Bare Bones Biology

Light energy is converted to organic energy by the ecosystem, then it is used up and released as heat energy that can not be recycled. The organic energy (red) is used to do all the myriad jobs required by living things to maintain the unbroken stream of life (green) through time (blue).

Bare Bones Biology 010 Transcript

Evolution Terms

Before we go further on the subject of genetics and evolution, let’s make sure we are all using the same words to mean the same things. You don’t need to remember these words; if you are still interested when we finish today, you can check the transcript that will be posted on Wednesday.

We already talked last time about biological evolution. It is a change in the gene pool over time.

A gene pool is all the genes in a species or other group of interbreeding animals. A species is a group of organisms that do or can interbreed. That’s like all the dogs, or all the cats, all the people, or all Post Oak trees, and that sort of thing. All the organisms in one species share a gene pool. The gene pool is all the genes that could be passed on because all members of the gene pool are capable of breeding together. Whether or not they do.

A gene is a unit of function that can be passed on to the next generation. Every gene has one function (OK, there are exceptions). Almost every gene has one function inside a cell or inside your body. Usually the function of a gene is to code for a protein that does the actual function. For example, there is a gene and a protein that have the same name, that is tyrosinase, and the function of the protein is to make pigment in your pigment cells. That’s it. Genetics at its bare bones really is that straightforward. Each gene makes a protein and each protein has a function. And the genes are physical entities, they’re molecules that can be copied and transferred to the next generation.

The functions of the genes result in real traits in the organism. I am looking right at you and you do have pigment in your eyes, your hair and your skin. You have pigment in your pigment cells, and I happen to know what gene is responsible for the enzyme in pigment cells that causes pigment to be made. That would be, tyrosinase. Your pigment is normal, therefore your tyrosinase protein is normal, therefore your tyrosinase gene has a normal genotype. If your tyrosinase gene were not normal you would have an albino phenotype. The phenotype is your physical trait that results from a certain genotype. The genotype describes whether or not your gene or genes that control a particular trait are normal. Every different kind of gene controls a specific function that regulates a specific trait.

All of your genes together — all the genes together, all the different kinds of genes, control all the inheritable traits in your body — these are your genome. Your genome is all the genes in your body. This is different from the gene pool that is all the genes in all the bodies of the same species. I will use the word phenome to describe all of your phenotypes that result from your genome — you are a person with black hair and brown eyes and a short chin and a certain size and so and so and so.

All of the genes in a whole species, all humans for example, is the gene pool. The gene pool is associated with the physical characteristics of the whole species, another example, a certain species of spider is an animal that is of a particular shape and color and builds a certain kind of web to catch its food. All the inheritable physical characteristics of this species are associated with the genes in the whole gene pool.

The evolution of the whole ecosystem is based on the relationships between and among the gene pools of all the different species that make up the whole living earth ecosystem. This is the most important ecological concept that I know, and as far as I know it does not have a name.

Shall we name it?

Bare Bones Biology 012

If you see me sitting in my car way out at the end of the driveway on a Sunday morning at 6:55, you will know I’m trying to listen to Bare Bones Biology to make sure I post the correct transcript. And here it is.

Evolution. How it Does Work

It will not surprise you to hear that the nose of a pug dog is different from the nose of a greyhound. Those traits are known as phenotypes. In fact all inherited traits are known as phenotypes, and these particular ones are caused by differences in the gene pools of pugs compared with greyhounds. The shared gene pool of Chihuahua dogs does not include genes for large size, while the shared gene pool of St. Bernard dogs — does. Those are also phenotypes. The behaviors of a normal Poodle and of my Catahoula Hound are very similar because they are both dogs with all the common traits of dogs. But some Poodle behaviors are quite different from the innate chasing and killing instinct that is bred into most hunting hounds. These behaviors are also phenotypes. The phenotype is the physical expression of the genotype.

These differences among the dogs did not happen by magic. They are the result of human selection over many generations. They happen because humans in the past chose which of the many pups born in a generation were able to pass on their genes to the next generation. That’s known as selection. Certain dogs were selected for reproduction. And so by selection, we humans changed the gene pools of the different breeds of dogs, and when the gene pools were changed the phenotypes changed.

We humans should not get big heads over this. We have not and can not change the laws of nature. What we did was to learn how the natural law works and we used it to make domestic animals that suit our needs. Humans used the natural law of selection to change the gene pools of domestic animals.

Biological evolution is a change in the gene pool over time as a result of selection. At its most basic it is just that simple. A change in the gene pool as a result of selection, only in the case of nature it’s natural selection rather than human selection. It is not survival of the fittest according to how humans imagine fitness. It is the successful transmission of genes to the next generation by those individuals who best fit into the balance of nature. So there is no point arguing about this aspect of evolution, because there are many, many proofs, both in domestic animals and in nature.

Evolution is happening all around us, all the time. Living things, to stay alive, must constantly interact with the changing realities of life, or they wouldn’t stay alive very long. Humans must adjust to change to stay alive. We must be able to come in out of the cold and find our food. Our digestive system needs to know how to respond if we eat a loaf of bread or an omelet. We have to breath. Our living bodies can do all this because of our genes. All the genes in our bodies, that is our genomes, working together in response to the conditions of life.

The requirements of life are fundamentally the same at all the levels of life. The information for a cell to survive comes from the genes in the cell turning on and off so they change the phenotype of the cell in response to conditions in its environment.

The information for you to survive depends on the behaviors of your genes as they turn on or off at the right time and place in your body, making proteins when and where they are needed, so your nervous system can react to the hot stove and your digestive system can respond to the first sweet wild plums of June that we picked yesterday. Your genes turning on and off make it possible for you to respond to your environment and therefore stay alive.

The information for the ecosystem to stay alive comes from the gene pools of all the organisms that that live in the ecosystem and change over time in response to their environments. Changes in the gene pools over time is evolution. If there were no evolution there would be no life on earth because evolution is the process by which he ecosystem is able to respond to change and therefore stay alive.

Reductionism and Power – BBB009 Transcript

When science was co-opted by the Government, there was a huge argument among university scientists as to whether having the money was worth letting the Government control our research. Of course, I never would have had my career without that money, but looking to the welfare of mankind, I think it was not a good idea, because the Government then got taken over by big business and it has recently become obvious that neither the politicians nor the business-persons understand the power they are unsuccessfully trying to manipulate.

We have ended up somehow believing that we have the power to change the basic laws of nature that permit life to exist on earth. We can’t, and so this is a very dangerous idea. But even if we could, I don’t know about you but I would not want Bill Gates advising God how to run the world no matter how good his intentions. It would be nice to have a someone in power who understands how God does run the world, but we’re still waiting for that.

Anyhow, the bottom line is the basic science was taken over by the government and then the government was taken over by big business, and now we have mostly technology instead of basic science because the goal of big business is to make money. Basic science is the discipline that figures out what are the basic laws of nature. Technology is the discipline that then uses the basic laws of nature to make things for humans. Originally for making tools and toilets and useful conveniences of that sort, but lately mostly to grow wealth.

One of the results of this is that biology has become overwhelmingly reductionist. That means we spend more and more time and money studying smaller and smaller phenomena. This has been very exciting for me as a basic biologist, because my original goal was to understand how genes regulate pigmentation. I wanted to know every thing from the change in a gene — let’s say to make a mouse be an albino that otherwise would have been black — to the change in the phenotype. The phenotype is what it looks like — either black or albino or something else. And we did learn all of that in one century. We learned it by comparing the specific functions of the genes with the phenotypes they control. The questions, of course, are why and how, but I will not answer those questions today because that also is not the point of what I am trying to say.

My point for today is that trying to understand how the albino/nonalbino gene causes pigmentation is not nearly as important as understanding how genes function in general. And that is not nearly as important as understanding how mice and people are alive and stay alive. I have colleagues who study pigmentation and don’t even know what it looks like. Most of our scientists are looking so hard at the trees that they can’t see the forest. Our questions as responsible basic biologists should be about nurturing life as it was created on earth. Because we can not control life, even though we can control individual lives and individual people, and we can cause enormous pain and suffering by trying to control life.

The early biologists were not reductionists. They were lumpers. Linnaeus’ big understanding was lumping together all the organisms that have the same characteristics. So, all the people are lumped and given a name (Homo sapiens), and all the plants were lumped and classified in the plant kingdom, and all the cats, and so on. Out of this lumping came the most fundamental biological understandings of all human time — and no they are not whether or not the cat in the box is dead. That is not biology. They are the sciences of genetics and evolution that know how information maintains the balance of all of life on earth. And how — if we continue to unbalance the smaller things of life — eventually we do have the power to unbalance the entire flow of information through the ecosystem.

Bare Bones Biology will discuss genetics and evolution for the next few weeks.

Bare Bones Biology 008-Balance

I just spent nearly a whole year writing a book that explains that the earth ecosystem is alive and what it requires to stay alive (just like every other living thing) is balance.

And now someone has redefined the word balance. So let’s be clear. What I mean is sustainable balance. Balance is when things stay where they are without anybody pushing. Like the teeter-totter that sits gently on the midpoint, or if you don’t know teeter-totter, think of the scales of liberty. Balance through time. That woman is holding the scales away from her body and they are completely free to move, one side down or the other side down. They don’t move, of course, because she’s only a statue — or a picture — but if those scales were real and they stayed even, through all of time, t hat is balance. Or maybe I will refine my definition, since the business folk have undefined it, by saying sustainable balance. Balance means balance — sustainably. Two ounces of gold at sea level at a certain temperature is perfectly balanced by two ounces of gold at sea level at a certain temperature, or by anything else that has exactlt the same weight. Or we could do as Rob Hopkins has done and change the words. He likes to talk about resilience, which is a very important and related concept, but not quite the same thing as balance, and balance is what I mean, so I’ll stick with it. Sustainable balance.

A primary function of the ecosystem is to sustain a balance among all the things that are part of the ecosystem, including:
Carbon dioxide
Oxygen
Carbon compounds
Mice
Elephants
Palm trees
Water
Dandelions
Us
Energy
Information
Slugs, and
Fire ants,

And a million million other things that are made inside the ecosystem and all are a part of how she stays alive.

How she does this is too complicated for humans to understand. I’m sure if we could make life, we could make our own ecosystem and the moon would be blooming with life. But in spite of what you may have heard, humans cannot make life. We can change it but we can’t make it, because the ecosystem is so much bigger and more complicated than we are that we can’t even think of all those parameters, and basically there is no life outside of the ecosystem. At least none that we know about. So, how can we humans claim to understand something that is more complicated than the number of nerve endings in our brains? And if that is true, how come I claim to understand it?

I do not claim to understand all of it. However, the living earth ecosystem runs by natural laws that do not change. The problem for anyone who wants to understand it is to clear away the clutter of all the details — or better use all the details in a repeatable, measurable way to understand the basic laws of nature as they apply to life. That would be what we do in the science of biology – which is the scientific study of life — and we know all that we need to know to begin giving the ecosystem what she needs to survive in balance. Sustainable balance, not some idiot corporation’s idea of sustainable growth.

There is no such thing as sustainable growth. You know that as well as I do. Everyone does. You can’t raise ten horses on one acre of land unless your neighbor raises hay.

Look out there. Post up that lovely picture taken from the moon of the beautiful living earth. There aren’t any neighbors raising hay, and no human technology can change that fact, no more than airplanes modify gravity or no more than our prayers can change the way God made the universe to function. So, if we want to do something that really will help human kind to survive into the generations with some kind of reasonable quality of life we will have to stop pretending that we can tell God how the world should be, and start changing our behaviors to conform with how the world really is.

Bare Bones Biology 007 – Can’t Do Nothing

I’m sitting on my back porch in the dark, watching the lightning flash, listening to the thunder growl over the little hill behind my house, drinking a cup of green tea, and remembering just such a night five years ago, when I sat in a Japanese hot bath at the Green Village Youth Hostel in Niibo-Uryuya listening to the grumble and crack of just such a storm.

For two months I had been reading Huston Smith, the Dalai Lama, Terry Tempest Williams, and the story of the living earth described by James Lovelock. And trying to write. To write anything that might help the children of human technology understand the most important bits of biological reality. But what is the use? I will never be a Terry Tempest Williams, and I don’t see any sign that the children of human technology are interested in what I have to say. Why try to write, when the books I read express my worldview so much better than I ever could say it?

That Japanese night I was reading, The Pine Island Paradox, by Kathleen Dean Moore, holding the book high over neck-level water, when she said. “You can’t do nothing . . To love a person or a place is to accept moral responsibility for its well being.” And so I hauled myself out of the bath and climbed up the stairs to my room to try again.

But Kathleen, you didn’t say. How do we know what is best for the well being of the one you love? Almost everyone I talk with thinks they know what is best. As a biologist I know that most of them — no matter how convicted and well intended — are simply wrong about what this place needs. Biologically. If we care about anything we can’t do nothing, but isn’t it even more important that we should not do something that will cause more harm. And it’s way past time we can care about one place on earth without caring for the whole of it, because it is all one life.

The answer came at that time from Huston Smith, in his book, Why Religion Matters.

“My way relates to world views. I am convinced that whatever transpires in other domains of life — politics, living standards, environmental conditions, interpersonal relationships, the arts — we will be better off if we extricate ourselves from the worldview we have unwittingly slipped into and replace it with a more generous and accurate one.”

I think he means we should listen to each other and compare notes before we decide what we should do. But I can’t make anyone else do that, and I can’t just sit here in a hot Japanese bath or on the back porch of my own home and smile and remember that I have had the best of life, so it won’t really affect me very much, whatever happens, and watch the younger folk working their little hearts out trying to fix the mess we have made, convinced they are doing something new and different to help, and making all the same mistakes we made, but with a great deal more power behind their efforts. If we care, we can’t do nothing And so finally that Japanese night I fell asleep while the storm grumbled and cracked outside my window.

The next day I got an email “where are you and are you having fun
Where am I? I haven’t moved from this place that I love.

Am I having fun? When someone asks an irrelevant question, should you answer the question or ask a better one? Were we put upon this earth to “have fun?” On my headstone, what? “She wasted her one shot trying to have fun?” Wall Street wants me to have as much fun as possible; should I dedicate my life to Wall Street? And a few more questions along those same lines, at least one of which might contain the words God, love and responsibility.

I don’t remember what I really said.

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.