they need to survive. These are mostly proteins, lipids, nucleic acids and carbohydrates. Every living thing in the ecosystem gets the energy and the molecules of life, either second or third our fourth, handed on from photosynthesis. (Except a very few really odd bacteria the live in strange places.)

At every step in the network of energy transfer from one creature to another, about 10% of the energy is wasted. It goes away as heat without doing any life work. Except of course to help keep us warm. The more work we do, the more heat is released in our cells. If we are very cold, we run around flapping our arms and we wear clothing to trap this released heat next to our skin. But eventually all the energy that was in the original plant is lost and we get more energy by eating.

But in the meantime, while the organic materials are circulating in the ecosystem, all the plants and animals of the entire ecosystem are keeping their bodies alive by metabolizing the organic molecules. Metabolism is the process — actually it is thousands of processes — of changing those organic molecules around to make all the different parts of our bodies: muscles, heart, eyes, all the structures of our bodies are made of organic molecules or they are made by organic molecules.

That is a lot of work!

The energy to do this work comes from breaking down the glucose molecules in the tight control of the cells so that the released energy is captured, still in the form of chemical bond energy. The energy is taken from the glucose to energize some other important cellular function, possibly your muscle movement, or perhaps the light receptors in your eyes, and so the glucose atoms are no longer bonded together and are released from the cell as carbon dioxide and water. Oxygen bonds with carbon or hydrogen because it is a downhill reaction — the energy bonds (added together) contain less energy in the carbon dioxide and water than they did when these atoms were bonded in the glucose molecule. Notice that it requires oxygen to burn glucose, but it wouldn’t be correct to say that we are burning the oxygen because the oxygen itself is going from a smaller molecule or atom to a larger one with more energy bonds. The energy is released from the glucose – just as energy is released from the organic compounds in wood or gasoline when these are burned in the presence of oxygen. The oxygen is required to remove the waste products (carbon and hydrogen) of the reaction so the energy can be released and used to make other molecules in the body.

The formula for breaking down glucose can be written:

But of course it is not just one reaction. It is a series of dozens of reactions that are catalyzed by enzymes. The overall process is known as Cellular Respiration. Cellular respiration is the intracellular process of breaking down glucose to release energy, carbon dioxide and water. In eukaryotic organisms, these reactions are organized in organelles known as mitochondria. Mitochondria are organelles that are specialized to direct the process of cellular respiration.

You probably already know that plants release oxygen that the animals require to breath, and the animals release carbon dioxide that the plants require to “breath.” Almost everyone knows this, but did they tell us why we need to breath? Or did they let us believe the plants are here on earth so that people can breath oxygen and eat?

No Way. Our lungs and heart are helper organs. They help to get the oxygen to the cells so that the cells are able to release energy by doing cellular respiration. One-celled animals don’t need the lungs and heart, but they do need the oxygen in their environment.

Plants “breathe out” oxygen, because it is a waste product of photosynthesis and carbon fixation. They need to get it out of the way so they can do more photosynthesis and carbon fixation.

Animals and plants “breathe in” oxygen so that each cell of the body will have the oxygen it needs to do cellular respiration to release the organic energy it needs to stay alive.

Animals and plants “breathe out” carbon dioxide because it is a waste product of cellular respiration.

Plants “breathe in” carbon dioxide because it is a substrate in the process of carbon fixation the process that provides food for the whole ecosystem.

It is the miracle of life that life supports life and life requires life. Nothing dominates, not even that lion in the diagram below; everything interacts so that all may survive, so long as the balance is maintained.

”One of the penalties of an ecological education is that one lives alone in a world of wounds. Much of the damage inflicted is quite invisible to laymen. An ecologist must either harden his shell and make believe that the consequences of ‘science’ are none of his business, or he must be the doctor who sees the marks of death on a community that believes itself well and does not want to be told otherwise.” Aldo Leopold

Energy Flows-Or Nothing Happens

Light is energy. There are many things about light that we don’t understand, but why should we understand everything? We only need three bits of very well established scientific fact to cover the most important aspects of how energy flows through the ecosystem to keep all of life alive.

1. Light is energy. We have defined energy as the ability to make actions happen, and light can make actions happen. For example, when light hits your eyes it activates molecules in a nerve cell that sends the message to your brain. That is one kind of work. Energy is the ability to do work.

2. According to the second law of thermodynamics, pushing anything from a lower level of organization to a higher level requires work. Work is necessary to push any kind of action “uphill,” but “downhill” actions can happen without help. It requires energy for you to climb the stairs to the top of the Empire State Building, but it requires no energy to get to the bottom if you fall off. In a more relevant example, anything that is more complicated or more powerful is “uphill.” To make a cake requires energy, but it can fall apart by itself. Cake is more complicated than flour. Life is the most complicated thing on earth. Cells require energy all the time in order to maintain their complex organization. But the important thing is that the entire system always is in balance because the downhill slide of energy balances its uphill push to the system. This is possible because energy comes in different forms.

3. Some forms of energy are “uphill” from others. For example, light energy can change to heat energy by itself, but heat energy can not spontaneously change back into light energy, because heat is a lower form of energy. Plants use light energy to make what I am referring to as organic energy (in food). Light energy is a higher form than organic energy, and organic energy is a higher form than heat energy.

So, the bottom line is that life maintains its complexity, even though it is always working “uphill,” because the entire ecosystem is provided with organic energy. For some people, this is the definition of life. Life is working, working, working all the time to keep itself from falling apart, and — if it stops working — it does fall apart. It dies.

That’s why people are alive and cake is not. Once you turn off the oven, the cake has no way to maintain its high level of organization and eventually it will fall apart. The miracle of life is that it can use light energy to keep itself organized and functioning — and it does it inside of itself. Inside every cell in our bodies and every organism in the ecosystem. So far as we know, nothing else in the universe can do this. Only life.

So the first half of our life story is about the amazing way that plants, and some bacteria, are able to capture light energy and convert it to food energy that we have referred to as organic energy. The process happens only in green plants and bacteria and it is called photosynthesis. Photosynthesis is the process of making organic molecules using the energy from light.

Capturing, or absorbing light energy is no problem for a pigment molecule such as the chlorophyll of plants. Pigment is any substance that absorbs light. Absorption of light energy happens all around us; it is what makes the colors. Light from the sun includes several different kinds (different wave lengths or different energy types) of light. We see some of these in rainbows, and we can see them because our eyes are activated differently by the different wave lengths of light energy.

So we see a cat because sunlight hits the cat and bounces off the cat into our eyes and energizes some nerve cells. This cat is orange, because only the orange light bounced off her. The other wavelengths were absorbed by the pigments in her hair. (We wrote a whole book about hair pigments, soon to be published, called The Colors of Mice, but that is blatant advertising and has nothing to do with our story here.)

The wavelengths that bounce off — that are not absorbed by the pigment — are still light energy; the wavelengths that are absorbed into the hairs change to a lower form of energy. For example, heat energy; that’s why the cat is stretched out in the sunlight on a cool day. It makes her feel warm and cozy. The pigment of a black cat absorbs most of the light that shines on it. A white cat reflects most of the different wavelengths of light. The green rug in this picture is reflecting green light back to our eyes and is absorbing the other wavelengths.

Plants, as you already realize, reflect the green light and keep the other wavelengths. Unlike cat hair pigment, however, the plant pigments (chlorphylls) do not allow the light energy to degrade into heat energy. Instead, the plant has a very complicated series of biochemical reactions that converts some of the light energy to make the energy bonds of large organic molecules. We will talk about the chemical reactions in some other post.

So, absorbing the light into a pigment molecule of (mostly) plants –and then using the energy to make food molecules — is the first half of the flow of energy through the ecosystem.

The second half is distribution of the energy so that all the parts of the ecosystem can stay alive. We discussed last time why an internet requires all its parts if it is to maintain resilience and sustainability.

So, to recap, the energy that does all this work comes from food. And of course you know what happens when you have no food. The only food we can use to stay alive is organic molecules, and the organic molecules are made by plants. If someone tells you that there is no limit to the energy available to us — because it comes from the sun — they are wrong. You and I both know we can not eat sunlight; our food comes from plants, and we are definitely limited by the amount of plants on earth, not by the amount of sunlight. If someone tells you we can make organic molecules for ourselves to eat, that is true, but unfortunately it takes more energy to make the food than we can get back when we eat it. Any anyhow food is not the only thing that keeps the ecosystem alive. The ecosystem is an internet; it requires a lot of things, and the most important is to keep all those things in balance.

The whole ecosystem stays alive by keeping a critical balance among all the different life forms that do the various ecosystem jobs we talked about last time, and a balance among the three forms of energy, light energy, organic energy and heat energy.

The ecosystem survives because the energy from the sun flows from one of its life forms to another to another to another, doing the work of keeping cells alive. Cells of plants, cells of bacteria, cells of turnips, cells of your body, cells of trees, cells of potatoes, cells of tigers, cells of worms, cells of mosquitoes, grass, horses, fish. You get the idea but if you want a visual cue you can look to the elegant, if simplistic, diagram below.

Every time we eat a bite of food (with the energy it contains) and then our body breaks down the food to release the energy bonds, and uses that energy to do the work of keeping our cells alive — every time we do any of those things, some of the energy is lost as heat. Nobody can eat heat, so then some plant somewhere in the ecosystem must capture more light energy to make more organic energy for our next bite.

Of course we know energy is not the only good thing we get from food. We will discuss other things — primarily carbon, hydrogen, oxygen, nitrogen atoms and small molecules like water and carbon dioxide — in the third section of this book when we explain how the ecosystem recycles these materials into and out of our food. The point here is that the energy does not recycle. It is lost as heat. That’s why the plants must be constantly making more organic molecules to keep the entire ecosystem alive.

For the whole ecosystem to stay alive, it must provide food for every living part of itself. It must maintain the balance among the numbers of plants and the number of organisms that eat plants and the organisms that eat other organisms. And even more, the ecosystem must maintain the balance between the light energy that it uses to make organic energy, and the heat energy that is released when organic energy is burned to do work.

That’s why we have global warming. The energy balance is off. It has been for a good while.

Therefore, the only long-term cure for global warming is to help the ecosystem to restore her balance. We could do it, but not if we try to use any method that causes more heat to be released into the ecosystem. We can not cure global warming, and the starvation that comes with it, by burning anything or by growing our economy or our population. Because growth within our living ecosystem burns organic energy.

And too much growth is what caused the problem in the first place.
“Men are not flattered by being shown that there is a difference between their purposes and those of God.” Abraham Lincoln

The First Requirement of Life; Energy Flows Through the Ecosystem

Energy flows both vertically and laterally through the network of levels of organization that make up the living Creation. The question, of course, is why and how does the living earth ecosystem accomplish this flow of energy. We have already introduced most of the components of this process.

Energy
is the ability to do work. If this definition seem to you impossible to understand, you are understanding. The definition an observational one. We do not see and we do not fully understand energy, but we need the word to describe the processes that we do see, without exception, in the living and nonliving parts of the earth ecosystem — and in the whole universe, so far as we know.

The Second Law of Thermodynamics is a another observational definition of the reality of how the whole of The Creation functions. The whole universe, so far as we can know. The second law says that everything will naturally tend to become less organized on it’s own. Energy can spontaneously convert from a higher to a lower form (nuclear > light > heat), but not the other way. Also physical things can fall apart (because it is energy that keeps them together), but it requires energy to do the work of putting them back together. The rock will roll downhill, fall into the river, and be buffeted about by the water that is running downhill into the ocean, but it requires energy to build a pile of rocks or to carry the water back uphill. So, for our purposes, work is anything that can cause a change from a lower (less organized) to a higher level of organization of energy or of matter. If the second law of thermodynamics seems difficult to understand, it is. But within the ecosystem we need only to understand that energy and matter exist in lower and higher levels of organization and it requires energy to make things more organized.

Life on earth is organized into levels of energy and complexity: the cell, the organism, the ecosystem and the whole earth ecosystem are the major levels of complexity.

Living organisms are able to use the natural flow of energy to do the work that is required to stay alive, but they can not change the laws of thermodynamics (or any other basic law of nature). Basically, living organisms (plants mostly) change light energy into organic energy, in the form of food The plants are able to make larger organic molecules and macromolecules from small molecules.

Energy is required to make something big from something small.

The plants capture light energy from the sun and change the light energy into what we are referring to as organic energy. We define organic energy as the energy of the “bonds” that join together carbon and oxygen and hydrogen and nitrogen (and other atoms) to make organic molecules.. The bonds that join organic molecules are not different from energy bonds that join inorganic molecules, but there is a whole big branch of chemistry that studies energy bonds between and among different kinds of atoms. We don’t need to understand allo the different kinds of energy bonds that function to make big molecules not fall apart, and so I have lumped them all in the category of “organic energy.” For our purposes, we need to know that molecules are held together by energy bonds and bigger molecules contain more energy than smaller molecules. This amazing accomplishment uses the second law. A higher form of energy is converted to a lower form — light energy is converted to organic energy. The higher energy form (light energy) contains more energy than the lower form. Some of that energy is used by plant cells to make the energy bonds of organic molecules and someof the energy is lost as heat.

Macromolecules are large molecules that are composed of molecules that are joined together by energy bonds.

Molecules are composed of atoms that are joined together by energy bonds.

Living things are composed of atoms and molecules and organic macromolecules that are joined together by energy bonds.

Atoms contain energy and matter (matter is the stuff of things that we can see and feel and it has weight if it is in a field of gravity). Again, there is a nice picture book on this subject, by Theodore Gray and Nick Mann, that shows the different elements of which the earth ecosystem is composed. That is, the different kinds of atoms. Everything we know is composed of atoms (matter and energy). The atoms join together to make molecules, and they do this according to energy relationships that depend on the specific matter/energy characteristics of each different kind of atom, that is, the kinds of energy bonds they can form. We do not need to study all these different energy relationships to understand that different atoms are more or less likely to form various kinds of energy bonds, that big molecules contain more energy than small molecules because of the energy bonds that join together the component elements, and that the particular atoms that make up most of the organic molecules are carbon, oxygen, hydrogen and nitrogen. And that plants capture the light energy from the sun and use that energy to join together atoms to make organic molecules.

Our food — also all of our other energy-containing carbon compounds (oil, gas, coal etc) – consists of organic molecules that were made by plants at some time in history. This is why some people propose to use live modern plants to make fuel for our cars.

In fact, the energy that runs all of the living earth ecosystem, comes from organic molecules. High energy organic molecules are circulated through the network of levels of organization of the whole earth ecosystem, first by plants. Organisms that can not do photosynthesis get their energy by eating plants, or other organisms. At every step of energy exchange (whenever organic molecules are eaten or burned) some of the energy is changed to heat and is lost from the system.