Bare Bones Biology 203 – Gary’s Question #3, Genetics

The process of evolution results in a change in the gene pool over time so that each species separately and the entire ecosystem, if it can respond to its environment, can stay alive. The ability to respond to the internal and external environment is the definition of being alive and of being a Life form, whether a cell, or an individual organism or a species or the entire Biosystem. That the Biosystem is a life form is not an opinion; it is a fact, or if you prefer, a definition.

140506-flowers-asc_8951SsIt’s also true that inheritable mutations are not altogether random, but we are not talking about mutations here, we are taling about evolution, and as I tried to explain previously in this series (Bare Bones Biology 201 – Genotypes, Phenotypes and Evolution), evolution works on the phenotype, not the primarily the genotype. The genotype is all the genes in one individual organism: the phenotype is the sum of the physical characteristics of an individual organism: Evolution is a change in the gene pool of a species (not an individual, that is impossible) over generations of time: the gene pool is all the genes in all the individuals of the species or of the ecosystem.

The process of natural selection, which is part of evolution, selects FOR survival and reproduction of phenotypes that function well in the environment. If and only if that genotype is heritable, then the entire gene pool may be change to favor one gene or, much more likely, a combination of genes, that are best suited to whatever environment is operating at any given time.

It makes no difference to evolution whether or not mutations occur, what those mutations may be and whether or not mutations are random. Evolution does not select genes; evolution selects phenotypes that function well within the Biosystem at any given time and place.

The function of the genes has primarily to do with the survival of the individual and of the species, and it is two-fold. First, the genes turn on and off during growth, development and survival in response to cues from the environment. These actions are studied by cell biologists, physiologists, developmental biologists. This level of activity is what you referred to as epigenetics – that is how genes know what is happening in and around your body so they can activate the appropriate responses. This is how we stay alive, day to day. It does not change the genes; in fact the basic function of the genes is to not change but to provide the information necessary for the organism to respond to environment, and the second function of the genes is to pass on all of that information to the next generation without changing the genes but reorganizing them, so that each individual has a slightly different phenotype. The variability of the phenotype is the connection between the genes and the process of evolution.

The most common kind of genomic variability is recombination of genes. Recombination ensures that every individual organism in a species is slightly different from every other organism in that species. Another way that variability is generated is by mutation.

140506-flowers-asc_8953SsGiven that every cell in the body has a full set of genes, and all these genes are copied billions of times, it is not surprising that mistakes (mutations) occasionally occur. It would be surprising if they did not. Some of the mutations can be passed on to the next generation. Therefore every organism does have a small percentage of mutations and every species carries a large number of mutations in its gene pool; should any of these ever become useful to the survival phenotype of the species – evolution will select for those mutations.

This whole story of nested processes is the language of Life, as it has been created. Unlike the languages of man the Language of Life is completely honest, and yet it is far, far more mysterious and empowering and glorious than the concept of personhood, which places God and his works subordinate to the narrow mind of man.

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This is not yet the end of the story. I’ll talk about punctuated equilibrium next week.

This is Bare Bones Biology a production of FactFictionFancy and KEOS radio 89.1, in Bryan, Texas.

Bare Bones Biology 097 – Climate Change-So the Earth is Alive, So What?

Probably I’ve convinced you, or you already knew, that the climate of the whole living earth can change, and that the life forms of earth make your food, air and water, and the whole earth ecosystem functions as a living thing, a giant super-body that has characteristics similar to those of all other living things. First among these, it can adapt to changing conditions by changing itself. That is one of the standard definitions of life.

So how can there be a debate over climate change? At least I thought that was what the debate was about because that’s what they kept saying, so I thought – Duuuh, how could it not change, it’s a living thing? But maybe this is another case of people not saying what they mean. Maybe the real question is – why should we care?

Mostly we should care because we are part of that living super body known as the earth ecosystem. What happens to it happens to us. Think of yourself as a flea on the backside of the ecosystem. What happens to the flea when the dog dies? No, we can not jump off on the moon. We tried that.


The life of the earth consists of millions of different species of organisms. We are one. The life cycles of all these organisms interact in ways that maintain the life cycles of each other. I have described the cycle of carbon and oxygen and water as it relates to people. That cycle also relates to all the other species of organisms that use oxygen to burn carbohydrates, so we are all interconnected in that way.

Some bored mathematician once figured the odds that we are breathing in the same oxygen atom that Cleopatra breathed out, that has cycled around through the biological system all these years. The probability was surprisingly high. If he had been a biologist he probably would have figured the odds that we are breathing in the oxygen atom those fleas breathed out. We are all connected to life by the necessities of life, and most organisms have very strict requirements for staying alive. Organisms, individual organisms, cannot “evolve.” They can change, for example their temperature, but evolution requires a change in the genetics, and it takes multiple generations. Therefore, only species can evolve. And only sometimes, if the changes are slow enough.

So these millions of species of organisms, plants, animals, fungi, microorganisms, that create the circulatory/respiratory system of the living earth, the species that clean up after us, worms, buzzards etc, the species that make good rich soil. Every one of those species requires a particular climate to stay alive. For example, good rich soil, in just one spadeful are millions of different kinds of organisms and micro-organisms. These organisms interact with each other and they interact with plants that are growing there.

The different plants also have special requirements for staying alive. Soil and plant relationships are delicately balanced to local conditions of climate. All the parts of the climate, the temperature, amount of sunlight, airflow, amount of water, everything interacts with the organisms and the organisms interact with each other. Every kind of organism has very specific requirements to stay alive, and it has taken millions of years for all these relationships to evolve to the point where we can see that the earth has come to function almost like an organism, with all of its internal parts helping to keep it alive, in a parallel way to how our internal parts keep us alive.

Some people believe that organisms, including, people, can adapt, and that adaptation is the same as evolution, so we could adapt to a higher temperature by evolving, but that’s not how evolution works. What will happen is happening, the species will die because they cannot live in the rapidly changing conditions. They will die and new species will evolve over the future millennia. In God’s time = ecosystem time. Not human time. Way too late to help us maintain the climate we need to stay alive.

Huge numbers of species have already died. This is not a computer-game fantasy, and there is nothing to debate. We do know how we are causing these problems and how to stop causing them. But we don’t want to stop causing them — we like things the way they are. Or I should say the way they were.

Bare Bones Biology 097 – Climate Change-So the Earth is Alive, So What?
KEOS FM 89.1, Bryan, Texas
Audio download available later this week
here and at http://BareBonesBiology.com

Recommended References: BBB093 – Climate Change II https://factfictionfancy.wordpress.com/2012/02/05/bare-bones-biology-2/ Bare Bones Ecology Evolution Handbook is available for download near the lower right corner of my blog

Bare Bones Biology 094 – Climate Change III

Oh, and yes, all these physicists who believe that they understand life because they have some convenient information about the basic laws of the universe. As far as anyone knows, life is not the center of the universe, and while life does operate according to the laws of physics, it is not studied by the science of physics. As far as anyone knows, life is the whole of the reacting, breathing, interacting earth, and physics says nothing about the higher Levels of Organization (and) beyond the properties of energy and matter. Well, not nothing. Physics is very important because it informs us about fundamental natural laws like gravity and energy that everything must obey.

Life couldn’t exist if it did not obey the fundamental laws. But of course, EVERYTHING obeys the fundamental laws, or it wouldn’t be here. That’s what fundamental means. And everything is not life. The purpose of biology is to learn to understand what is the difference between life and everything else.

Everything must obey the law of thermodynamics, so biologists study that. But all the non-life also obeys the laws of thermodynamics. Thermodynamics is not what makes life alive. It is necessary but not sufficient.

Biology is the study of life, and therefore biology is the study of the whole earth ecosystem and how the living earth and all its parts is different from non-life and – more importantly — how we can stay alive without causing harm to the whole earth ecosystem that gives us our lives.

The ecosystem stays alive because of interacting cycles of functions and properties, of energy and matter, because of the ability to transmit information by genetics so that the ecosystem can respond to change, and because of the ability to flow energy from the sun into plants and from plants into every other living thing. And the ecosystem also stays alive because of the ability of itself to recycle the key materials that it needs to stay alive – like carbon dioxide and oxygen and water. Carbon and oxygen and water recycle through the living earth just as they recycle through our own bodies. They are a part of life. They are the climate – the respiratory system – of the living entity we call the earth ecosystem. If they didn’t change – if the climate didn’t change – the earth would not be alive and we would not be here.

There is no debate among biologists about whether or not living things change. There would be no life if it couldn’t change in response to what is happening around and within it. That is the foundational necessity of being alive, and all illness, disease and death are the result of not being able to change in response to one’s environment. Climate change is real, the fake debate is about politics, not about life. And the function of the fake debate is to prevent we the people from figuring out what to do about it, because what we must do about it would diminish the preposterous wealth and power of the corposystem.

So what can we do to give a gift of fitness to our human future within our living earth? We have three options, at least. 1) We can do something useful to help humans — that is, to help the earth maintain a climate that is suitable for human life. That’s what most biologists prefer to spend their time thinking about. 2) We can do something that is harmful to the health of the living earth. That will cause devastation to the future of humans on this earth. Or 3) we can do nothing and let the climate rebalance itself without regard for our needs.

The trouble with doing nothing is that it will result in unimaginable suffering because of the vastly greater number of people, animals, plants and other living things that will be affected, and that’s why I prefer option number one, do something useful to help humans.

And the way to do that is to find a way to stop the growth that is causing the ecosystem to rebalance and readjust all its millions of cycles of life, in response to our waste products.

Bare Bones Biology 094 – Climate Change
KEOS FM 89.1, Bryan, Texas
Audio download available later this week
here and at http://BareBonesBiology.com

Recommended Readings: Bare Bones Ecology free download on my blog.

Bare Bones Biology 091 – Evolution

Last time I told you what I know about the reality of our human position on the earth, and more importantly what we don’t know and therefore cannot control. Next I’ll tell you a little why and how story of the past couple of hundred years that have grown our destructive modern economies.

The theory of evolution was a brilliant breakthrough that took place a couple of hundred years ago. After that, it was studied rigorously until the evolutionary scientists and the geneticists realized they were all studying different parts of the same creature, and they got together. Now, 200 years later, we know a great deal more about how this beautiful life form, the whole earth ecosystem, manages to survive through the millennia by changing in response to changing conditions. We know that these changes are mediated for the most part by organisms that, by their interactions with each other and with the environment, carry the genetic information for the life of the whole system forward from one moment of time to the next. The correct term for this kind of study is evolutionary ecology. We left Darwinism in the dust at least a hundred hears ago.

The corposystem and modern politics and economics do not want us to know about evolutionary ecology, I guess because they have a strong foundation in that little nonsense phrase: “Survival of the fittest.” You have heard me say many times: “That’s not how it works.” I didn’t tell you how it does work for two reasons. One is that I don’t completely know how it works – nobody does – the other is that evolution is so complicated that most people don’t even TRY to understand how it really does work. Not even a massive computer could do the job because we don’t know all the parts of the whole earth ecosystem, so we can’t plug the information into the computer. We don’t even know all the species that do the work of keeping us alive. That’s why biologists are concerned about us humans killing them off – the other species – without even knowing what they are and how they contribute to our well being. The bottom line is that our modern corposystem is partially justified by a false or fake belief in survival of the fittest.

It is true that tooth and claw is an important reality of life. It’s also true that tooth and claw is a necessary component of life because it contributes to the flow of energy through the ecosystem, but tooth and claw is only a subset of how evolution works. How does it work? I lay out the background in pages 32 onward in Bare Bones Ecology Energy Handbook you can download from my website, FactFictionFancy. The shortest version I can tell you in a five-minute spot is that life evolves by generating functionally effective systems out of pre-existing systems.

A cell is a functionally effective system that is made of thousands of molecules – the key is that all these molecules work together perfectly. The problem, from our point of view, is the millions and millions of functional systems that did NOT work together perfectly within the system and so they became extinct. The way evolution works is to generate millions and millions of functional systems, by recombining the older systems, until a new system emerges that works together positively with the whole of life. That one SYSTEM (species) out of all the millions that unbalanced the systems of life, that one survives over time to become a part of the living whole earth ecosystem. We are unbalancing the life systems of the earth. The difference between us and all the other species is that we KNOW these things.

And the reason I am trying to explain this to you is that I see some new social movements coming up that are based on the reality of evolution instead of the failed models that were in part based on a false view of evolution. I’ll talk more about these in future.

Bare Bones Biology 091 – Evolution
KEOS FM 89.1, Bryan, Texas
Audio download available next week
here and at http://www.BareBonesBiology.com

Summing Up

Evolution happens. Not only it happens, but it is one of the most powerful and fundamental forces in all of living nature, along with the laws of thermodynamics, gravity, cause and effect.

In chapter one, we said the entire ecosystem requires energy to do the work of staying alive. We said the laws of thermodynamics describe how energy can or can not flow through the ecosystem. Survival of any living thing is a constant push against entropy, and entropy is a natural law of the whole universe, living and not living, that describes the natural tendency of anything to become un-complex — to fall apart, like a rusty old car in your back yard, compared with the shiny old Model T that you have kept in good repair.

We have also said that life is one of the most complex things that we know about in the universe. It requires energy to keep it that way and nobody is pottering around keeping it in good repair. Life stays alive because of the way the ecosystem works as a whole to keep itself going in spite of the natural laws of the universe. It does this, as we have said a large number of times, fundamentally by three uber-processes that we have discussed in our three chapters.

Chapter One – The flow of energy through the ecosystem, utilizing every bit of organic energy between the time it is created by the plants using sunlight as energy source, until it is lost forever in the form of heat. Every corner of the ecosystem, if it is to continuing doing its function of helping to keep us all alive, must have energy. It is one of the defining characteristics of life that it can keep itself in good repair. This is accomplished by the flow of organic energy from its creation in the plants through all the levels of living organization, the herbivores, carnivores and the organisms that live on dead and decaying matter that still contains organic molecules.

Chapter Two – The recycling of materials is the process that is easiest for us to understand, and yet the apparent simplicity is deceptive, because this recycling, again, relies upon all the interconnected levels of organization of the ecosystem so that, for example, carbon is made available to all of the levels of life from the time the plants use it to make organic molecules until the breakdown of the organic molecules returns it to the atmosphere.

The biggest difference between the materials and the energy is that materials are atoms or molecules of matter that have mass and occupy space. So the maerials just get pushed around on earth from one place to another.  Whatever energy is — it does not stick around to be used again. With respect to the ecosystem it is used primarily as organic energy that is created by plants using light energy from the sun. As every living thing (almost) uses the organic energy, the organic energy changes to heat energy and can never again be used to maintain the processes of life. Heat energy is also useful, but it does not run our generators, so to speak. So materials and energy flow through the ecosystem along the pathways of the levels of organization. The difference is that materials can be recycled but energy can not.

Chapter Three – The flow of information causes all the above things to happen as they do — that is genetics, from the DNA to the gene to the chromosome to the genome of an individual organism to the gene pool of the speces to the evolution of that species to the ability of the whole ecosystem to respond to conditions inside and outside of itself.

Life can be defined as the ability to respond to the environment, from the ability of a cell to find a safe place to live to the ability of your gut to digest organic molecules to the ability of a bird to build a nest to global warming. And beyond that to integration of the entire living earth that we will discuss in the next few posts.

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.

Why do cells and organisms require oxygen to stay alive? Because oxygen is necessary for the flow of energy. It is required for our cells to capture the energy from organic molecules, through the process of cellular respiration. Oxygen is provided to us by the ecosystem.

Why does the ecosystem require the recycling of materials to stay alive? So that the plants can use the materials, along with energy from the sun, to make more organic molecules, through the process of photosynthesis.

Why does the ecosystem require the deaths of individual organisms, so that it can give life to more individuals? Because the deaths of individual organisms are necessary for the flow of information through the ecosystem to continue, and the flow of information IS the innate, internal ability of the ecosystem to respond to the environment. That is, the flow of information is the most basic essence of life itself.

Those three most basic of all life concepts – the movement of energy, materials and information over time — will also be the basis for our summing up in the next few posts.

Genetics

The genetic code directs our biological functions — yours and mine and Bitsy (the dog) and Buttermilk Pie (the cat). Every new cell of an organism receives a copy of its own code of life, and then it uses the code to direct the proteins that do all the work of the cells, as we have described, by specifying the functional shape of each protein and producing them when and where they are needed in our bodies. Just for one example, this process makes available all the proteins required to do cellular respiration and so provides the energy that the cell needs to do all these tasks.

The more you think about all the tasks a cell and a body must do to stay alive, the more you recognize cycles inside cycles connected with other cycles. This is why life only comes from other life. When any one of these cycles is broken it not only stops its own task, but also all the other tasks that rely upon it for their functions. For example, the processes of mitosis, meiosis, DNA replication, cell division, all require organic energy that is made available by the process of cellular respiration, and cellular respiration would be impossible without all mitosis, meiosis, etc.

And the purpose of this one individual life seems to be meiosis and the fertilization of an egg by a sperm, a zygote, that will require proteins and energy to grow into an adult to repeat the cycle. These cycles more or less describe the flow of energy through the individual organisms. Even more elegant is the way in which they also participate in the flow of information through the entire living ecosystem.

Because of the processes of meiosis and cellular respiration, each new zygote is unique. It is correct for its species. For example, the new mouse cell contains 20 different kinds of chromosomes, two of each kind, two complete sets of chromosomes. Each kind of chromosome (numbered 1 through 20) contains the correct kinds of genes. For example there is a gene named tyrosinase in about the same position on every chromosome number one of the mouse. So every mouse has two tyrosinase genes. One came from the mother on chromosome number one and the other from the father on his chromosome number one.

However, the new zygote has a different genetic code than either the mother or the father, first because the chromosomes were assorted during the first division cycle of meiosis, and second because all of the genes (though they are of the same kind) are not identical to each other. The tyrosinase gene, for example, is responsible for making pigment in the pigment cells of mammals. It can be normal or it can be abnormal. If it is normal it does its function correctly; otherwise not. If the zygote gets two abnormal tyrosinase genes (one from each parent) then it will not have any normal gene to do the job of making pigment in the pigment cells. Of course, a zygote is not a baby. It is only one cell. However, that cell will make copies of itself until over time there are millions of cells until eventually some of the new cells will become pigment cells.

The genetic code is programmed to make tyrosinase in pigment cells. If the pigment cell is not able to make tyrosinase, then the new mammal will be an albino. If it is able to make tyrosinase, then it will have normal pigmentation. This is an example of just one kind of gene that is found in one location on one kind of chromosome. Similar relationships are possible for any kind of gene on any of the chromosomes. The function of meiosis is to reassort the genes. The function of fertilization is to make new combinations. Every individual zygote is therefore unique. Through all of time, every new generation of every sexually reproducing species consists of individual organisms that are not identical to each other. Every different phenotype is therefore also unique.

The phenotype is the physical nature of the body that results when a gene does its function. For example, the genotype of a normal tyrosinase gene could be referred to as Tyr+. The genotype of an abnormal tyrosinase gene could be referred to as Tyr – . Of course we already know that organisms have two of each kind of gene, so if a person, for example, has two normal tyrosinase genes, then we could write the person’s genotype as Tyr +/Tyr +. That person would make pigment in her pigment cells.

The function of the tyrosinase gene is to make the tyrosinase protein that causes the pigment cell to have pigment. That is, a pigmented phenotype. So the person has a pigmented phenotype.

If we want to refer to all the genes in one person, we use the term genome. If we want to refer to the entire phenotype of a person we could use the term phenome. Most people do not use this term, but I need it for the remaining part of our discussion because the phenomes of organisms, the variability of the phenomes, basically are the source of information flow for the entire ecosystem. They are the code of life of the ecosystem, as we will discuss later. Meantime, this discussion has become sufficiently complicated for today.

To sum up, living things can respond over time to conditions inside their bodies and outside their bodies. If they can not respond to conditions they do not stay alive. It’s not possible to respond to anything unless there is information flow (communication of some sort) between the conditions (cold temperature for example) and the response (putting on a coat). This is even more true of the automatic responses, for example, digesting your food. The ecosystem, to stay alive, also requires information flow. Information flow in individual organisms is a result of the genotypes of their cells. Information flow in the whole ecosystem is the result of the many different ways in which organisms interact with each other at the level of the phenome.

And that is the end of the story of information flow within organisms (genetics) and the beginning of the story of information flow across all the levels of organization of the ecosystem (evolution). Whew!

And don’t forget that every bit of this story requires organic energy or it does not happen.

Evolution

The third requirement for a living ecosystem is communication. The cells of which you are made all communicate among themselves so that you can stay alive. Your nervous system responds to short-term activities, for example by telling you to get your hand off that hot stove, ASAP. Your hormonal system balances your body and all its processes over the long term. That balance is essential to your survival and also to the long-term survival of the species. The sperm must somehow “know” how to fertilize an egg; the egg then must know how to divide; all the little cells need to know whether to live or die depending where they are in the blastula or the gastrula; then a few billion cells later the nervous system begins to form and by the time of birth the mother and baby must both “know” how to see each other and respond together.

Other organisms do more or less the same balancing act, though the methods differ. Plants don’t have a brain with nervous system, but they do have hormones. The individual cell, the most basic organism, communicates more directly with its environment. Most of this activity, the behaviors of all the billions of cells, is directed by the code of life, the DNA in the nucleus of each cell.

The whole ecosystem, of course includes all the behaviors of all the cells, plus all the behaviors of the multicellular organisms. That is the various behaviors of the organisms interacting with other organisms of the same or different kinds. Mating, eating, parasitism, commensalisms, singing, laying eggs.

To imagine this sort of interaction you can think of a small stock tank (pond) in your pasture. The fish and the insects and the plants and turtles, and the water and temperature. All of those things interact in various ways to maintain the balance of all of life in the pond. This is the living ecosystem maintaining a balance within itself; that is the same kind of balancing of energy resources, materials and information that your body maintains by its physiology and an individual cell maintains by the processes of its biochemistry. These interactions represent the flow of energy through the ecosystem, as we discussed in chapter one, and the cycling of materials through the ecosystem (chapter two), but they also represent the flow of genetic information that ties together the whole ecosystem, through time, as one living thing.

I do not know a name for the process of information flow through the entire ecosystem from cell biochemistry; to the physiology of individual animals, plants and other organisms; to the communal behaviors of organisms. However, it is not difficult to show that the result of all these interactions is the coordinate evolution of the ecosystem that is mediated by the code of life in the chromosomes of every cell.

Biological evolution is the process of change in the code of life over time.

No we are not going to argue about evolution because there is no reason to argue and many, many reasons not to argue. The most important reasons to not argue about evolution are:

1. Evolution is not Darwinism. Darwin was a person with some ideas and opinions based in 100-year-old science. Evolution is a natural process — like the sun rises and sun sets is also a natural process — natural processes do not have opinions and they don’t do science. But we can. We can use measurable facts and the scientific method to unequivocally demonstrate that evolution does exist and it is functioning now. And we are part of it. So that takes care of half the question; the other half is not science.

2. Evolution has nothing to do with religion, because science is the study of measurable facts using the scientific method. Religion is not the study of measurable facts and it also does not use the scientific method. There is no reason why it should; it is not science, and the scientific method is a dreadful way to do religion.  Religion has its own best methods.

3. In whatever way life was created, the creation obviously also involved the natural processes that are necessary for life to exist. These include the flow of energy (chapter one), the recycling of materials (chapter two), and the flow of information that is what we are talking about. Without these, there could be no life on earth. How did we come to be in a place that provides the conditions that are necessary for our survival? I don’t know, but that is not what we are talking about, so it doesn’t matter to this story.

4. We all need the same things for our survival and one of these is the survival of the ecosystem.  So I can not think of one good reason to waste time arguing over something that happen not less than 10,000 years ago and probably a lot more than 10,000 years ago, when we could be working together to save what we need right now.  We can’t do that by guess and by gosh, as we have so far been attempting; the more we know about how the ecosystem functions — the better citizens we can be.

Oh, I think I went off on a rant.  What was the question again? How does the code of life have anything to do with cellular biochemistry, physiology and the higher-level behaviors of organisms?

The answer is, it is mostly about proteins.