Molecules are Composed of Atoms

At least this is a useful way to think of these entities that are so small and at such a relatively low level of organization that we (meaning the physicists) can’t see, touch or imagine precisely how they function.

But we can make a model that describes the things we know about how they function.

Atoms are made of mass and energy. Mass means they have weight (where there is gravity) and volume. On earth there are a little over 100 different kinds of atoms. The mass of an atom can be thought of as protons and neutrons that make up the internal portions of the atom. Protons have positive energy that attracts electrons. Electrons have negative charges that make up the outer portion of the atom where it can come in contact with other atoms. (These negative energies are very similar to minute units of electricity). Atoms with more protons also have more electrons because the opposite charges attract each other.

Different kinds of atoms are attracted to each other according to their different electron energies. If the energy attractions are strong, then different kinds of atoms can make energy bonds between themselves to form molecules.

A molecule is two or more atoms joined together with energy bonds that we can describe according to the following diagram.

Water is two hydrogens joined with one oxygen by energy bonds.
Carbon dioxide is one carbon atom joined with two oxygen atoms, CO2.

Energy bonds are not random. The innate energy characteristics of a particular kind of atom determine if it will bond and how it will bond with other atoms. This is another one of those laws of nature that humans can not control. We can change atoms around — we can bombard them and break them because we have powerful technologies, but we can not change the nature of the energy interactions. Energy interactions happen according to the Second Law of Thermodynamics.

That’s what we really need to know. We don’t need to know all about the physics of atoms and molecules to understand how living things are able to use these characteristics to flow energy through their selves.

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.

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.

Levels of Organization

The Ecosystem is a Network of Levels of Organization

The diagram below needs explanation, but it won’t be easy, because the ecosystem is so complicated that it is impossible humanly to represent or to fully understand.
If you find it mind boggling to comprehend the levels of organization, all interacting among and between themselves, then you are just like the scientists, the politicians, the religious and everyone else. Fortunately, we do not need to understand all the little details of the system in order to have a good idea of how it functions — the structural and functional requirements for it to stay alive — and that is our goal. A basic appreciation of the beautiful idea of networking. and of the levels of organization. is background for understanding the flow of energy, and of other things, through the living ecosystem. Life is possible because of the internet of living and nonliving things through all the levels. The basic format of these realities is outlined in the below diagram.

The ecosystem consists of sets and subsets of living and nonliving entities that interact between and among themselves. We can not represent the entire system in a diagram for two reason. One is that the sets and subsets (levels of organization)
are flexible, a fact that is necessary for their survival (sustainability). The other is that there are just too many interactions to understand or represent.

For example, looking to the diagram, there are ecosystems within ecosystems. I am a functioning part of the pasture ecosystem and the East Texas group of ecosystems and in fact all the ecosystems in the world because I contribute to the materials (such as carbon dioxide) and the energy flow and many other activities that occur within each of these ecosystems and the whole earth ecosystem. If I could draw all the lines of interaction between myself and all the other ecosystems and all the other levels of organizations, the entire page would be black. So I drew only one or two or a few lines to feebly represent just a few interactions.

Imagine that everything interacts with everything on this diagram in some way(s) and also everything interacts with millions of other entities that make up the living system. For example, your heart interacts with every other component of your body; your resilience and therefore your survivability (sustainability) would be unlikely if any of these interacting components of your body were missing. All the organs work together to maintain your life. This is represented by the lines between the heart and kidney and skin on the diagram. However, it is true of every organ in your body. They all interact. Similarly, the leaves, bark and other organs of a tree all interact with each other to make the tree alive, and the tree interacts with nearly everything else in the ecosystem, including us.

We are only one component of the metabolism of the ecosystem. Our lungs breathe the oxygen that is provided by plants; our food gives us the energy we require for life; the environment degrades our wastes, so that we are not suffocated in a dung-heap of the unused byproducts of our metabolism. These processes are carried out by other organism that all are interacting within all the big and little ecosystems of life on earth. We could not survive without the other elements of the ecosystem, and we also contribute to the other elements of the ecosystem.

Levels of organization are shown on the diagram by the large headings on the left side of the page. Levels of organization are a special type of interaction that we have discussed before. Everything in the universe is composed of other, smaller things. These relationships are referred to as levels of organization. A very few example relationships of this kind are shown in the diagram with vertical lines. To summarize some of the levels of organization that exist:

1-The whole earth ecosystem is made up of smaller ecosystems and organisms. The whole earth ecosystem is the biggest (most inclusive) unit of life on earth.
2-Organisms are made up of organs and their environment
3-Organs are composed of specialized tissues and their environment.
4-Tissues are composed of specialized cells and their environment
5-Cells can be organisms or they can be subunits of organisms. The cell is the basic unit of life. Below the cellular level of organization, life as we define it is not present in the interacting systems of which it is composed.
6-Cells would not be alive without the precisely organized organelles, macromolecules and molecules of which they are composed.
7-Organelles are subunits of the cell that perform specific functions. For example, the chloroplast is an organelle that is made up of macromolecules and molecules that, in the environment provided by the cell can do the processes of photosynthesis. Photosynthesis is the process of changing light energy to chemical energy that is used to form the energy bonds of macromolecules.
8-Macromolecules are organic molecules joined together with smaller molecules by energy bonds.
9-Molecules are made of atoms that are joined together in very specific ways by energy bonds. The kinds of energy bonds and the kinds of relationships between the atoms are not random. They depend upon the fact that different kinds of atoms have different characteristics.
10-Atoms can not be seen or directly measured individually. However, if we collect a few million/billion atoms all together in one place we would call that an element. There are not very many elements that (in their special combinations as molecules) make up all the living and nonliving things of the ecosystem. These elements/atoms are diagrammed by chemists in the “periodic table.” A lovely book by Theodore Gray and Nick Mann describes and illustrates all these basic elements (and atoms) of our existence.

Atoms are studied by physicists. There are many metaphoric descriptions of atoms, but the bottom line is we do not fully comprehend atoms from our perch so much higher up in the levels of the ecosystem (just as we do not fully comprehend things that are at levels of organization over our heads. Our sensory organs are designed to function in our own level.) What we need to know is that atoms are matter (they have mass, which means they have weight and volume. Everything from your desk to your grandmother is composed of atoms). Atoms also carry the energy that we require to do any kind of action in our lives or in the ecosystem. The energy of atoms determines how the different atoms can make energy bonds with other atoms so that molecules can form, and macromolecules.

It is important to know that humans do not understand most of these interactions. It’s also important to remember that any system that has more interactions, to a point, is likely to be more resilient (suggested reading linked by Albert-Laszlo Barabasi). Resilience is largely the result of complexity and is essential to life. Increased complexity of a network increases resilience because it makes available “fail-safe” options by providing several methods of accomplishing each process. Increased complexity can also increase the efficiency of energy usage (notice these elements also can be true of social organizations).

However, this does not mean that more complexity is always better than less complexity. Complexity is not the only element of life that is essential, and complexity must be maintained in balance with all the other essential components of ecosystem viability. Too much complexity can be as harmful to the balanced organization of a network as too little complexity. We could not be alive if the nature of the chemistry and physics of our environment were different than they are, or if the interactions within the ecosystem ceased to function. All the levels and all the interactions make us what we are.


When I was growing up, and when I was a productive member of the work force, my goal was to save and to share with the future (to sustain) the “American dream.” Of course, that wasn’t my only goal, but it was foundational, and it defined the boundaries of my personal dream. The whole point of “my” dream was that we all can have different dreams so long as my dream does not cause harm to you or your good dream. Of course, that’s an ideal — an impossible island within which to function. Therefore, the other half of my dream is a continual process of negotiating the boundaries of our individual dreams so that our community is a positively functioning whole.

It was only after retirement that I realized some of the people I worked with — and with whom I shared a mutual commitment to the “American Dream” — it wasn’t the same dream at all. We had never explained ourselves to each other, never negotiated our ideas, and so we all were seriously trying hard to sustain different and incompatible dreams. This was a shock to us all, and we very soon were arguing/debating/fighting rather than sustaining. It became clear that we can not build an American Dream if we don’t know what it is and discuss it among ourselves before we start to fight over misunderstandings that we don’t know exist. We cannot understand each other unless we define our words.

Sustainability a word that we must understand if we are to build a future for ourselves, first because Americans have multiple different ideas of what should be sustained, and more importantly because the word was deliberately co-opted by the economic community, following the green revolution, to mean the exact opposite of what it means. The idea of sustainable growth (which is impossible within the living earth ecosystem) has overcome the actual meaning of sustainability. The implications of this reality are, to me, genocidal. I see this campaign to change the meaning of the word sustainability as a deliberate attack on the life and health of the whole earth ecosystem for the profit of a few. Worse, the attack seems to have succeeded, and the result, literally, is a Ponzi type of growth scheme that is manipulating the resources of the entire world. Unfortunately, however, it is not sustainable. The fact of sustainable growth is physically impossible, even though the concept of sustainable growth has become embedded in our culture as a synonym for sustainability.

So the word sustainability is a problem because it seems that most or many Americans believe that it means sustainable growth, and the earth ecosystem can not grow. The size of the earth ecosystem is fixed. The ecosystem has become more efficient in its use of organic energy (it did this primarily by increasing diversity), but we can not change the size of the ecosystem, because the ecosystem functions according to natural laws such as gravity and the second law of thermodynamics that we can not change. If we continue to try to grow the ecosystem, the result will be the same as it sooner or later is with all Ponzi schemes, because sustainable growth is impossible in a living system. Growth in the ecosystem is limited by the ability of plants to convert light energy to organic energy, and we are destroying our plants in our efforts to grow.

If the word “sustainable” has communication problems, another approach might be to use some different words to explain the physical realities of the ecosystem and the things she needs to survive. Rob Hopkins likes to describe ecosystems in terms of “resilience,” and describes resilience as a reflection of the relationship between diversity and survivability, and this is very important (download pdf from Google, title Resilience Thinking). Diversity is one of the basic realities of life systems; higher levels of diversity generate higher probabilities of survival because the living system is a network. As is true of the computer network, diverse possible pathways make for fewer crashes (well described in “Linked: the new science of networks” by Albert-Laszlo Barabasi).

In the human body we might think of cancer as a threat because of the decrease of diversity when one type of cell overtakes the myriad other cell types that individuals require for their survival. A good general discussion of how this has played out in human populations is found in the historical events described in Jared Diamond’s book “Collapse.”

It is also true of ecosystems. The high survival value of diversity in living systems is easy to demonstrate. Still, diversity/resilience is not the only essential element of ecosystem survival, is not identical in its meaning to “sustainable,” and none of these terms refers to growth of either the economy or the biomass on the earth.

The most widely quoted definition of sustainability is the “Brundtland definition” of the 1987 Report of the World Commission on Environment and Development: “meeting the needs of the present without compromising the ability of future generations to meet their own needs.” According to your computer dictionary, sustainability is: “Able to be maintained.” Or, in relation to smaller ecosystems: “exploiting natural resources without destroying the ecological balance of a particular area.”

We have already stressed the requirements of the ecosystem:

1 – A forever balance between the amount of available organic energy that flows into the system and the amount of organic energy that is used up within the system (remembering that we are within the system);

2 – A continual flow of information through the system (this is mostly genetics, genes in all organisms carry the code of life and are passed to future generations). In brief, the effective flow of information increases the survivability/diversity of living systems. For example: (a) we know that some people are genetically more susceptible to certain diseases; when the flu comes around, some people are hit harder than other people. If everyone were the same, then everyone would be equally as likely to die of flu. This is a biological survival value for the human species. (b) Similarly, each small or large ecosystem is composed of many different species. The many species permit the ecosystem to use more of the available organic energy to do more kinds of work before all the energy is converted to work or heat and lost. (c) Again, the whole earth ecosystem is composed of a diversity of smaller ecosystems. Clearly, resilience, as defined by Prof. Hopkins, is importantly based in diversity, and is essential to maintain life on earth.

3 – The third major factor that must stay in balance if the living earth is to survive is the cycling of materials such as water and oxygen and carbon dioxide through the whole ecosystem. That we will discuss information flow and materials cycling in separate chapters.

The bottom line is that all these definitions are accurate, and for once the computer definition is excellent and the simplest definition of “sustainability” is: “Able to be maintained.”

We have said that LIFE is not the same reality as A LIVING THING, and that is essentially because a living thing is not sustainable. That is why we all have hopes and dreams of a sustainable ecology/economy for our grandchildren, and that is why our various versions of the “American Dream” always involve pictures in our heads of the children and the grandchildren working the land as we do or boating on Lake Bryan as we do, or celebrating Hannukah as we do or enjoying whatever world view that we enjoy.

But dreams and pictures and words of today are not a reality for tomorrow. It is not the function of the living earth to fulfill our dreams, but to maintain her own life. If we really want our grandchildren to be a living, laughing presence upon this living earth we MUST understand what the ecosystem needs to stay alive and then we must give it to her, because otherwise our own rampant growth upon the earth, just like a cancer in our own bodies, will reduce the resilience and upset the balance to such an extent that the productivity of the earth ecosystem will be reduced and unable to provide enough organic energy to nurture our grandchildren.