Tomorrow I’ll post the latest transcript of Bare Bones Biology, on the subject of world views, or frames. This is yesterday’s sunset, unretouched except to take out a dirt spot or two.

After the Storm

Bare Bones Ecology – Fini

The full moon set and the sun rose, as I swung my camera back and forth from West to East.

BareBonesEcology, our ongoing project that describes the flow of energy, the recycling of materials, and the enormous power of the information that guides life on earth. Cest fini!

All that remains is to edit for print. !!!!!!! 🙂

For our blog, this now leaves Sunday and Thursday free for random thoughts and new projects. And the days between for random photographs of the ecosystem. After today I will be working on the upcoming course (Bare Bones Ecology – Energy, to be held at the Brazos Valley Museum of Natural History) and will probably put notes from that project.

In the meantime, on Wednesdays, I will continue to post the transcript of the week’s radio spot that airs on KEOS (98.1) on Sunday morning at 6:55 and Tuesday evening at 8:55.

Today we are celebrating.

Limiting Factors

We have shown that the most important requirement for life of a cell or of an organism or of an ecosystem is to maintain a balance among all the conditions necessary for life, most of which involve energy, materials and communication.

We have shown that the behaviors of the different species of organisms are responsible for distributing energy throughout the whole ecosystem.

We have shown that the behaviors of the different species of organisms are responsible for distribution the materials of life, atoms and molecules, throughout the ecosystem.

We have shown that the behaviors of the different species are responsible for the ability of the ecosystem to react to conditions inside and outside that might be a threat to her life.

We have said that the more species an ecosystem is supporting, the more balanced and resilient that ecosystem is, because every different species has a slightly different behavior. So any little problems that happen with one or another species will have only a minor impact on the balance of the ecosystem. Other species will be able to do the same job in a slightly different way, and the more such species are available the more likely the ecosystem is to survive.

Now let’s talk about how the ecosystem protects herself in the case of some species over-running the ecosystem, like a cancer over-runs an individual organism, and so threatening the lives of the other species hat are required for balance and resilience and life of the ecosystem. For the most part, this function is performed day by day and year by year by limiting factors that are a part of the balance of the whole.

Let’s take for example a species that lives in the desert. The usual limiting factor in a desert is water. If there are too many individuals, then the whole community is likely to run short of water, and most of the individuals will die. So then there are not too many. Those that remain are the individuals who are best able to live without water, and these will pass on their genomes to the next generation. The result is that deserts are filled with organisms that have evolved intricate adaptations to the desert climate.

Water is the limiting factor in this environment that drives both balanced populations and evolution.

Suppose for one year there is more than enough water, then the population of desert mice, for example, will bloom, and the mice will begin to eat up all their food supply, until it is gone, and many will starve. In that year, food is the limiting factor.

If food is not limiting, then predators are likely to take the surplus mice in the next following breeding season. After a bloom of mice, there is likely to be a bloom of foxes, as the ecosystem uses her innate behaviors to maintain the balance that is necessary for her life.

If this fails, then the overcrowded conditions of the mice is likely to provide excellent conditions for the evolution of viral or bacterial diseases.

Notice that these limiting factors are not enemies of our species or of the ecosystem. They create the perfect conditions for any species to survive over long periods of time in an earthly ecosystem. If we really do want to survive, then we will need to understand limiting factors as friends and allies, and manage them accordingly.

The next limiting factor, if a species manages to work its way past all the previous, will be that the population becomes so large and begins to use so much energy that the waste products begin to threaten the balance between the source of energy (plants) and the using up of energy (food) until the waste products begin to affect the environment (as in global warming).

Experiments have been done, using rats or mice that are provided with all the food and water they could possibly need. When populations become so great that they are crawling all over each other, then their behaviors become “nutsy:” infanticide, murder and war increase.

At this point, the species is probably doomed to extinction by destruction of all the things it needs to stay alive.

The only difference between us and the other species is that we understand what we are doing to God’s Garden of Eden — or we can understand if we want to, because the information is available. And because of our brain — we get to choose whether or not we want to continue trashing the ecosystem. If we decide we want to provide a reasonable life style for a reasonable number of humans on the face of this earth, we must begin passing out the birth control to everyone who wants it IMMEDIATELY.

In this way our technology might save some of us.

No human technology can change the basic laws of nature that keep the ecosystem alive. No human technology can remove the limiting factors or safely unbalance the ecosystem.

Our human environment now is the whole earth ecosystem, and we are now using more resources than the ecosystem can consistently produce. I have seen what happens to mice that overpopulate their environments. Those pictures are in my mind as I see the choices we are now making.

But we are the only species in history that has been given the freedom to choose.

We can help to balance the ecosystem — the flow of energy, the recycling of materials and the balance of species.

Or —


Genetic Variability and Evolution

We have already shown that evolution is a foundational reality of life on earth. We showed it in two ways. The first proof we gave is that we can do it. If humans can manipulate genetics to evolve new breeds of dogs, cats, cattle, horses, and other species, then of course evolution does exist. Even further than that, we can do genetic engineering. Not that we really want to discuss genetic engineering of plants and animals in this chapter, but I’m sure you have heard of it, and we can point to the fact that genetic engineering is possible only because we understand the basic principles of life that are required for evolution:

1. Genetics. The fact that genes are passed from parent to child;
2. The variability of phenotypes among all living creatures that is assured by sexual reproduction;
3. Selection of some genomes rather than other to pass on genes to the gene pool of the next generation.

The other evidence we have given for evolution is that life is defined by its ability to respond to external and internal change, and that the response involves inherited behaviors that preserve the life. This is true of cells that have chemical messengers and their receptors — and organisms that have brains and nerves and hormones — and it is true of ecosystems through the phenotypes of the organisms. A phenotype is a physical characteristic of an organism that is caused by a gene or genotype of that organism.

So now we want to describe how evolution functions in nature to preserve the lives of ecosystems. Next time, we will describe the basic processes that are required for evolution to happen.

First we’ll do a quick run through of genetic terms. We remember that each individual gene (usually) has one function that it regulates by making a specific and unique protein inside of some cell. Maybe this gene is responsible for your red hair, for a simple example. Mc1r is the name of the gene. Red hair is the name of your hair phenotype. Obviously, it takes more than Mc1r to make all of you, and in fact there are thousands of genes in each of your cells. Each pair of genes has a particular function that is associated with a particular phenotype. If you add them all together, the resulting phenome is YOU. All the genes that make up YOU are your genome. Your genome is not exactly the same as my genome. For one thing, your Mc1r gene codes for red hair and my MC1R gene codes for not-red hair. So we all have hair genes, but that does not mean we are all identical. Your genome is not identical to my genome.

A species is a group of animals of the same kind that could or do interbreed. So humans are all of the same species (Homo sapiens). Because humans can interbreed and often do, therefore we all share the same gene pool, whether we have red hair or not-red hair or kinky hair or unpigmented skin we all share the same gene pool. All the genes in all the humans is the gene pool of humans. The gene pool is even more variable than any of the genomes. This variability is the result of sexual reproduction (meiosis followed by fertilization) and is extremely important for survival of both the species and the ecosystem. It is the communication system of the ecosystem.

Different species do not interbreed (that’s the definition of a species) so they can not share the same gene pool. Every different species has its own function in the ecosystem. For example, most of the species of plants are producers, because they can make organic molecules using energy from the sun. Animals of different kinds are consumers. Consumers cannot make organic molecules (we have to eat them). One of our jobs is to help recycle the materials, carbon, oxygen, nitrogen, that the plants need to make more organic molecules. The energy can not be recycled, and that’s why the life of the entire ecosystem depends entirely on plants. And there are species that do all the other various jobs that are necessary to keep an ecosystem alive.

All the different species do their jobs in the ecosystem by their behaviors. So the ecosystem ocean of all the gene pools of all the different species is made up of a vast array of behaviors.

That’s the background.

Now I want to use an example to explain how this communication system functions. These are from two different species of flowers that I found in my front yard when I drove back home this afternoon.

Here is the first species. Maybe you can tell me what it is. All I know is that most of the plants have pink flowers, but this plant has white flowers. Let’s assume this species of plant has a job to do in the ecosystem, or it probably wouldn’t be here, even if we don’t know what the job is. We do know what flowers are for. The purpose of flowers is to do sexual reproduction so the plant can make more plants of the same kind. Sexual reproduction involves the fusion of sperms with eggs. Or in the case of flowers it involves finding some way for the pollen to get to the egg, and usually that involves some kind of insect, maybe a bee or some other kind of insect that is attracted to this flower. The genome of the insect determines its behavior. The genome of the flower determines its behavior. The two behaviors are both required for the flower to reproduce. In this case a mutation in one plant has caused the flowers to be white instead of pink. How might this affect the whole collection of organisms that do all the jobs in the ecosystem?

Are any of the regular pollinators attracted to white flowers?
Are the white flowers able to get pollinated?
Is some other pollinator possibly attracted to the white flowers?
Are the white flowers maybe MORE attractive to the normal insect or some other insect that normally doesn’t visit this particular kind of flower?
Do the white flowers for some reason survive better in our drought conditions of the past two years?
Which of these plants will make more babies for next year, the pink ones or the white ones?

Depending on the answers to those questions and many more questions during the development of the plant we will see next year either more or fewer of the white flowers. This is the process of evolution. This is life. This is the ecosystem being responsive to its environment by making available many different species that all have:

1- different behaviors
2- variability in the behaviors because there is variability in the gene pools of the species.

Without the ability to respond to internal and external changes, the ecosystem could not be alive.

The requirements for this responsiveness are two:

1- Phenotypic variability must be available, and this variability must be inheritable. We have already stated that most phenotypic variability is the result of genotypic variability. Genotypic variability is the result of sexual reproduction that we described previously. It is the norm in our ecosystem. If God invented sexual reproduction, it was not for your pleasure. It was to provide the variability that is necessary so the ecosystem can respond to environmental conditions.

2- In any species, on the averages, the individual organisms (and their genomes) that successfully raise babies are those that pass on their genes to the next generation. Natural selection is the process of choosing which genomes (out of the entire gene pool of the species) will be passed to the next generation. Natural selection consists of (on the averages) the combination of the phenotypes and conditions that both change with every breeding season. The genomes that can make offspring that survive best in the conditions of that particular growing season will be more likely to pass on to the next generation. The result of natural selection is that the some percentage of the gene pool is passed on to the next generation. In the next breeding season there will again be variability, because of sexual reproduction, and again only those organisms with the phenotypes that are most compatible with whatever the environment is that year — they will be the ones that breed and rear their young to make the next following generation. This is the process of natural selection.

Evolution is a change in the gene pool over time as a result of selection. Evolution is not a theory. It is a proven fact of life.

Evolution is NOT survival of the fittest.

Evolution is survival of the organism that helps the ecosystem to maintain its viable balance among all the thousands/millions of jobs that are done by the millions of species that make up the ecosystem and must be maintained in balance for the ecosystem to stay alive.

What remains, in our next blog, is to discuss are some of the methods the ecosystem uses to get rid of species that threaten this balance.

Life Is

Life is the innate, internal ability to respond to the environment rather than just sit there and be destroyed by it. The flow of information sustains life because it senses the environment and cues the living response. The hand on the hot stove is a reasonable example of this process, but very limiting as a concept because we need the whole of the ecosystem information system to stay alive — in addition to our own nervous system.

Life at any level is maintained by:
1. Flow of energy
2. Recycling materials
3. Flow of information that maintains the balance among all these things.
4. The ability to balance all of the above.

To visualize the flow of information through the whole ecosystem, we need to imagine the functions of the various species of organisms within all the smaller ecosystems that make up the whole. Textbooks often use a pond ecosystem as an example, because it is easier to imagine than a gigantic whole that has no inputs or outputs. Ponds, of course, are in contact with land and air, which helps them to keep their balance. The whole earth has no such buffer to help her maintain herself in space.

But here is the pond, and lets take only four species of organisms. An ecosystem with only four species could not possibly maintain a balance, but let’s pretend.

A water weed
A plant-eating bug
A bug-eating animal
A fungus that eats dead things.

The sun shines on the green water weed. It’s job in the ecosystem is to use the energy from the sun to make organic molecules by photosynthesis. It uses carbon dioxide and oxygen to make organic molecules. It uses the energy contained in the organic molecules, and also the carbon and oxygen, and nitrogen that its roots bring from the bottom of the pond, to make the cells of its own body. The plant also does cellular respiration. So the plant is very important to the life of the pond. It has made organic molecules using energy from the sun, nitrogen from the earth and carbon dioxide from the air. It breathes out more oxygen than it takes in. The plant “knows” how to be a plant because of all its genes that work together to cause all the right functions to happen in the right cells at the right time of its development.

The plant-eating bug eats the plant and uses the energy from the organic molecules, and also the carbon and nitrogen and oxygen to make the cells of its own body. It breathes in oxygen to do cellular respiration and it breathes out carbon dioxide, because all the energy for it to stay alive comes from the process of cellular respiration that breaks down the organic molecules of plant that the bug ate. The animal “knows” how to eat plants and also how to digest them and how to make its own cells because of all its genes that work together to cause all the right functions to happen in the right cells at the right time of its development.

The bug-eating animal eats the plant-eating bugs and uses the energy from the organic molecules, and the carbon and nitrogen and oxygen, to make the cells of its own body. It breathes in oxygen and breathes out carbon dioxide and for all the work of staying alive it uses the energy that was stored in the organic molecules of the bugs that it eats. The behaviors of this animal are also directed by all its genes. It “knows” how to catch bugs and also how to digest them and how to make its own cells because of all its genes that work together to cause all the right functions to happen in the right cells at the right time of its development.

All of these organisms die and defecate, and fall to the bottom of the pond, where the fungus digests the remaining organic molecules, releasing the nitrogen back to the soil and more carbon dioxide into the water. It uses the energy that was stored in the organic molecules to do the work of staying alive, until all or almost all of the organic molecules are broken down and there is no more energy available until some other organisms in the pond defecate or die. Even the fungus “knows” how to do what it does because of the genes that control whatever enzymes and other proteins are produced in its body at the right time and in the right place.

So there are three reasons for explaining this tiny ecosystem to you:

1. Such an ecosystem could not survive for very long because there are not enough different kinds of organisms doing all the jobs. For example, think what would happen if the environmental temperature changed so that species of plant could not survive in that pond. The whole system would crash. The more different species are doing the same or similar jobs, the more likely the pond is to stay alive. This is what Rob Hopkins refers to as “resilience.” It is essential to survival of an ecosystem that it maintain a balance among hundreds of different species that have similar functions but slightly different genomes, so that some of them may be able to survive if the conditions change.

2. Do not imagine that these are the only functions necessary for an ecosystem to survive. Another reason why many hundreds of species are required to do the job of maintaining balance in an ecosystem is that there are many hundreds of different jobs to do. I only listed four basic jobs. Energy flow, recycling of carbon and oxygen and recycling of nitrogen. Many hundreds of molecules need to be recycled, and many hundreds of species are required to ensure the proper flow of energy to every portion of any ecosystem so that the whole may stay alive.

Ecosystems can die.

3. Notice it is the behaviors of the organisms that direct the flow of energy and the flow of materials through an ecosystem. Behaviors of organisms are controlled in large part by the genome of the organism, that is all the genes in the organisms. The gene pool of the organism is all the genes in a particular species. The gene pools of all the organisms and all the species in an ecosystem ARE the flow of information through the ecosystem. Again, Rob Hopkins is correct that the resilience of any ecosystem is much greater, the more variation there is in the ocean of all the gene pools of all the organisms in that ecosystem. Just in case some change happens in or around the ecosystem, if there is a lot of variability in that ocean of genes, then it is more likely that the ecosystem can survive, because it is more likely that some organisms will survive that are required to do all the jobs of energy flow and materials recycling.

This IS evolution.

It is simply silly to argue whether or not evolution exists. Evolution is one of the most important laws of nature, along with gravity and the first and second laws of thermodynamics and the law of cause and effect, that the Creator gave to The Creation so that it can exist. If there were no evolution there would be no life on earth today.

Evolution is NOT survival of the fittest individual within a species. It is survival of a species that helps and does not harm the balance of jobs that are required for the whole ecosystem to stay alive.

Bare Bones Biology 005 – Gaia


Ohh, sorry to be late posting today, I was out in the wilds of Dallas where they have no web access. Here is the transcript of BBB 005.

In July of 2005 I went to Japan to write a book that may be completed this year. I’ll let you know. But at the time I thought I was writing the book, it turned out I was just learning what questions needed to be asked, and of course I kept a diary. On this day I had walked from the youth hostel where I was staying about a mile into the littleone-road town of Niibo-Uryuya. It’s a beautiful place, surrounded by a green expanse of rice fields, and beyond the rice a circle of low volcanic mountains.. And I’d like to read you an excerpt from the diary.

Midafternoon on a shizukana Monday in Niibo Uryuya is quiet and peaceful, but if you walk along the paths and the car-width roads you find a day filled with relaxed activity. People are meticulously fixing, mending, weeding. I am sitting, eating an ice cream cone quick, before it melts, and reading Gaia, the new edition. The mockingbird-equivalent screeches long high notes from the electrical wire, while the local hawk paraglides the survey of his territory

Spiders hide in the hedges, behind their webs, apparently with their bellies full of dragonflies, judging by the remains. In Texas this time of year the dragonflies range under the electrical wires and over the goatweed, about head high to a horse, in territories about two meters square. Sometimes they switch territories with a neighbor, but they maintain an equidistant cruising mode. Someone said they are hunting fire ants. Anyone who lunches on fire ants is OK by me, so I like to sit and read and watch their iridescent air dances in the middle of the afternoon when it’s too hot to do anything else.

Here in Niibu Uryuya there are no fire ants, but I’m sure there is a fire ant equivalent because today for the first time the dragonflies are flashing red over the rice fields in little equally spaced territories, about head height to a horse. If there were horses. I wonder if it’s the same species of dragonfly, and then I wonder if it matters. Amateur naturalists love to learn the names of things, but I’m having trouble remembering Japanese words, which right now I could really use, and I already know there is an animal to inhabit every lifestyle on this earth – the Japanese mockingbird equivalent and the hawk and the dragonflies, all are fulfilling the same purpose, doing the same job here that they do, whatever the species, in Texas, and that is one reason the world does not grind to a halt. The magnificence of this whole of creation, where every little bit fits perfectly into the whole fabric of life, far surpasses words for explanation. Gaia indeed.

In fact, that’s why I never read Gaia the first time round. The so-called “Gaia hypothesis” is one of those beautiful ideas, like evolution, that clicks open a door of the mind to a new view on the reality of creation, as it has to be (or it wouldn’t work). If you take the time to learn all the reasons why people have discovered these concepts they seem so obvious, after they have been discovered, so elegant, so necessarily true (or we wouldn’t exist) that the reading of the book, which by the way was written by James Lovelock — no matter how well it’s written, is anticlimactic — a comparatively pedestrian recitation of specifics that clip the wings of the beauty of the creation it is trying to describe.

But I am reading the book, so I can give the guy credit for calling our attention to the beauty of our one common reality, the living earth.

And then I have to try to write about it.

The Spirit of God

“In the beginning God created the heavens and the earth. The earth was without form and void, and darkness was upon the face of the deep; and the spirit of God moved over the face of the waters.”

That’s my favorite quote from the Bible.

It doesn’t say exactly how He did it. But here we are in this very fine Garden of Eden, the only living thing within light years, in the midst of a universe of fire and ice. It is indeed miraculous. If a miracle is something that our little pea brains can’t understand, then we are surrounded by miracles and it would be better that we don’t forget it.

Whether or not we can feel the spirit of God moving among the miracles, and even though nobody understands everything, we do know some of the basic natural laws that keep this life alive. Werner von Braun, who I think was a physicist, said: “The universe is hostile only when you do not know its laws. For those who know and obey, the universe is friendly.”

So how do we get to know its laws? I expect he was thinking about the laws of physics, and I expect he was right. We would not get very far trying to pretend we can walk on clouds (even though it makes you want to try sometimes, looking down on them from an airplane) and we wouldn’t get very far without wheels and combustion and all of that kind of technology based in the reality of natural phenomena. And we won’t get very far pretending that life can exist in absence of what it needs to be alive. The word of man is not more powerful than the works of God that lie all around us and proclaim themselves for us to see and understand. And obey — or not. We have the freedom to choose — and as we continue to choose unwisely, the universe becomes more and more hostile.

We are even pretending that we don’t need what we do need for life to stay alive. Right now we need the ecosystem to stay alive. How can we not understand that the ecosystem is a living thing with all the needs of living things? I don’t know the answer to that question, but let’s talk about the needs of all living things. The natural laws of being alive. Boiled rigtht down to the bare bones, they are threefold, and they are the same for the tiniest cell as they are for you and me and for the whole great earth ecosystem that you can see from the moon. If you were foolish enough to go to the moon.

We need food because it requires work to stay alive, and there is a universal law of energy that says no work can happen without energy. We get energy to stay alive from our food. Food does not come from supermarkets or from the sun. It comes from plants, that is from our garden of eden. Once we have eaten the food — we can’t eat it again. Actually we could, but most of the available energy has already been used from the food by the time we defecate it, and energy does not recycle.

We need to recycle materials such as oxygen and carbon dioxide and nitrogen and carbon and all the elements that are part of life. That is another reason we eat. Also it’s why we breathe. And to direct all these activities, every kind of life needs to have the information available that tells it how to use the energy, by digestion and all that, and how to recycle the materials, for example by breathing, in order to stay alive.

All processes require information. We do the processes — we do everything that we do because of our genes. Our genetic code. We can be alive because our genetic code knows exactly when and where to make an enzyme to digest the meal we just ate, and exactly when and where to make a nerve cell or a pigment cell or a muscle cell, or exactly how to think.

These three things — energy from plants, the recycling of elements and compounds, and the genetic code to direct all the whole processes — these are required by every living thing, from the tiniest prokaryotic cell to the entire whole ecosystem itself.

How do we know this? Because without any one of them, life ceases. We do not know everything about anything, but we know that — if God created life — then that’s how he created it to be.