3: What is Life?

Chapter Three: What is Life?

When Charles Darwin was born, people had taught and accepted for centuries that a creator created all plants and animals as separate entities. For many centuries, the religious views had been required, with an aggressive inquisition hunting down people who were thought to be non-believers, with those who were convicted often executed. By the mid 1800s, the religious repression was being relaxed, somewhat, and people who had other views were not being hunted down and punished. But most people in Europe still accepted the basic premise behind the religious teachings. They believed that all of the plants and animals on Earth had been created pretty much as they were at the time. There had been no change.

In 1859, Charles Darwin published ‘Origin of Species,’ a book that challenged this premise. Darwin proposed that it is possible that all life on Earth had a common primordial origin. The change happened over a very long period of time; through a process he called ‘natural selection.’ Here, he explains the idea that got him into a great deal of trouble with the people who accepted the standard view:

On the principle of natural selection with divergence of character, it does not seem incredible that, from some such low and intermediate form, both animals and plants may have been developed; and, if we admit this, we must likewise admit that all the organic beings that have ever lived on this earth may be descended from some one primordial form. (Link to source, Origin of Species by Charles Darwin.)

In popular parlance, this is called the ‘theory of evolution.’ Scientists call it the ‘universal common ancestry’ theory, or ‘UCA.’

In the early 2000s, the invention of mechanical gene-sequencers allowed scientists to test Darwin’s theory. All life on Earth is based on a molecule called ‘deoxyribonucleic acid’ or ‘DNA.’ The DNA has sequences of ‘codons’ that contain the codes that DNA uses to build the proteins and other complex molecules needed for life.

Qqqq DNA sequencing image

If different organisms had different origins (in other words, if they weren’t all descended from some one primordial form), these complex molecules would have been determined by various different DNA codes in different organisms. In other words, the code that related the sequences of atoms that go together to make the proteins to the ‘steps’ on the DNA would be different. Scientists can sequence genes from widely divergent organisms, say the Treponema pallidum bacteria that causes syphilis, on the one hand, and chimpanzees on the other. They can then compare the sequences. If the different organisms had different origins, we would not expect the codes to be the same. We would expect different codes to be used to create the same atomic structures in the different organisms.

This is a testable theory. In the early 2000s, Douglas Theobald and a team of researchers at the University of Colorado obtained funding to use advanced gene sequencing techniques and statistical analysis to test the UCA theory: They published their findings in 2010. They found that the coding mechanisms used for the various proteins in the different life forms were not just similar; they were identical in all living things they tested. They used standard tests to determine how likely this is to be a coincidence. Here are their findings, from their paper:

UCA is at least 102,860 times more probable than the closest competing hypothesis. Notably, UCA is the most accurate and the most parsimonious hypothesis. Compared to the multiple-ancestry hypotheses, UCA provides a much better fit to the data (as seen from its higher likelihood), and it is also the least complex (as judged by the number of parameters). (Link to source.)

What does this mean?

The sequences were identical. This might be a coincidence, or it might indicate a relationship existed between the different beings. They could use standard statistical tools to determine how likely the observed results were to be a coincidence. In this case, they found that the odds against a coincidence were 102,860 were to one against. In other words, if you were in a position to create DNA based life in separate events, and put together the DNA of different organisms in separate acts, without any attempt to make the different DNA based beings match each other, you would have to do this 102,860 times before you would wind up with one set of beings that has the observed similarities as a result of random chance.

To put this into perspective, scientists have determined that there are about 1082 atoms in the entire universe (Link to source.) There have been about than 1017 seconds since the big bang. If life could come to exist by random processes as many times as there are atoms on the universe, and this happened anew once each second for all of the time that has passed since the big bang, life would have come to exist a total of 1099 times. If you had 102,760 identical universes, each of which is the same size as our universe, and conducted this test that many times, only once in all of these times (only on one atom in one second in one universe) would random chance cause the genes to align as we observe.

This basically means that the mathematical probability that Darwin’s theory (the universal common ancestry theory) is wrong is zero, or a number so close to zero that there is no difference in practice from zero. All beings on Earth share a common ancestor.

Where Life Came From: ALL Possibilities

We don’t know exactly when this common ancestor lived but we do know it must have lived here more than 3.58 billion years ago, because we have evidence of some life—clearly descended life existing as of that date.

There are only four possible ways that the universal common ancestor could have come to be on Earth when it arrived:

1. It could have evolved from some non-living thing here on earth.

2. It could have been intentionally created here on Earth.

3. It could have evolved or come to exist spontaneously somewhere other than earth and found its way to Earth, with no intention being involved.

4. It could have been created intentionally somewhere other than Earth and then sent here.

In order to understand exactly why the first four options are not possible, we need to understand a little bit about the way the process we call ‘life’ works, from a mechanical perspective, in all things that are ‘alive’ here on Earth.

I want to warn you in advance that the information that follows is intellectually challenging. I have spent a great deal of time learning it, many years in fact, both in university classes and through independent study in very difficult and challenging fields. I will condense this information a great deal and simplify it as much as I can, so you can see the general ideas needed to understand the essential points of this chapter. If you find this kind of analysis interesting (and I hope that you do; there is a great deal more work that could be done in all of the fields discussed below), the internet provides a treasure trove of information and virtually any university in the world will have classes in the key fields from which this information is drawn. I have tried to make the discussions as simple as possible, given the topic, and expect that most people should be able to get it if they are willing to go through it slowly.


First a little physics:

Before 1905, scientists only had theories to tell them that the things called ‘molecules’ exist. There was no proof. Scientists had never seen molecules, or done any experiments that allowed them to tell if molecules really existed.

In 1905, Albert Einstein got a paper published called ‘Investigations on the theory of Brownian movement.’ In this paper, Einstein presented mathematical evidence that the movement of pollen grains that were suspended in water, called ‘Brownian motion,’ could be explained by collision with tiny ‘particles’ of water. The math showed that, if water formed itself into ‘particles’ with one atom of oxygen and two of hydrogen, the weight of these ‘particles’ colliding with pollen grains would be exactly enough to account for the observed motion of the pollen grains.

This was seen as proof that molecules existed and were real things.

Over the next few decades, analysis of molecules advanced a great deal. The next great milestone came in 1939, when Linus Pauling published the book ‘The Nature of the Chemical Bond and the Structure of Molecules and Crystals: An Introduction to Modern Structural Chemistry.’ This book used various different tools to show how nature puts atoms together to form molecules. Pauling’s book explained how to determine the exact distance that the atoms were from each other, and the angles that separated them. It explained how to calculate the bond ‘strength,’ or the amount of force holding the atoms together and the amount of energy needed to separate them.

This passage is from the jacket material for this book:

For the first time, the science of chemistry is presented as the natural result of quantum mechanics operating at the level of the chemical bond. Observable chemical properties such as melting point, boiling point and bond strength resulted from molecular structure; molecular structure resulted from the bonds that held the atoms in position; and the bonds resulted from the quantum nature of the atom.

With this information, researchers could begin to make scale models of molecules for the first time. They could and did get tiny balls made of some porous material (Styrofoam) and sticks, and physically put them together. Pauling’s book explained how far apart the atoms must be, and the exact angles of the bonds. Scientists could put together even very complex molecules as if assembling a puzzle.

Prior to the 1953, the term ‘deoxyribonucleic acid’ or DNA simply referred to an acidic substance of the nuclei of cells. By the 1950s, researchers were starting to realize that DNA was no ordinary substance. DNA formed itself into shapes that could be seen under microscopes as very complex. It reproduced itself to make exact copies of these shapes in incredible numbers. There are more than 5 trillion cells in your body; each of them has an exact copy of the DNA that is your genetic code.

DNA appeared to be a truly enormous molecule, one that clumped together into collections of atoms so large that they can be seen with microscopes (we can see ‘chromosomes’). DNA appears to have special properties that no other molecule had. Researchers began to try to figure out how DNA could do the seemingly impossible things it did.

In 1953, three researchers at the University of Cambridge in England, Francis Crick, James Watson, and Maurice Wilkins, used calculations in Linus Pauling’s book to make physical models of the components of DNA. These components are called ‘amino acid bases:’ they include adenine (abbreviated A), cytosine (C), guanine (G) and uracil (U). After they had models of the bases, they worked out ways to fit them together to see if they could make a model of this complex molecule.

They found that they only fit together in a very specific way only, a way that explained the special properties of this molecule.

A could only bond with U and U could only bond with A. G could only bond with C and C could only bond with G. These bondings created something called ‘base pairs.’ The ‘base pairs’ then became something that looks like the rungs of a ladder that takes the shape of a double helix.

Qqqq dna model left.

The chemical bonds holding the base pairs together in the middle are very weak. (Technically called ‘hydrogen bonds,’ they are a kind of ‘semi bond,’ which is not nearly as strong as true chemical bonds.) The bonds that hold the atoms that make up the side rails of the DNA ladder are very strong and the bonds that hold half of the rung of the amino acids to the side rails are very strong, but the bonds the center of the rungs of the ladder together are very weak. This allows the ‘ladder’ to split in the middle; under the right circumstances, it will ‘unzip’ almost like a zipper, turning the molecule into two ‘half ladders.’

Note about Thiamine and Uracil:

These are basically two names for the same amino acid. You will find some texts use Thiamine (T) and some use Uracil (U) for this acid, leading to some confusion. Most commonly, when talking about DNA texts call it ‘Thiamine’ and when talking about RNA (the ‘half ladder’) they call it Uracil. There are tiny quantum mechanical differences in these molecules, which is the reason they have different names, but these differences don’t affect anything that would have any impact but the most ardent quantum mechanical researchers. (I think that many scientists like such complexities, as it makes their field seem far more complex than it really is, allowing them to impress people more easily.)

Each rung of the ‘half ladders’ can only bond with the appropriate other ‘base amino acid,’ as described below. A can only bond with U, U can only bond with A, and so forth. Once a DNA molecule has split into two ‘half ladders,’ molecules found in the nuclei of cells can then ‘rebuild’ the two half ladders into two brand new ladders.

Human DNA has about 3 billion ‘rungs’ in its ladder. In the new ladders, the rungs are identical to those in the old ladders, with each of the 3 billion ‘base pairs in the exact same sequence in the new ladders as in the original one.

The new molecules (‘ladders’) are exact clones of the original.

You could think of the information in the DNA as like a coded message. If you start with a ‘half ladder,’ each ‘half rung’ will be one of the four ‘amino acid bases,’ either A, C, G, or U. There will be 3 billion ‘half rungs.’ The sequence of the ‘letters’ in the genetic code is used (as we will see shortly) to create the physical molecules needed for the processes we call ‘life’ to take place.

This coded message can make exact copies of itself. Under the right circumstances, each of the coded messages can turn into a new independent living thing.

Crick, Watson, and Wilkins discovered these things in the spring of 1953.

This was an amazing discovery.

But even more amazing discoveries were to come.

The Second Coded Message In DNA

There is also a second, far more complex code within DNA.

This code is responsible for producing the ‘worker molecules’ in living things, called ‘proteins.’ Proteins are very complex molecules that do things in life.

Hemoglobin is one example of a protein. The hemoglobin molecule is red in color; this is what gives blood its distinctive color. Hemoglobin is a complex molecule that has the ability to ‘soak up’ oxygen when it passes through the lungs. The hemoglobin then carries that oxygen to the cells of the body, which all need oxygen for their life functions. When a red blood cell containing oxygen-saturated hemoglobin gets to cells that need oxygen, it releases the oxygen and sends it through the cell wall. The cell then sends carbon dioxide (a waste product of metabolism) back through the wall. The hemoglobin inside the red blood cells then ‘soaks up’ the carbon dioxide. The red blood cells then travel back to the lungs where the hemoglobin releases the carbon dioxide as air (which you will then exhale). The entire process then begins again.

Hemoglobin is one of more than 2 million different known proteins in the human body.

All of them have to be manufactured by the body; none of them can come from food:

The reason for this is that all proteins are far larger than the openings in intestinal walls and can’t get through from food to the bloodstream. It is true that you can eat proteins. But these proteins can’t go directly from your food into your cells. In your intestines, bacteria break down the proteins into amino acids (which all proteins are made of). The amino acids are small enough to get through the intestinal wall. Once they are there in the bloodstream, your body sends them to cellular factories that ‘reassemble’ them, through the process described below, to make the exact mix of new proteins that your body needs.

These new proteins do the ‘work’ needed to keep your life functions going.

The second code in DNA is the code the body uses to reassemble the amino acids as needed into new proteins.

Researchers have found that there are exactly 20 amino acids in all living things on Earth. (You will find them all listed in the table below, marked ‘the genetic code.’) No living thing has more or less than this. The DNA ‘codes’ for these 20 amino acids in a very specific way that Crick, Watkins, and Wilkins discovered and catalogued in the fall of 1953.

Here is the short version of how this process works (you can find as detailed of explanations as you want on the internet):

If your body needs a protein, certain worker molecules (proteins) go to the DNA molecule and split the ‘ladder’ into two ‘half ladders.’ One of these half ladders then ‘grabs’ the amino acids needed to reproduce itself and turn it back into a full ladder. That replaces the original molecule. If it is needed again, it is there to be used again.

Now you have a full DNA molecule (the replacement) and a ‘half ladder.’

The ‘half ladder’ is called ‘messenger RNA.’ It holds the ‘messages’ needed to make the proteins. Each set of 3 rungs on the messenger RNA is called a ‘triplet’. For example, if there are three ‘rungs’ that are each made of Uracil, the triplet is UUU. There are 64 possible triplets. (In other words, 64 possible three letter combinations, where each of the letters may be one of four amino acids.)

The chart to the right shows all of the possible combinations. Each three-letter combination corresponds to one block in the chart, and each block contains the name of 1 of the 20 amino acids. (Note that there are 64 possible combinations but only 20 amino acids, so each amino acid is coded by more than one triplet; in some cases there are 2 and in some cases 3.)

This relationship, between the ‘triplets’ of letters and 20 amino acids, is called ‘the genetic code.’

Qqqq genetic code here.

Crick, Watson, and Wilkins discovered the mechanism living things use to manufacture the worker molecules needed for life processes to take place. Here is how it works:

A specialized protein called a ‘ribosome’ ‘grabs’ onto three of the ‘rungs’ of this half ladder. The ribosome then ‘reads’ that triplet and ‘decodes it,’ figuring out which of the 20 amino acids it represents. For example, if it ‘sees’ UUU, it knows that the required amino acid is Phenylalanine; if it ‘sees’ UUA it knows it needs Leucine. (You may want to refer to the chart to the right to see that these are the corresponding molecules.) Once the ribosome ‘knows’ which amino acid is required, it ‘grabs’ that particular amino acid from its surroundings, where all of the 20 amino acids are available. It ‘attaches’ the required amino acid to the three ‘rungs’ it is ‘holding.’ It then ‘walks’ down another three ‘rungs.’ It ‘reads’ the code to see which amino acid is called for; it ‘grabs’ that amino acid, and it ‘attaches’ it to the three ‘rungs’ it is ‘holding.’ It then walks down the ‘ladder’ again to get to the next three ‘rungs’ and does the same thing.

At a certain point, it will come to a code that tells it that the protein is finished. At this point, the ribosome will work with several other proteins to ‘cut’ the long chain of amino acids loose from the ‘half ladder’ of messenger RNA. After the new protein has been removed, the messenger RNA (the ‘half ladder’ that we started with) is available to make another protein, if another is needed.

This leaves a long chain of amino acids in the right sequence that is floating in the cell. This is not a finished protein yet, because all proteins are 3-dimensional molecules and this is just a long chain. The protein is a worker; it can’t do its job unless it has been ‘folded’ into the proper shape by other worker proteins. Every atom has to be in the exact right position for the molecule to do its job.

Specialized proteins come in to ‘fold’ the chain into the required shape. Now the protein is finished and can be sent out to do whatever job it was designed to do.

Here is an example so you can see how this works: Hemoglobin is a protein. It has exactly 137 amino acids. These amino acids are coded in 438 of the 3 billion ‘rungs’ in your DNA. Each 3 ‘rung’ combination (triplet) represents 1 of these 137 amino acids. If your body needs hemoglobin, it signals to the cells to make some. Proteins divide a DNA molecule into two ‘half ladders’ (if there is none already divided) and ribosomes begin making the 137-link chain. Once the chain is complete, other proteins cut this chain loose from the half ladder (allowing the half-ladder to make another hemoglobin molecule, if necessary).

The hemoglobin molecule is not finished yet. It is a 3 dimensional molecule and can’t work as a chain. Other proteins then ‘fold’ this hemoglobin into the required shape.

Now the hemoglobin molecule is finished. Your body needed the hemoglobin to make red blood cells, the only cells in the body that use hemoglobin. Bone marrow is the only place in your body that makes red blood cells, so the hemoglobin and all of the other proteins needed to make red blood cells must be transported to the bone marrow. Once all of the parts needed to make red blood cells are available, the marrow makes them. It then sends the blood cells out into the blood stream to start their working life.

Your body replaces all of its red blood cells every 90 days, so the old cells are constantly being removed from the body and replacement blood cells are being made. To supply the needed hemoglobin, your body makes millions of molecules of hemoglobin (by the above process) every minute of every day you are alive.

Hemoglobin is one of roughly 2 million different proteins that your body needs to operate. They are all made the same way. A single strand of DNA contains all the information needed to make every one of these proteins.

This is not a theory.

A theory is a guess about how something might work by people who don’t fully understand the exact mechanism. People make such guesses and then test them. Once they have tested the theories and confirmed them, the information is called a ‘fact’ not a ‘theory.’ The mechanism discussed above has been thoroughly studied. It happens this way.

This is the way life works.

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