Bare Bones Biology 201 – Genotypes, Phenotypes and Evolution

Living things have the ability to respond to their environment. That means both the internal environment and the external environment. For example, you as a living thing – your physiology and your behavior change if you get too hot or too cold. An ecosystem also responds to heat or cold. It is also a living thing, and it responds to its environment by changing the species of which it consists.

Organisms respond to change using the processes studied in embryology, physiology and behavior — the ecosystems and the Biosystem use evolution to respond to change.

Your physiology, and also your embryology and development, and behavior, are regulated by all the genes in your body interacting with your internal and external environment, so that you can take food and air and water, and use them to become what you are. In that way the genes, responding to your environment, produce you as a “thing,”

Put into my model of Life that I described in last week’s Bare Bones Biology blog, you can be thought of as a node produced by the network of processes that maintain your Life. The processes can be thought of as the invisible Life force, and you are the solid object that results. Solid objects (nodes, things) have phenotypes.

I’m sorry we must add another uncommon word to this story, but the word phenotype is important. Your phenotype is everything about you, from your red hair to your behaviors to your physiological responses to the environment. Mostly your phenotype is caused by the processes that are regulated by your genotype, and those processes are studied in the science of Genetics. Accidents (amputation for example) can influence your phenotype but not your genotype. Accidents are not inheritable. Your culture can be inherited, but only by your training, not by your genes.

140227-tree-ASC_8143RSs copyHigher Life forms, such as an ecosystem or the Biosystem, also respond to change in the environment. Their responses to change are regulated by evolution, the natural Law of Life. Your body uses processes regulated by your genotype to grow and respond to change (and so be alive). The ecosystem uses all the phenotypes in the system – interacting with five other processes we discussed in order to grow and respond to change (and so be alive).

It was Darwin’s genius to recognize that living “things” (he was looking at organisms, but it could have been cells or ecosystems) all have slightly different phenotypes – color, behavior, health, any characteristic of a “thing” can be selected for or against, and so long as it can be inherited by the next generation it is a selectable phenotype that can respond to the power of the Law of Evolution.

In the Cosmos example, tameness was the phenotype selected for. This is the portion of evolution that Darwin recognized and we have come to think of as “survival of the fittest.” That term is nothing more than a silly reductionist sound bite, good for the human ego, but if we want to understand how evolution really does function and conceivably save ourselves by conforming to the Law of Life, survival of the fittest will be of no use to us. For one thing we are very far from the fittest species, because we would rather have money than survival. We will have to modify our own phenotypes (behaviors) so that we affirm and support the Life of the whole.

But that’s an aside, what we want to explain today is that natural selection or artificial selection act upon phenotypes, and most phenotypes are generated by genotypes. The genotype of each living thing is unique because of the way genetics works, which we are not discussing today. At all the various levels of organization of life from the most simple cell to the most complex Biosystem.

Genotype → Phenotype -→ Evolution

But remember that the processes of evolution can only use phenotypes that are inheritable from one generation to the next.

And we said all that so we could answer one of Gary’s original questions about epigenetics. Epigenetics is the study of heritable changes in gene activity that are not caused by changes in the DNA sequence.

Epigenetics is not relavent to evolution. Epigenetics is relevant to genetics, such as how genes are mixed around in cells, and how genes are regulated in cells to turn on and off. We have not been talking about genetics except to say that any trait or phenotype can be used in the process of evolution if it is inheritable.

To download the podcast of this blog, the direct download URL is:

Bare Bones Biology 200 – What Depends on What?

Here is the direct download of the podcast from a question posed by Sheila.

If you want to go to the podcast, I cannot make the link work here, but the address is:
and in front of that you must put http://

The blog is quite a lot more inclusive and will be posted on this weekend.
Sorry to be late, but Bitsy and I are moving to a location that has no internet access and this requires adaptation.


What does a system depend on? The answer is that everything in a system, more or less, depends on everything else in a system, and if the system changes, then everything else in the system must rebalance itself. This is what is meant by sustainability, and it is a definition of Life that we have been using in the past few blogs. If the system cannot rebalance itself, then it crashes – or dies.

The other question is “How did the system originate, so elegantly balanced?” And the answer is that the Law of Evolution creates sustainable systems. That’s what it does, and how it does this is fairly well understood in the disciplines of embryology, evolution and ecology. I certainly cannot explain it in 600 words, but I keep on biting off chunks of information that – if you keep trying to understand them – will ultimate convince you that systems evolve by maintaining their balance when conditions change. (Or they die if the conditions change so rapidly or dramatically that the system cannot rebalance.)

That information does not answer the God question, of course, but in my opinion, if God created the universe, then God created the universe to function the way it does function . I do not claim to understand God, but I do know a lot about what God has created, and I would far rather study and try to understand the works of God than the products of the human ego. If God created the universe, then God created the laws of nature to work the way they do work.

There are several laws of nature that are studied in different disciplines. The natural Law of Gravity describes some properties of matter. Matter is things that have mass and/or weight. The natural laws of Thermodynamics describe how energy functions. Energy does not have mass; energy is the ability to do work, and work is done, basically, when something happens. Energy is required for processes to do work. The natural law of Evolution describes how living systems maintain themselves, using matter and energy. Last week I described six qualities that define both Life and the Natural Law of Evolution, which is the Natural Law of Life

To appreciate any of these natural laws it is important to think of ourselves, and all of Life as systems, rather than “things.” A system is a group of processes that function together, each supporting the functions of others in the system, to maintain the whole system.

Life on Earth is a system, the Ecosystem, or Biosystem. Ecosystems are the subsystems of the entire Biosystem. Populations are subsystems of ecosystems. Individuals, such as you and me are subsystems of populations, but even we are not independently “things,” because we could not exist without the Earth system of which we are a part, and we could not exist without the subsystems that are a part of us – our lungs, kidneys, heart, digestive system – and those are systems composed of living cells.

A system is a network of interacting processes that function together to maintain the whole system. “Things,” such as ourselves, are simply temporary nodes – like the jewels in the metaphorical “net of Indra.” Or like the nodes (web pages and other nodes) of the internet. “Things” are objects with phenotypes. Things (nodes, objects with phenotypes) are necessary to maintain the integrity of the processes and to cause the processes, as I said above to function together, each supporting the functions of other processes — rather than each process functioning randomly or separately. Evolutionary selection acts upon the nodes (things, phenotypes) of the network and the network of processes generates the things.

For example, an airplane is a thing that brings together all the processes necessary for commercial flight. If you take away any of the processes, or change the configuration of the processes and/or the environment in which they function, the thing may not work.

A system consists of processes that do the functions (actions, behaviors) of the network of which the system is composed, and “things” are the nodes, connecting points, intersections of functions that join together the processes so as to maintain the integrity of the system. My favorite metaphor of a system is one of those stick figures that can be generated by a computer.

The stick figure is a model, usually a cartoon, that can move and change its shape. It consists of dots (representing in this model, things, nodes, jewels) joined together by lines (representing processes). All the processes work together to maintain the functions of the whole, while the nodes represent the ways in which the processes interact to maintain the integrity and the phenotype of the whole, so it is able to respond to the law of Evolution and thus maintain itself.

This model is applicable at all the levels of Life. Each node of a complex system represents a subsystem that is also composed of processes linked by things. For example, you are a system. One of the nodes of you as a system is your heart. Furthermore, at all levels, the things (nodes) are also subsystems. Our heart is a self-sustaining system consisting of things (nodes) and processes. Thus, everything interacts with everything else at the nodes, and in a way that maintains the balance of the whole complex of interacting systems.

I believe this may be the meaning of the mathematical concept of a multidimensional universe. I have no way to check the math, but that’s OK, because for me it makes a whole lot more sense to study the reality of Life itself. Especially as we humans have reached the point where the things we create are destroying the balance and the links that maintain the integrity of the nested set of process that is Life itself.

If you have trouble imagining this you should realize that NOBODY CAN understand the balancing interactions of the whole system of Life itself. There are far more links and nodes in the whole of Life than in our brains and computers combined. This is why we should not try to change Life systems without using the precautionary principle – that is, we should look at ALL the possible results of our meddling, both good and bad, because all actions cause both good and bad results. That is a very important meaning of yin and yang – the balance must be maintained or the system will change itself into something we won’t like, and that is indeed happening, partly because our culture is more interested in controlling what we believe to be bad – or pretending that it does not exist – than dealing with the reality.

NOTE: for the image, go back to a previous blog and refer to the chart of levels of organization:

The function of our corposystem is to use biological links and nodes to make money. These links and nodes evolved to exquisitely regulate Life itself – not for profit. We humans are redirecting the interactions of Life to the purpose of making money, and this unbalances the links and nodes that are necessary for Life Itself to exist on earth. And so, the re-organization of the nodes and links changes Life, because that’s what is unique about Life. It changes when its environment changes – because that’s how the Law of Life (evolution) maintains Life. If it cannot change using the links and nodes it has available – it dies (crashes, as our corposystem is now crashing as a result of imbalance.). And then a different system grows by the coming together of a different configuration of links, nodes, environment and overall function. Evolution does not change existing systems that are unsustainable. What it does do, if the existing system is unable to respond or (as we are doing) tries to fight against the needs of nature — is get rid of the existing system and start over using evolution to build a whole new set of interacting nodes and processes beginning with lower levels of complexity – such as a more primitive animal, or even the cell.

This is really good (really hard) question contributed by Sheila and produced by FactFictionFancy and KEOS radio 89.1 FM, Bryan, Texas.

Next week the other really hard question that we have been working up to, from Gary: If evolution acts as described in Cosmos and in nearly all basic genetics courses, then why doesn’t it operate gradually?

Bare Bones Biology 199 – Evolution

In Bare Bones Biology 198 ( and in the blog that was posted to FactFictionFancy the following day (, I listed six characteristics of all living things that make them responsive to the world outside of their own bodies.

That is an important definition of Life. Life and living things are responsive to the environment, and their environment is everything that is outside their own bodies. They are also responsive to the internal environment, which is everything that is going on inside their own bodies. Within physiological limits, Life is able to respond to change. If it can’t – it dies.

Most people notice this and think it is ordinary – of course — ! It is ordinary to us. We are alive. We eat, we walk, we talk, we try not to run in front of cars. But in the universe, so far as we know, the interconnected systems that can reproduce their own kind and recycle the materials of which they are made, and find food and use it to do those things – this is not ordinary.

110825droughtasc_3018sls-copyIt was the greatest and most marvelous event after The Creation itself, when a group of processes came together, to form a unitary system that was able to respond to the environment by moving toward food or moving away from noxious things. It was the creation of Life. Life is a system composed of a set, or sets, of processes that function to respond to the environment in which it lives by reproducing its own kind.

Six qualities that make life possible, that I listed in those last two blogs are: 1- Inheritance of traits; 2- Variability of traits; 3- Reproduction; 4- Death; 5- Transmission of traits to the following generation; 6 – Interconnectedness of the processes of one living system with all the other living systems on earth.

Those qualities are essential for all living systems and their subsystems — all species – to maintain Life on Earth. And the original “invention” of Life was the coming together of a group of processes that maintain life by responding to the environment in which they live.

Evolution is the Law of Life on earth; Evolution makes Life possible because Evolution is how Life responds to its environment. Without evolution there could be no Life as we know it on earth, because Life and living things must be able to respond to their environment or they could not stay alive. Think of the first breath of air that a newborn infant inhales. Think of the color of your eyes, or of your skin, that you inherited from your grandparents, or great-grandparents. If there were no evolution, Life could not respond to conditions in the environment and there would be no Life.

A living thing is a system that is able to respond to its environment to find food, water, air so that it can reproduce itself and continue staying alive generation after generation. It is the natural Law of Evolution that guides and balances all these processes of Life (and a myriad more) within all organisms and between all organisms and all other systems on Earth as the entire interacting set of systems continues to use the energy from food to respond to the environment and so to stay alive.

Evolution is NOT primarily survival of the fittest. Evolution is the natural process that permits living systems to respond to their environments and so to maintain and BALANCE all the processes that are required for living systems to stay alive — including life and death, reproduction, using food energy and cycling the water and nutrients through the whole interacting set of systems and subsystems. Therefore – if you still think of Evolution as “survival of the fittest,” or any other sound bite that is more simplistic than the holistic balancing act that Evolution actually is, you cannot understand climate change, and regardless if you are one of the bad guys or one of the good guys – if you win or if you lose — you cannot help to make wise plans for the future of humans on this living earth.

This is Bare Bones Biology, a production of FactFictionFancy and KEOS FM 98.1, Bryan, Texas. A copy of the podcast can be downloaded here: