Introduction to the Mathematics of Evolution
In the next chapter we will begin our detailed discussion of how DNA fits into the issue of evolution. But first, it is necessary for the reader to understand what a "protein" really is and how proteins are made in the body.
Think, for a minute, about a wooden rocking chair. If you look at the individual parts which make up the chair you will see the 4 legs, the seat, the structure the person leans back against, the wooden rods to strengthen the back of the chair, the curved wood which allows the chair to rock, and so on.
If you took the rocking chair apart, piece by piece, you would see several different kinds of wooden patterns which are put together to make the chair.
There are hundreds of different kinds of cells in the human body. Each type of cell in the human body has many structures in them which can be compared to a rocking chair. Each of these cell structures are made up of smaller structures, much like a wooden rocking chair is made up of smaller wooden rods and other pieces.
In a cell, the individual parts of the chair can be compared to proteins. The entire structure of the chair might be called a "protein structure." The pattern to make the different designed parts of the chair (i.e. protein structure) come from sections of DNA called "genes."
For example, let us consider the "ports" in the cell membrane through which food and other things pass into the inside of the cell. Essentially a "port" is a hole in the side of the cell membrane. However, it is a "hole" which is made of proteins which are bound together to form a structure.
The "port" is a protein structure which is made up of proteins with different shapes. The DNA includes the templates which are used as patterns for making the different shaped proteins used in each port.
Just like a person would look at a blueprint before starting to build the individual pieces which make up a wooden rocking chair, the body turns to the DNA to find the blueprint (i.e. template, pattern or cookie-cutter) to make the pieces (i.e. proteins) which make up the structures inside of cells (or on the surface of the cell or outside the cell).
Protein synthesis, or protein biosynthesis, is the process by which the genetic information in DNA (deoxyribonucleic acid) is converted into proteins. All of this occurs inside the cells. The term "proteins" in this context includes proteins, enzymes and some other complex molecules which are made from polypeptides, which will be discussed below.
A gene is a pattern, or cookie-cutter, or blueprint, which is used by the cell, during protein synthesis, to make the individual proteins needed by the cell. The DNA is the starting point for making proteins.
DNA is like the blueprint of a building, however, DNA also includes the blueprint for the construction of the building, including the supervisors (supervisor proteins), the laborers (laborer proteins), the messengers (messenger proteins), etc., all of which are functions accomplished by proteins inside the cell.
The DNA does not become the proteins, rather it is used like a "copy machine," it simply allows other molecules to "copy" its patterns over and over again.
As one example, in certain kinds of bacteria there is a protein structure called a flagellum. The flagellum is like a long tail which sticks outside of the bacteria cell, by which certain bacteria swim around. It is a large protein structure. The "motor" which turns the tail is inside the cell. Both the motor and the tail are made of proteins.
However, this large protein structure is made up of smaller protein structures. Taken together, this large structure has been compared to an outboard motor engine for a speedboat.
Here are some of the smaller protein structures which make up the flagellum, which is itself a large protein structure:
Hook (similar to universal joint)
Filament (similar to propeller), meaning the long tail
Rod (similar to drive shaft)
S ring and M ring (similar to rotor)
Bushing, L ring and P ring
Stator, studs and C ring
Inner (plasma) membrane
and so on.
The point is that each of these smaller protein structures are made up of individual proteins, which came from patterns on the DNA.
Building this large protein flagellum requires supervisors; just like building a skyscraper would require supervisors. The supervisors who oversee the construction of the flagellum are proteins.
The workers which actually put the proteins in place, as they are built, are also proteins. The accountants who tell the DNA which proteins to make next are also proteins. The messengers who provide information to the DNA for repairing damages to the structure are also proteins.
The entire process by which the flagellum is made is done by proteins, even the communication processes are accomplished by proteins.
The process by which these patterns on DNA are used to form proteins is the subject of this chapter on protein synthesis.
The terms used in this chapter will be used freely in subsequent chapters, so it is important to understand the process of protein synthesis, especially the last step.
While the process of protein synthesis may seem complicated, in reality this chapter is a highly simplified overview. An entire book could be written on all the complexities and exceptions which occur in different organisms with regards to protein synthesis.
This chapter will describe what goes on in a eukaryotic cell and especially in bacteria.
Step One - Phase One of Transcription
Transcription is the actual act of using the DNA as a template to create a new protein.
DNA resides in the nucleus of the cell. DNA consists of about 3 billion "nucleotides," or to be more accurate: 3 billion pairs of nucleotides.
Step one is to convert a section of DNA into RNA, which is a molecule similar to DNA. RNA itself will later be used in the process as a template in the process of choosing the sequence of specific amino acids which will actually make up the protein. It is the amino acids which become part of the protein, not the original DNA or even the RNA copy of the original DNA.
Thus, transcription takes a stationary blueprint (the DNA) and copies it onto a traveling blueprint (the RNA) which will travel to a different part of the cell (outside of the nucleus) where the protein is actually built.
In other words, the DNA will stay in the nucleus, so it can be used over and over again, but the copy of DNA, the RNA, will travel outside of the nucleus and will become the actual pattern which will be used to make the protein.
Transcription, the conversion of DNA into messenger RNA, or mRNA, is actually in two phases.
In phase one of transcription, a molecular machine (called: RNA polymerase) unzips a section of DNA. However it should be noted that RNA polymerase does not act alone. Each type of cell provides different "helper proteins" to help the RNA polymerase do its job for that type of cell.
Starting at one end of a gene, called the "promoter sequence" or "promoter region," and continuing until it reaches the "terminator" sequence, it starts building a type of RNA called "pre-mRNA" (i.e. pre-messenger RNA) or "Nuclear RNA" because it is inside the nucleus of the cell.
In other words, the RNA polymerase "unzips" a section of DNA so that the double helix is now two single-sided helix strands (it unzips only a single section of DNA). The unzipped section is not the entire DNA, only the section of DNA needed for this particular job.
This process picks one of the two sides (a specific side) of the DNA and uses it as a template to make complementary single-sided RNA, namely pre-mRNA.
On a DNA strand, an "A" always has a "T" next to it on the DNA (unless there has been a mutation). However, when converting a side of DNA into pre-mRNA, an "A" is actually paired with a "U" (uracil), as the following chart shows:
An "A" on the DNA becomes a "U" on the pre-mRNA (uracil).
A "T" on the DNA becomes an "A" on the pre-mRNA.
A "C" on the DNA becomes a "G" on the pre-mRNA.
A "G" on the DNA becomes a "C" on the pre-mRNA.
These combinations are called "complimentary" because if you know one of the nucleotides, you automatically know its "complement" (i.e. what is on the other strand).
Thus, DNA has nucleotides: A, C, G, T and RNA has nucleotides: A, C, G, U.
RNA polymerase has been described as a "battery-powered spider" as it crawls along the DNA unzipping a section of the DNA.
The gene portion of DNA, which is what is unzipped, contains alternating sequences of exons and introns. Exons and introns are segments of nucleotides, but like all segments of nucleotides, they have names to identify their functions.
Exons are the section of the gene which will actually "code" for proteins, meaning the exons actually become the finished blueprint for making the protein.
Introns do not code for proteins, thus they do not become part of the proteins, but are thought to be instructions to determine which exons are needed for the specific protein being requested.
For example, the average gene in human DNA can be used to create 10 different proteins. Some genes can create 50 different proteins. It is thought that introns contain the instructions on how to put together these different proteins from the same gene.
In any case, in this step of transcription; both the introns and exons are kept and are put on the pre-mRNA. The pre-mRNA is an exact copy (actually it is a complement) of one side of a section of DNA, except that a U replaces a T. More will be said about exons and introns in the next step.
Step Two - The Second Phase of Transcription
In the second phase of transcription (also called "RNA splicing"), the pre-mRNA is itself copied, and its copy is called mRNA. mRNA is the actual blueprint to make the protein.
In copying pre-mRNA into mRNA the introns are left out of the copying, meaning they are "spliced" out of the RNA and are not part of the mRNA.
Thus, pre-mRNA contains both exons and introns, but mRNA only contains exons.
However, it is also in this phase that "RNA splicing" removes some of the exons. In Step One all of the exons are copied to the pre-mRNA. However, in this phase, not only are all of the introns spliced out, but also some of the exons are intentionally spliced out.
Why are some of the exons left out? The reason is that the DNA is being used to create one protein at a time, even though it is capable of creating ten different proteins (in this example). In other words, there are enough exons to create ten unique and different proteins, but it only creates one protein at a time, thus not all of the exons are used in the creation of a single protein (the protein at this point is still an mRNA).
That is why, in the process of creating a single protein, many of the exons are left out during the second phase of transcription.
It is in this RNA splicing that different patterns of exons are combined together to ultimately be the pattern to create the exact protein which was requested!!
If you think this is simple, consider that some human genes can create 50 different proteins. The exons on the DNA must stay in the same sequence (i.e. order) on the mRNA, but different exons are left out for each type of protein. Try to figure out how to do that in your spare time!!
The intron, as it is spliced out, no doubt provides the intelligence to determine if the exon, which is next to it, is also spliced out or if it stays to become part of the mRNA. This is called "alternative splicing" because different sets of exons lead to different proteins.
Thus, pre-mRNA and mRNA not only differ in the fact that there are no introns on mRNA, but they also differ in that there is only a subset of exons on the mRNA, so that a specific protein can be manufactured later in the process.
Step Three - Moving the mRNA out of the Nucleus
In eukaryotic cells (OK, in most eukaryotic cells) the DNA is protected inside of a membrane called the "nuclear envelope." The nuclear envelope has two layers. The envelope has many ports which are called "nuclear pores."
mRNA is made inside of the nuclear envelope, but processing of the mRNA occurs outside of the nuclear envelope. Thus, the mRNA must travel through one of the nuclear pores. Each nuclear pore is itself built of many proteins.
Ribosomes (to be discussed next), which are also proteins, are also created inside the nuclear envelope in a subnuclear body called the nucleolus. Ribosomes also must pass through a nuclear pore.
So how does a large molecule pass through a nuclear pore? The answer is a "carrier protein." The carrier protein must be able to latch onto the mRNA and guide it through the nuclear pore. This is how one website describes the carrier protein:
"Each carrier protein is designed to recognize only one substance or one group of very similar substances. The molecule or ion to be transported (the substrate) must first bind at a binding site at the carrier molecule, with a certain binding affinity. Following binding, and while the binding site is facing, say, outwards, the carrier will capture or occlude (take in and retain) the substrate within its molecular structure and cause an internal translocation, so that it now faces the other side of the membrane. The substrate is finally released at that site, according to its binding affinity there. All steps are reversible."
Wikipedia - Carrier Protein
Actually, various molecules are constantly passing through the nuclear envelope in both directions.
Step Four - Translation
Once the mRNA is outside of the nucleus it then heads for a section of the cell which includes the ribosome. The ribosome area of a cell is one of the most fascinating areas of a cell. It is also one of the most complex areas of the cell.
The ribosome looks like a large ball of yard. In other words, it looks like a sphere that is made of yarn. This is how one website describes the ribosome.
Ribosomes are among the biggest and most intricate structures in the cell. The ribosomes of bacteria contain not only huge amounts of RNA, but also more than 50 different proteins. Human ribosomes have even more RNA and between 70 and 80 different proteins!
. . .
For many years, researchers believed that even though RNAs formed a part of the ribosome, the protein portion of the ribosome did all of the work. Noller thought, instead, that maybe RNA, not proteins, performed the ribosome's job. His idea was not popular at first, because at that time it was thought that RNA could not perform such complex functions.
Some time later, however, the consensus changed. Sidney Altman of Yale University in New Haven, Connecticut, and Thomas Cech, who was then at the University of Colorado in Boulder, each discovered that RNA can perform work as complex as that done by protein enzymes. Their "RNA-as-an-enzyme" discovery turned the research world on its head and earned Cech and Altman the 1989 Nobel Prize in chemistry.
The New Genetics, Chapter One
It should be noted that the discovery of Cech and Altman also helped the evolutionist cause by helping evolutionists explain that complex enzymes did not need to exist to perform some of the tasks needed for the "first living cell." It you want to win a Nobel Prize, discover something which helps the evolutionists.
Rachel Green, however, later discovered that the RNA nucleotides were not needed for assembling a protein. Instead, she found, the RNA helps the growing protein slip off the ribosome once it's finished.
By the way, ribosomal RNA is called rRNA. There are many different kinds (i.e. functions) of RNA.
Well, now that the history lesson is complete, let us look at what really happens in the ribosome area.
First, the mRNA, which came through the nuclear port, and at this point is as straight as an arrow, is attached to the ribosome. Once attached, the ribosome can do its work.
There are four terms which need to be understood at this point:
First, the mRNA (which contains instructions/patterns taken from the DNA)
Second, amino acids (proteins start as a string of amino acids)
Third, polypeptides (polypeptides are the resulting string of amino acids)
Fourth, proteins (proteins are polypeptides which have been folded into the shape of the protein).
Study that list for a few moments.
Ribosome looks at mRNA three consecutive nucleotides at a time. How many different ways can three consecutive nucleotides be ordered? The answer is 43 or 64. The '4' is the number of different nucleotides and the '3' is the number of nucleotides which are looked at at the same time by ribosome.
Three consecutive nucleotides are called a "codon" or triplets or tri-nucleotide sequences.
Now we have a problem. There are only 20 different kinds of amino acids. We have 64 different codons, but only 20 amino acids. Try to figure out how 64 codons can make 20 different amino acids.
Not to worry, the ribosome can make the conversion. The "dictionary" which controls which codon is matched with which amino acid is called the "genetic code" (though the genetic code is not universal between species).
However, three of the 64 codons do not translate into an amino acid. The codons: UAA, UGA, and UAG serve as "stop-translation" signals, which terminate the making of the polypeptide. AUG can be a start codon or can be made into the amino acid methionine.
Within the cell are free-floating amino acids. A type of RNA called transfer RNA (i.e. tRNA) captures these amino acids and takes them to the ribosome. Actually there is a different type of tRNA for each type of amino acid and each tRNA can correspond to one or more codons.
The ribosome analyzes each codon and then selects the correct tRNA, meaning the correct amino acid is chosen to add to the growing polypeptide. It does this until it reaches a "stop-translation" codon, which tells the ribosome to "stop" the building of the polypeptide and release it.
The rRNA then helps the polypeptide be removed from the ribosome and you then have a free polypeptide.
All of this happens amazingly fast!!
This step of protein synthesis is far more complex than anyone truly understands. But given enough time, scientists will figure it out in even more detail. Much is already known about tRNA, but I will not discuss the details here.
Step Five - The Folding of the Polypeptide
OK, at this point we have a polypeptide which has been removed from the ribosome. We can think of it as being "straight as an arrow" at this point, just like the mRNA was.
But proteins are not straight; they have a very specific shape. Actually, it is the shape of the protein which determines its ability to be integrated into a protein structure. Actually, it is more complicated than that.
Not only is the folding of the amino acids (i.e. polypeptide) important for the protein structure, but also at certain locations on the shape certain amino acids must be located so the different proteins will bind together or repel each other, etc.
In other words, in order for a protein structure to be strong, it must not only have proteins which have the right shape; so they can fit together like a puzzle; but the proteins (i.e. the amino acids) must "stick together" or repel each other, at just the right points. This is accomplished because some amino acids (remember a protein is nothing but a chain of amino acids) bind to other amino acids.
Also, some amino acids repel each other, which is also important in some cases. Some amino acids repel water and other amino acids are attracted to water. And so on. The point is that it is not only the shape of the protein which is important, but also the order and types of the amino acids on the protein which is important.
So how do polypeptides get folded into the proper shape of a protein?
Polypeptides are folded, and in many cases chemically altered, in order to become proteins. A full discussion of this topic is far beyond the scope of this book. Instead a couple of key paragraphs from a book will have to suffice:
The explanation for the cell's remarkable efficiency in promoting protein folding probably lies in chaperones, a family of proteins found in all organisms from bacteria to humans. Chaperones are located in every cellular compartment, bind a wide range of proteins, and may be part of a general protein-folding mechanism. There are two general families of chaperones: molecular chaperones, which bind and stabilize unfolded or partially folded proteins, thereby preventing these proteins from being degraded; and chaperonins, which directly facilitate their folding. Chaperones have ATPase activity, and their ability to bind and stabilize their target proteins is specific and dependent on ATP hydrolysis. Binding of chaperones to partially folded proteins suggests that the folding process could be regulated at intermediate steps.
Molecular Cell Biology, by Lodish, Berk, et. al.
Here is a section of another paragraph:
Proper folding of a small proportion of proteins (e.g., the cytoskeletal proteins actin and tubulin) requires additional assistance, which is provided by chaperonins. Eukaryotic chaperonins, called TCiP, are large, barrel-shaped, multimeric complexes composed of eight Hsp60 units.
Molecular Cell Biology, by Lodish, Berk, et. al.
Suffice it to say: polypeptides are folded, and in some cases chemically altered, as they are converted into proteins.
Note the vast number of critical chemicals that are in your body, such as the amino acids. These come from foods. Now you know why your mother told you to eat healthy foods.
Step Six - Placing the Protein In the Cell
At this point we have the protein (so in a sense "protein synthesis" is complete), but the protein is not in its proper place in the cell yet.
A protein can basically be placed into one of three places:
1) Inside the cell, such as part of a protein structure,
2) Built into the cell membrane, such as a "port," where each port is composed of many proteins, and is itself a protein structure,
3) Placed outside the cell membrane, such as to "bind" to something or as part of a protein structure which extrudes outside the cell (such as the flagellum).
At this point the new protein has to be placed into the proper place. In many cases the new protein needs to be integrated into a complex biological structure, such as a flagellum, which is in the process of being built or repaired.
Guess what? More proteins come into play at this point to guide the new protein into the proper place.
However, at this point we need to pause and reflect.
In Step One above, the RNA polymerase was activated to start the process of converting a gene into a protein. What initiated or ordered the RNA polymerase to create a protein? The RNA polymerase is a puppet, doing only what it is told; so what is the puppeteer which is telling the RNA polymerase what gene to use?
For example, suppose a bacteria cell has just divided and it needs to create a flagellum so it can glide through fluids. Which proteins in the flagellum would logically be created first; the proteins in the base of the flagellum or the proteins in the tip of the tail of the flagellum?
Obviously, the proteins in the base of the flagellum would be created first.
We can compare this to the construction of a tall, one-hundred story building. What if the purchasing agent/accountant for the construction company ordered 20,000 desks to be delivered to the construction site before the foundation for the building was even dug? Would the construction workers be happy about having to navigate through 20,000 desks sitting on the ground as they went to and from the building site? Probably not.
First, you build the foundation, then you build the steel frame, then you pour the concrete for the floors, etc. etc.
Likewise, when a new cell (created by cell division) needs to start construction on a flagellum, it needs the proteins for the base before it needs the proteins for the tail.
The point is that the order of the creation of the proteins is very important. Something has to control which genes the RNA polymerase uses first, to create the proteins.
In the book: The Edge of Evolution, also by Dr. Michael Behe, he describes the creation of the celium and flagellum in certain kinds of bacteria. He describes the various kinds of "control elements," "checkpoint proteins," "boss proteins," "subboss proteins," "helper proteins," the proteins which actually become part of the structure, the switching on of genes, etc. etc. All of these functions are done by different proteins.
It is actually this phase of protein synthesis which controls the first phase of protein synthesis, meaning the order in which the proteins are requested to be manufactured.
It is impossible for this book to duplicate what Dr. Behe has done in explaining the complex processes involved in building protein structures in a cell. The reader is strongly advised to obtain a copy of Dr. Behe's "Edge" book and study chapter 5 in detail. This chapter in this book is only an introduction to the process.
Perhaps in 20 or 30 years a complete, detailed schematic of what happens when the cell has to create a complex protein structure, such as a flagellum, will be written. But for now, scientists are just beginning to see the light at the end of the tunnel.
Do you see a pattern here? Proteins are everywhere in the cell, doing all of the vast number of different complex jobs in the cell. Not only that, it is proteins which become part of the protein structures.
The DNA must contain all of the patterns for all of the proteins in the cell, which include the many different functions and structures which are needed by the cell.
An "irreducibly complex" system is a "complex" system which cannot function until all of its parts are completely in place. Dr. Michael Behe coined the phrase and wrote the book: Darwin's Black Box, which was written about this subject.
Evolutionists do not like Dr. Behe's books because they do not like the concept of "irreducibly complex" systems because these systems imply a "design," which implies a "designer," which is what they really don't like.
But the fact is that protein synthesis (and I have just scratched the surface and given a broad overview) is an irreducibly complex system.
For example, without RNA polymerase there would be no protein synthesis and no proteins. Without ribosome proteins and rRNA there would be no protein synthesis and no proteins. Without a folding mechanism there would be no complex life on earth. And so on.
Science, which fanatically tries to segregate the theory of evolution from a "designer," would say that the protein synthesis of the "first living cell" was simple and that as animals got more and more complex the protein synthesis mechanisms slowly got more and more complex.
What evidence is there for this theory? None. It is pure pie in the sky. There is no "simple" cell on the planet earth. All of these imaginary "simple cells" only exist in the minds of evolutionists. Likewise, a "simple" protein synthesis is also pie in the sky.
Shall we talk about other things that go on inside the cell, such as the mitochondria, ATP molecules, glucose, pyruvate, the Citric Acid cycle, the Electron Transport Chain (ETC), and so on? All of these things are necessary to provide energy in the cell and involve the mitochondria, which, by the way, have their own DNA (though it is very small DNA).
Science has not even proven that a "first living cell" could have formed. Nor has science explained what imaginary protein synthesis existed in the imaginary "first living cell."
The same protein synthesis which exists in human beings also exists in single-celled bacteria. There is no "increasingly complex" protein synthesis in any living thing on the planet earth!! All of it is incredibly complex. The concept of an "increasingly complex protein synthesis" is a pure scientific fairy tale.
While it is true that protein synthesis in prokaryotic cells is a little less complex than in eukaryotic cells; even the protein synthesis in prokaryotic cells is far too complex to have happened by accident. It too, is highly, highly irreducibly complex.
It seems that all of the "evolution" of protein synthesis occurred in a long, long sequence of species which are all now extinct. How convenient. The "evidence" is dead and gone.
Actually, the evidence is not gone. The evidence never existed.
Is the theory of evolution a "proven" fact of science? Considering that there is no "simple cell" on the planet earth, and even evolutionists admit that random events could not create a prokaryotic cell in a prebiotic pool, it would be safe to say that the theory of evolution has no factual basis. It is a "theory," and a very unscientific theory at that.