Bigger ≠ better, and
Stronger ≠ winner.

Ask a dinosaur.

Long-term success requires
a sustainable and usable balance
between size and speed,
and between strength and agility.
And between income and outgo.

the view from my mailbox

I do love the views in April

World View Three

There are some things about which we have no choice. Most of these are not human realities. Human realities often have a lot to do with matters of opinion, and so they can be changed if enough people want to change them. The things which nobody can change are not so very many, and they relate to the laws of nature that permit life on earth. The laws of energy mostly. They are easy enough to understand if we want to understand them, but we can’t change these by any of our human power ploys. Hitler did not change the laws of energy, and neither did the Buddha. This is good, because if the laws of energy were to change, life on earth could not continue. However, that leaves only one other option: people need to change whenever they run afoul the laws of energy.

The way it usually goes, some people will try to understand the environment well enough to benefit from it; others will try to dominate it. In the long run, the effort to dominate will inevitably fail. Humans can kill, but we can not dominate life.

Fortunately, people are very changeable. Mostly we don’t change; I don’t know why we would rather suffer than change, after we reach a certain age, but we can change if we care enough about something or other.

So the question is: are we better off to keep trying to understand the bigger picture, to keep modifying our world view closer and closer toward a reality we can never fully understand? Or to keep trying to reinforce whatever information and opinions we already understand.

I wonder if this question might go a long way to explain our current political situation. And if so, then I wonder why anyone would care enough to fight over a difference in world view, when we really all want the same thing and our common problem primarily has to do with our relationship with the immutable laws of energy transfer in the universe. I could see fighting, but I don’t understand fighting over something that is not the real problem. When we could be trying to solve the problem.

More World View

Even if it were true (and clearly it is not)
That everyone in all of history
Lived inside a dog-eat-dog world view.

That is not a reason for me to suffer
Inside their heads.

——————————

“If we always do what we always did;
We’ll always get what we always got.”

Mitosis

Inside the nucleus of each of your cells is an exact copy of the DNA that you received from your parents. As you know, every eukaryotic cell consists of molecules — water, proteins, lipids, carbohydrates nucleic acids and some other things — all organized inside a membrane. The membrane is referred to as “semi-permeable.” This means some things can cross the membrane and other things can not. In a normal environment, the cell controls what is inside and what is outside of itself. The organization inside the eukaryotic cell is complex, and includes many organelles. Organelles are lipid-bound structures that contain molecules organized to do specific functions, for example photosynthesis in plants, cellular respiration in nearly all cells, and my favorite, pigment granules inside pigment cells. Prokaryotic cells (like bacteria) are equally well designed, but they don’t have membrane-bound organelles inside themselves.

The nucleus of eukaryotic cells is the central core of the cell. It has two membranes around it, and it contains the DNA. DNA is the genetic material that is passed from generation to generation as a coded molecule made of nucleotides (we discussed in the last few posts). DNA is a physical molecule that is kept safe in the nucleus of your cells and copied exactly every time a new cell is made. It does not shift around or change its code (unless there is a mistake, which is very rare). It also does not leave the nucleus of the cell.

DNA has nothing to do with our political lives and is not found in our behaviors or our social structures — Bill Moyers notwithstanding, and if anyone knows Bill Moyers I hope he will read this little book so he can do a more accurate job of representing biology. Our understanding of the limiting parameters of biology (and our response to those limits) will determine whether or not humans on earth can continue the lifestyle to which we have become accustomed. So to Bill Moyers I say:

“Democracy does not contain DNA, and biology is not a whim of human language. Biology is a fact of  nature that will be here whether or not humans continue on this earth. It is far more important to our survival than either our democracy or our ability to make cute metaphors.”

Oh, oops, I got off on a rant, but you get the point. DNA is not a social reality. DNA in nature is designed to maintain the code of life and to regulate the biology of the cell. The DNA molecule carries the coded instructions for operating your body, cell by cell, and that’s all that it does. And that is one reason DNA is so carefully controlled in the cell, so it should not make mistakes in the code or wander out of the nucleus of the cell.

In the past few posts we have given an overview of DNA replication. DNA replication happens inside the nucleus of each cell when it comes time for the cell to replicate (that is when one cell divides to make two cells). To divide, the cell gets bigger, stretches out longer, and then pinches itself in half in the middle. Before it divides, the cell must make another copy of the genetic code, and then it must have a way to make sure that each new cell gets one of each of the chromosomes (the genetic code), so the two new cells are genetically identical. So that is when DNA replication occurs. We explained DNA replication in the last couple of posts.

After the DNA replicates, then the cell has two exact copies of each chromosome. Each chromosome is one enormously long DNA molecules, plus some proteins and other things that cluster around the DNA. All the DNA in all the chromosomes are your genetic code.

Because it is so long, the chromosome has to wind itself up into a shorter space before it replicates. These shorter, wound up (condensed) chromosomes are what you may have seen in pictures. The original chromosome and the copy chromosome (of each) remain attached to each other, and they all are still in the nucleus of the cell. Then, just before the cell begins to pinch itself into two cells, the nucleus dissolves. The condensed chromosomes line up in a space like a flat circle that is referred to sometimes as a “plate” between the two ends, preparing for mitosis.

Mitosis is the process of cell division that gives rise to two identical daughter cells.

The double chromosomes line up across the middle of the elongated cell, so that one of the duplicated chromosomes faces each end. Structures (microtubules, they are made of molecules) form in each end of the cell that look like little strings. The copy chromosomes are still attached to the original. The microtubules from one end attach to one of each duplicated chromosome, and those from the other end of the elongated cell attach to the other of each duplicated chromosome. Then one of each different chromosome is pulled to the left and the other is pulled to the right. The cell pinches itself in the middle until there are two cells that each have one of every different kind of chromosome, a nucleus forms around the chromosomes, and they stretch out long again so they are no longer condensed. The two daughter cells are genetically identical to each other and to the original cell.

This is the process of mitotic cell division (mitosis) and I’m sure you can find it on the web and in many books, in great detail, with lots of names for all the different stages of division. The detail is not as important to us as the bottom line, which is:

1. Every chromosome must replicate its DNA so each new cell will have the exact genetic code as the parent cell;

2. The replicate chromosome stays attached to the original chromosome while they line up in the center of the elongated replicating cell.

3. One copy of each chromosome is pulled to the left and another copy is pulled to the right in the elongated cell.

4. If all these processes are done properly, then each new cell has an exact copy of the DNA code of the original cell.

People Are

When your world falls apart, it is because the reality of life does not fit whatever is your world view of life. It’s a form of culture shock. Your choice is to somehow find yourself a more logical world view — one that better fits the facts. It is hard and painful work. Or the other choice would be to is to clutch more firmly your illogical world view and withdraw into yourself. My world view has been trashed several times, a painful event, but one that leads to a higher level of understanding as we put the pieces back together in a more logical way. Here is my new one. Because I am a scientist, I always try to base my views in measurable facts whenever they are available, and so I begin with an extremely well documented fact.

1. It is a fact that the anatomical and physiological makeup of humans is determined largely by their genetics, and that they inherit their genetics from their parents. This fact is demonstrated in many ways, but the most obvious is that we are able to change genes. If a change in a gene causes a change in a phenotype (phenotype is a physical or physiological trait), then the gene must somehow affect the phenotype. And there are many other proofs. It’s a well documented fact.

2. It is a fact that humans have brains and it is also a fact that our brains do many things for us that are common to all humans (are inherited from our ancestors) and of which we are not aware. We know this in general because of what happens to people whose brains have been damaged. We do not know very much about the specific.

3. In other words, there are some common characteristics of all humans that are different from other organisms, and some of them are common to us all, even if we don’t know it.

4. I believe that one of these human qualities is our ability to make logical sense out of our environments. In all my past ten years of searching around the world including the USA, I have found that every person has a life-logic that makes good sense if we listen to the foundations for that logic. Many life-logics are extremely damaging to the self or others, but they all make logical sense. Our life-logic has been called a world view.

I believe our brains are always looking for a world view that is logical. Whether or not our world view is factually valid is another question. Some realities are not measurable; some world views conform better to measurable facts than other world views. However, all world views are logical within their own construct.

5. I believe, once the human brain has reached a logic that makes sense, it will protect that logic with everything in its power, and the greatest of these is denial. Denial is an automatic human response to anything that threatens us or (specifically because that’s what I’m talking about) our world view. Of this, I speak from experience, and again I believe it is a universal human trait. This has at least two results:

• a. most people believe that every other world view is illogical and refuse to listen to what in reality is the logic of other people’s world views; and

• b. because we are afraid of the emotional black hole that would exist if our world view proved to be wrong (and we know that all world views are wrong in some respects), we create cliques, clans and wars. This is not for the purpose of finding out what is true, but to prove that our own world view is correct. Unfortunately, this is impossible because no world view is 100% correct, so most of the time we don’t know what we are fighting about because fighting proves nothing about the relative accuracy of the various world views, and so we make small problems bigger in order to prove something that is unprovable. Politically, this means that the “pendulum keeps swinging from one extreme to the other and back again.”

6. It is a fact that a very large part of the unique quality of the human brain is that it can adapt to environmental circumstances. In other words, we are all the product of our own experiences, laid on top of the basic qualities of the brain.

7. I believe that a very large element of our American environment (our culture) is that we are taught to believe we aren’t good enough unless we are “winners.” It doesn’t matter what we win, so long as we win something, then we are OK.

8. It is a fact that the scientific method is based in measurable facts. This gives us the option (for those who have access to the method) to build our individual and collective world views on the basis of measurable facts. Undeniably, the scientific world view is more likely than, say emotions, to approximate the reality of things that can be measured. This is demonstrated by the reality of technology. If we didn’t have a good grasp of some real universal law, our airplanes would not fly. So it’s clear that we can (if we choose to do so) get closer to factual reality if we base a world view in measurable facts.

9. Any good scientist knows the difference between things that can be measured and things that can not be measured, and also knows how to tell the difference beween a fact and an opinion or other non-measurable belief. That is why scientists don’t argue with people who are not interested in sorting these things out. There is nothing to argue about unless both sides are willing to acknowledge the portion of information that is proven or provable. There is no point to a big argument over whether or not gravity exists, for example, and working scientists are among the most busy people on the planet just trying to keep hold on their careers. Such an argument is not relevant to their world view.

Most good scientists enjoy a genuine search for knowledge. Most scientists are very committed to the general welfare. Once they know how we are causing harm to ourselves, they want to help fix it. Technologists are not scientists, but most technologists feel similarly. The problem is that the world view of most technologists is that technology will save us from the laws of nature. Unfortunately that is not a viable world view relative to the facts. Most other people also are positively motivated, in the sense of helping humans, but their world views usually have more to do with the opinion that either religion or politics will “save us.”

10. I believe that — religion is to spirituality as technology is to science. In other words, religion and technology represent different efforts of humans to build logical world views with which to control the laws of nature. Unfortunately, we know factually that we can not control the laws of nature and survive, because the ecosystem is structured with the laws of nature as its foundation. If we pull out the foundation stone the whole thing will crash. It is like a cell in your body trying to change the way your body. If the cell wins, you are dead. Fortunately we probably can’t do this to the ecosystem. As a religious friend of mine says:

“Lynn, you should not worry about the ecosystem. God has created a living earth with checks and balances so that it can protect itself.” True, but the fix will be tragic for humans, and I was actually more worried about the grandchildren.

11. American politics is about winning at any cost, whether or not it is for the general welfare. People in power know that they do not have the power over millions of other people. Therefore, people in power, whether they be corporate leaders or politicians, control the masses by creating false world views that they proceed to “sell” in any way they can.

• a. They can not sell a false world view using all of the real facts because people are by nature logical and would smell a fish;

• b. People are by nature logical, and will rebel if they can’t have a logic;

• c. Therefore people in power leave out factual steps in the logic they provide to pacify the people. They replace these with bullshit that sounds more attractive than the real facts. Thus they give the people two things that people by their nature want very much: a logical world view; and a happy story to go with it.

The problem for the people is:

• a. The leaders do have access to the facts;

• b. If the leaders can seize control of communications and education so that they can falsify or leave out important measurable facts, then the world view of the people will not approximate factual reality and that of the leaders will, with the result that the leaders will have the major control over the power. Factual reality holds more power than the logic of one’s world view because you can make real physical things work with factual reality, whereas world views are mostly composed of subconscious or emotional realities;

• c. The facts have three levels of physical reality that are different from each other.

Level One – individual comfort (I won’t give up my world view no matter what) – refusal to listen to other people’s equally logical world view.

Level Two – The human group welfare (this would usually be a clique, clan or worldview sort of group, but also could be any human political group) – whatever worked for my father is obviously best for my son and everyone else’s sons. Peer pressure and mob behaviors are included. This is where the pendulum swings but no progress is made toward success.

Level Three – over-all reality, which in the case of us is the whole ecosystem because we can not survive without it.

Thinking about our world view in terms of levels is very useful. It explains some realities that otherwise appear to be in conflict. For example, evolution.

Successful evolution is a sort of negotiation in which the basic needs of all the levels are met. Take cells for example. At level one, the cell that eats another cell changes nothing of significance to evolution, but only to himself. And then someone eats him. At level two, the cancer cell appears a big (political?) winner over all the other cells in the body. But as a result the body dies, along with all its cells, eliminating them all from further participation in any kind of life. At level three, the cells work together to keep the body healthy and thus are able to pass on their genes to another generation of bodies and cells. So if anyone tried to tell you that evolution is an exercise in “tooth and claw” their world view logic is somewhere between level one and level two and represents only a small part of the real picture.

Unless human kind can develop level three social skills, we will end up like the cancer cells, because the fact is that the overall ecosystem is a good deal bigger than any or all of us, and is probably not listening to any of our world views. Like all living systems, it will do whatever it will do according to the laws of nature (we do know how this will happen in a general sort of way) to save itself, so if we genuinely want our politics to benefit our sons we should find out what the ecosystem genuinely requires in order to stay healthy, and not what some economist (or military general, or president) says it should need according to his very logical world view that leaves out several important facts at the very base of its logical structure.

And this is why scientists don’t try to talk to people who won’t listen to real measurable facts of level three.

The fact is that level three will determine the true quality of life for our sons, and at level three we all want the same thing, which is quality of life. Therefore, it is a complete waste of our valuable logical brains to spend them unnecessarily muddling around in levels one and two when we could, instead, listen to the various ways in which we all express exactly the same needs, wants and desires. We could be using all that information to work together at level three to get what we all want, need and desire.

We will never get these needs fulfilled by killing off competitors at level one, or overrunning elections or the ecosystem at level two, because we cannot force level three to do what we want her to do. Our only option is a level three evolutionary compromise in which we adapt our fairy tales to the factual, physical, measurable needs of level three survival — if we decide that is more important than our own need to believe we are more powerful even than God. We are not more powerful than God, and I do not believe God wants us to trash His beautiful living ecosystem.

And unfortunately for our fairy tales, God’s laws respond to our behaviors — not our world views.

I wonder what the person said the next day after he chopped down the last tree on Easter Island? “Oops, shouldn’t have done that!”

DNA Replication

There is a difference between the elm tree, the horse and the dog, and all the grasses and weeds. In fact, there are several differences. For the most part, these differences are encoded in the DNA that is carried in every cell of the body of each of these organisms. Each kind of organism has its own DNA “code of life,” that has been passed from one generation to the next over all of the time of organisms on earth.

DNA is a molecule that consists of a long string of nucleotide molecules that are fastened end to end in a coded sequence by very strong covalent energy bonds, and fastened across the middle by weak energy bonds to another covalently bonded long string of nucleotide molecules that is its mirror image. Not surprisingly, the coded sequence of nucleotides in the horse is different from that in the dog and more different from that in the tree. Every cell in each of the organisms, carries an exact copy of the code for that organism. One of the biggest job of every cell is to make an exact copy of its own code whenever it makes a new cell.

Cells die all the time in the body of all living creatures. Your cells are dying while you sleep and when you work. There are so many cells in your body, doing all the work of keeping you alive, that some of them are replicating (reproducing by making a copy of themselves) and some are dying all the time of your life. Your old cells must die so that your body is composed of mostly new and healthy cells that are capable of doing the work of staying alive – cellular respiration, photosynthesis in the case of the tree and the grass, digestion and growing hair in the case of the horse and dog. Life is defined by death; your cells must die to keep you alive. If they did not die when and where they are supposed to die — then you would die before you even have a chance to grow. Some birth defects are caused by genetic mistakes in the system of how cells are supposed to die during growth and development.*

*(Editorial – If God created life, then that’s how He made it. It seems curious to me that we love God for creating life and at the same time we hate death. The fact is that without death the whole system would crash, and there would be no life as it exists on earth. We don’t have to prove that – just imagine all the ants crawling all over everything.  Life works because of how it works, and it does not make sense to love the one that gives us life and hate the same one who gives life to the future. We will not make our lives better by trying to change the most basic natural laws that give us life. First, we can’t change them, and second — do we love God and his creation or only our own bodies?)

But, back to our description of how things work to make life. Life is also defined by reproduction. All living cells are made by the replication of cells that are already living. This is one of the unique qualities of life on earth, that all life comes from life, and every living cell must contain the code of life. Humans have 36 pairs of chromosomes in the nucleus of every cell (except a few odd cells have none, like red blood cells that live off the other body cells). One of the biggest jobs of the cell is to make an exact copy of each of its chromosomes just before it divides to make a new cell, so the new cell can also have 36 pairs of chromosomes with the exact code of “me.”

DNA Replication is the process of replicating (copying) the DNA that is in the chromosomes. It happens in each cell just before the cell divides to make two cells. It happens in the following manner.

The long DNA code is composed of the nucleotides C, G, A, T as described in the previous post. DNA is referred to as “double-stranded” because the code side of the strand is paired up with the copy side of the strand. C pairs with G and A pairs with T.

So, if a very short piece of code might be

CGCTATCAGT (covalently bonded in series)

Then the copy strand, also covalently bonded in a series, would be

GCGATAGTCA

And the two strands are joined across the middle by weak energy bonds and they are wound up around each other. The two “backbone” strands of the DNA plus some proteins and some RNA make a chromosome.

When the time comes for the molecule to replicate, there is a set of enzymes in the cell that causes the weak bonds that are between the two strands to separate. The two strands to come apart in a controlled fashion. There are always nucleotides available in the nucleus of the cell, where the DNA is sequestered, and the nucleotides always want to pair in the same way. This is because of the specific shapes of the four different nucleotide molecules, they attract each other. C pairs with G and A with T. The two strands come apart in the middle, but they can not break the covalent bonds that keep them fastened end to end. When the strands come apart, for example when the C and G separate across the middle, the C molecule will attract a G molecule, while the G from the other strand will attract a new C molecule from those available in the cell. In this way, each side (each strand listed above in this example) attracts a new “other” side until each has a new other half of the molecule.

CGCTATCAGT attracts
GCGATAGTCA

And the same with the other strand

CGCTATCAGT attracts
GCGATAGTCA

As the new nucleotides slip neatly into their places, the enzymes in the nucleus use energy to make the strong covalent bonds of the “backbone” of each nucleotide strand. (The energy to do work in the cell comes from cellular respiration that is discussed in chapter one, available as a pdf on the right side of this blog. The energy is passed from one chemical reaction to another in the form of energy bonds that are controlled by enzymes.)

Then the two strands wind around each other and attract all the other components of the chromosome. The result is the cell makes an exact copy of each strand of each chromosome. At this time the cell containes twice as many chromosomes as normal. Then, when the cell divides, each now cell will contain one copy of each chromosome.

DNA Replication (part one)

DNA = the molecule that carries the code of life from one generation of cells to another.

DNA Replication = the process inside every cell (almost) of making an exact copy of the DNA that will be passed on to the next cell to maintain the genetic code of life. Replication is copying exactly.

DNA replication is the bottom line of genetics and heredity. We inherit genes from our parents. Those genes carry the instructions for every process that is regulated within our bodies. That includes the “uphill” processes that can’t happen without adding energy, and many of the “downhill” processes that must be controlled. The genes are the key to how we are alive. Besides genetics, we also require energy and materials to maintain life.

Energy is required to be alive because energy is the ability to do work and work is any action that is “uphill” relative to the Second Law of Thermodynamics. Energy is discussed in chapter one of Bare Bones Ecology that is available as a PDF from the right side of this blog. We could not live without energy that is provided by plants.

Also we could not live without the materials (nutrients) of which we are composed, that is mostly carbon, oxygen, hydrogen, nitrogen, a selection of other kinds of atoms, and of course water. Recycling of nutrients is discussed in previous blogs that will become chapter two.

Life is not so different with regard to energy and materials. Energy and atoms are available everywhere in the universe, but life is different in the kind of information it uses to run all the living processes — breathing, cellular respiration, photosynthesis, thinking, seeing. Everything. This is the most remarkable thing about life. It maintains the conditions that are necessary for itself to be alive, and life does this using the genetic code. The genetic code is made of organic molecules (called nucleotides) that the living cell puts together in just the right way, based on the code they receive from previous living cell(s). Today and in the Thursday post, we describe in a general way how this code is passed from one cell to the next.

The code has been passed forward from one generation to the next from whenever life began. We may not have the details about how life began, but we definitely know how the ecosystem, the organisms, and the individual cells are set up to transmit the genetic code from one generation to the next.

The best evidence of our understanding of anything is the ability to do it, and as you know, scientists and corporations are now “genetically engineering” organisms to have special characteristics that are not natural to them. This is done by adding new genes to the genetic code, and it is changing the cells and the organisms and the ecosystem, because this is the code that runs all of life on earth.

So it is good for us to know how the code works at all the levels of the ecosystem and ties the whole ecosystem together as one whole living process.

The genetic code is carried in chromosomes. Each chromosome is one giant molecule made of four different little nucleotide molecules that are fastened together end to end in a code. We will explain the specific code in a later post. The names of the nucleotides are commonly abbreviated A, T, C, G, as we explained last post. The DNA molecule is enormous, but it consists of the sequence of nucleotides. I will use an imaginary example code:

A-T-T-C-G-C-C-G-T-A-G-A-A-T-T

Because of the shapes of the nucleotides, there is a front end and a back end to the DNA molecule. For this example we will make-believe A is the front end of the molecule. The nucleotides are fastened end to end with very strong “covalent” energy bonds, that were originally created with the help of enzymes. Although mistakes can happen in the code, very rarely, normally the strong covalent bonds can not be created or broken without the help of enzymes. This maintains the code in a specific sequence so it can not spread all around like dominos scattered on a table.

This huge molecule is all folded up and kept safely in the nucleus of the cell. Remember the code of life also directs the functions of the cell. It does this by turning genes on and off at the right times in the right places. Turning on genes does not change the strong covalent bonds that fasten the ends of the nucleotides together. Turning on genes does not use the ends of the nucleotides; instead it uses their front sides. To prevent this happening at the wrong time and place, the cell has a way to block the front sides of the nucleotides with other nucleotides all the time, unless a particular gene is being used (how it is used – we will get to that later. This process also is regulated by enzymes, so it is important that the whole DNA molecule kept quiet and safe when not needed. Therefore the molecule must be maintained inert (inactive) most of the time. This is done by the DNA molecule being double-stranded.

The diagram above shows only one strand. We have already said that each nucleotide can bond very firmly to the next with strong covalent bonds, so the code is maintained in sequence for generation after generation. The nucleotides also have another relationship with each other. It turns out that the cytosine molecules are attracted to guanine molecules by a set of weaker energy bonds on the front side of both molecules. And the thymine molecules are attracted to adenine molecules, also by a set of weaker bonds. So a complete DNA molecule is double stranded. The sequence of nucleotides is the complete genetic code for the organism it is in. The inverse copy stays parallel to the code copy, attached to it by a zillion weak bonds, and it blocks the functions of the code copy of the DNA

A-T-T-C-G-C-C-G-T-A-G-A-A-T-T
T-A-A-G-C-G-G-C-A-T-C-T-T-A-A (and so on for millions of nucleotides)

The cell keeps this whole thing folded up inside its nucleus and saves it, so there is a complete copy of your own unique genetic code stored inside the nucleus of every cell in your body (except a few specialized cells like red blood cells).

And likewise every other living thing in the ecosystem, but of course their code is somewhat different from yours. All the codes contain the information that is necessary to maintain life, such as the ability to do cellular respiration. All the codes also contain information that is different from one individual to another, such as the color of your skin.

The code is very safe in there, and it can’t do any processes until the time and place when those processes are needed to sustain your life. And then it is the enzymes that control what happens. But before we talk about using the code to maintain life, we need to finish describing how it is passed from generation to generation over all of the history of life. That will be Thursday post.