DNA: Evidence for the Master’s Blueprint – Part 1

Family differences - not anything evolutionary.

Family differences – not anything evolutionary.

In this article, a history of the science leading up to the discovery of the DNA molecule and its encoded message for building life forms is considered. The history leading up to these many discoveries is amazing in many respects.  The synergy of scientific procedures and improvements in technology through time must be credited for the advancements in our understanding of molecular biology.  Our current knowledge of how biochemical molecules govern life was not led by any support from the evolutionary theory.  Each discovery was the result of a hypothesis, a proposition, or set of propositions, set forth as an explanation for the occurrence of some specified group of phenomena, either asserted merely as a provisional conjecture to guide investigation testing from deductive reasoning of previous research work or derived from experimental results.  Today, published research typically forces the data into the evolutionary paradigm.  Creativity and classic scientific methodology are not welcomed.

An honest reflection on the complexity of

Encoded Complexity!

Encoded Complexity!

life is independent evidence for a designer.  Not simply because life is tremendously complex, especially at the molecular level, but because this level of complexity defies natural processes no matter how they are combined.  No kind of chemistry exposed to heat, light, earth, electricity, water or time will create the kinds of molecules about to be discussed.  As a genetic engineer familiar with the purification, manipulation and recombination of such molecules as DNA, I am forced to the logical conclusion that life is the product of someone far more intelligent than me.  I am forced to admit that biology is a product of super-natural forces and intellectual planning.

Biological science has a long and fascinating history. For several thousand years people wondered about the origin of life and mechanism of inheritance, that is, how do living beings reproduce after their own kind; giving rise to the same form but with variations not seen before. A simple example may help explain. If you have brothers and sisters like I do, somehow we are all the same and

Variations in humans - no evolution here!

Variations in humans – no evolution here!

somehow we are all different. My older brother is 6’2”and he has brown eyes and brown hair, he is slim and bony but with great long muscles attached to those bones. We have a lot in common. We like the same things, the outdoors, music, and reading and of course coming from the same family we share a lot of history.  My brother looks like my uncle on my mother’s side. My older sister is 5 foot two and, well, she’s a girl. Her hair is brown her eyes brown; she looks like my mom. Then my little sister, she has a very fair complexion. She does not suntan; she burns. She’s 5’4″ and her hair is an auburn red. She is covered with freckles. She has always had to wear glasses to see well. And me? I think I was adopted. I have blonde hair, blue eyes, I am 5’10, and I am built like an early Neanderthal. I like to read. I like music. I love to grow plants and of course I do share the same history with my siblings.

So what makes us different? What are the factors that come together to create differences in people? What are the inherited factors that make some plants tall and some plants short? Why are there pink roses and red roses and yellow roses and coral colored roses and orange roses? How is it that some horses are born to run and others are born to pull a plow? Why is it that every time a dog gives birth, it gives birth to a puppy and not a kitten?

We might go back before the year 1859 to consider some ideas that at one time or another dominated the world’s thinking but let’s start with Charles Darwin whose publication On the Origin of Species came out that year.

In his book On the Origin of Species by Means of Natural Selection, Darwin understood that small variations could be seen in the offspring of every species. Although he did not know where the variation came from, he supposed that the small variations could potentially improve the success of the survival of the offspring under certain natural conditions and this could somehow continue to modify future offspring. Given enough time the accumulation of thousands if not millions of variations could result in a creature so vastly different from its ancient parentage that it represented a new species Thus he proposed that species might not have come into being as any special act of a Creator God but have arisen by the inheritance of modified characteristics.

Bird from dinosaurs?

Birds from dinosaurs?

This would only occur if the variations that arose added some survival benefit to the specie. Charles did not know how to distinguish a good variation from a bad variation only that the present forms of living things seemed to be perfectly adapted for their lifestyle; food supply, type of movement, ability to communicate and reproduce with its own kind and such.  This perfection he suggested was the product of millions of generations of nature selecting for the most fit variations.  Those variations then became somehow a permanent feature of the living being and this gave it the appearance of being designed to fit into its environment when, from Charles’ position, it was by chance and nature’s demands on survival that “created” these adaptations.  Ultimately, the complexity of living things and how they survive in the world were seen as the product of an mindless, random, evolving process.

In the year 1866 Gregor Mendel published the results of his investigations on the “factors” that controlled the variation in the garden pea plant.  Through rigorous study of his garden plants, Mendel was able to show that there was a consistent and fixed inheritance of traits such as the color of the flower, how tall the plant grew, whether the seeds were round or whether they were wrinkled. For the first time in history someone had demonstrated that variation could be tabulated, measured and experimented with, yet Mendel’s work went unnoticed.

It wasn’t until the year 1900 that Mendel’s principles were rediscovered in independent research and this is when the modern study of genetics began.  Most important to Mendel’s work is the unchanging fact that variation within a specie was fixed.  This means variation could be seen, traced through lineage, and that breeding efforts had a predictable outcome.  Interestingly, the science of genetics has since validated all of Mendel’s work and added volumes to the consistency, predictability and predefined

Mendel discovered the laws of heredity, debunking Darwinian evolution.

Mendel discovered the laws of heredity, debunking Darwinian evolution.

mechanisms of genetic inheritance by which these fixed ‘factors’ give rise to variation in the living beings of any kind.  Credit is given to Mendel as the discoverer of the Law of Inheritance; an unbreakable, consistent and predictable Law that explains how fixed variations of the characteristics of living beings are inherited.

Flemming was the first to view chromosomes in a configuration associated with the division of a cell (mitosis) and began to realize that this material may be associated with inheritance.

Chromosomes -stained properly they are visible when cells duplicate.

Chromosomes -stained properly they are visible when cells duplicate.

A few years later, 1902, Walter Sutton was able to show that there was a interrelationship in the study of cells and their shape and what was now called Mendelism or genetic heredity. Using the microscope, other researchers in 1905 through to 1910, demonstrated the existence of the sex chromosomes; the X and the Y.  Those organisms that were born having two X chromosomes were female.

Chromosomes determine gender.

Chromosomes determine gender.

Other scientists showed that some human diseases were due to the inheritance of inborn errors of certain proteins inherited from their parent. Others studied the simple fruit fly known as Drosophila. And it was shown for the first time that some changes in variation were linked to chromosomes. In the years to come a new proposal was put forth known as the gene theory; that each specific change or variation that was inherited from a parent was due to a gene. Yet no one knew exactly whether a gene was composed of a protein, or DNA or a whole chromosome or was some other chemical acting as the genetic factor -yet to be discovered?

Combined with chemistry and microscopy and using X-radiation, mutant forms of corn and fruit flies as well as bacteria could be produced. No improvements in any of these organisms were observed; only that the traits that were normally inherited under controlled and consistent conditions could be altered in ways that could be measured.  Those genetic factors could be destroyed and cause disease and, if not fatal to the first generation, could be inherited according to Mendel’s Law.

Throughout those first 50 years of the 20th Century, from 1900 to 1950, most of the scientists studying genetics were under the belief that it was protein that carried the genetic characteristics from parent to offspring; since proteins give function to the living organism. Along the way a very sticky molecule known as deoxyribose nucleic acid (DNA) seemed to act as a skeleton for the ‘genetic proteins’ that scientists were interested in. Most important to scientists of the time was to understand how inheritance could be transmitted to the offspring? It was thought that proteins might be the genetic message but what was this nucleic acid (DNA) doing there? Was it simply a scaffold that carried the proteins from sperm and egg to create a new individual?

Label proteins were not the genetic material.  Labeled DNA was responsible for the blueprints that make bacterial virus'.

Label proteins were not the genetic material. Labeled DNA was responsible for the blueprints that make bacterial virus’.

In 1952 Martha Chase and Alfred Hershey used radioactive sulfur to label proteins and radioactive phosphate to label DNA (click on the image and follow the DNA- the red string is radio-labeled DNA which instructs the infected cell to produce more virus) and they proved that it was the DNA molecule, not proteins that transmitted the genetic information, in this case, to make more viral particles.

It was DNA that held the genetic factors that were transmitted from generation to generation. What a breakthrough! This scientific evidence began to make sense of the importance of the chromosomes.  It was those long, sticky, polymers of nucleotides that contained some sort of information that could be duplicated and passed from cell to cell and from sperm to egg to produce a new individual.

In the year 1953 two scientists by the names of Francis Crick and James Watson had solved the three-dimensional structure of the DNA molecule. They showed that two strands of the DNA polymer aligned in opposite directions of each other and were held together by weak electrical charges found in the linear arrangement of the subunits that made up the polymer like beads on a string.  They further showed that this interaction caused the two strands to rotate along the length of the molecular strands forming what has now become the known as “the double helix”.

Double helix of DNA.  Strands run in opposite direction of each other but perfectly complement each other through the weak  molecular bonds that hold the code for the blueprints for life.

Double helix of DNA. Strands run in opposite direction of each other but perfectly complement each other through the weak molecular bonds that hold the code for the blueprints for life.

In the years to follow other researchers were able to show that when new cells were produced, DNA was replicated in a semi-conservative way. This means that when DNA replicates, each of the strands of the double stranded DNA serve as a template or photocopy for the new strand.  The two strands separate, each strand is replicated and the two new cells have a double helix composed of an original DNA strand and a brand new copy of that old strand.  This was termed semi-conservative replication.

In 1958 Arthur Kornberg had purified an important enzyme known as DNA polymerase 1. It was shown that this enzyme was responsible for creating the DNA duplex from a pool of nucleotides, the individual units of the “beads” that make up the strand of DNA. Some previously made DNA was also required as a template for making the DNA into a duplex of DNA.  This was done in a test tube, verifying the semiconservative nature of DNA replication and showing that proteins were responsible for replicating the DNA molecule.

Multiple proteins collaborate to duplicate the DNA molecule. Each new strand is composed of one original DNA molecule and one newly synthesized strand of DNA.

Multiple proteins collaborate to duplicate the DNA molecule. Each new strand is composed of one original DNA molecule and one newly synthesized strand of DNA.

 

In 1966, still other molecular researchers cracked the genetic code. They showed that the long string of nucleotide polymers that make up the DNA molecule, when transcribed into the RNA molecule, created a message. The message specified or directed the cell as to how to make a protein molecule. The alphabet that the RNA used was not like the alphabet that we use to create words. To create words we use an arrangement of 26 letters, each letter a single symbol. Collectively, a number of these symbols when aligned in a linear fashion create a meaningful word. But in the genetic code, when 3 of the 4 nucleotides that make up the substance of DNA are aligned in the proper order, they make a single symbol or “code” for each one of the 20 essential amino acids that are used to create proteins. The 3 letter nucleotide which represented the symbol for an amino acid was commonly called the “triplet” or  “codon”.   Sixty-four codons are possible from the alignment of the 4 types of nucleotides that make up the genetic molecule.

All 64 codons are recognized to have function. Many of those codons are be used for the same amino acid. Some of the codons did not code for any amino acids, rather they created information that told the cell to “stop” adding amino acids when creating a protein.  In other arrangements of nucleotides much longer that the 3 letter codon, alignments of nucleotides have much, much more to say to the cell.

From 1966 and throughout the next 40 years scientists learned to manipulate the DNA molecule. Many other enzymes were found that bound to the DNA molecule. Some of those proteins were responsible for winding up the DNA molecule. Other proteins were responsible for unwinding the DNA molecule. Other enzymes could digest the DNA molecule and others could recombine the DNA molecule.

The letters for the 'alphabet' of DNA language.  Triplet nucleotides sit side by side.  Each triplet is interpreted by the cell as the code for an amino acid.  Each amino acid has more than one code.

The letters for the ‘alphabet’ of DNA language. Triplet nucleotides sit side by side. Each triplet is interpreted by the cell as the code for an amino acid. Each amino acid has more than one code.

The real secret discovered by Watson and Crick was that the DNA was to be found as a double helix. This means that DNA, acting as a chromosome, was composed of two long, linear polymer chains. One of these chains ran from left to right and one of these chains ran from right to left. In molecular biology the terms right and left are not used; rather, one strand of DNA runs 5′ (5 prime) to 3′ (or 3 prime). The other strand of the molecule of DNA runs 3′ to 5′. Though the 2 strands run in opposite directions they complement each other in a way that each strand is the exact opposite copy of the other strand. They bind together through weak chemical attraction much like magnets stick to metal. But as they bind they tend to wind to from a “helix”. This is the secret of genetic inheritance.

When DNA is replicated, proteins open the double strands that complement each other and begin to replicate each of the two strands using the DNA polymerase protein. A number of other proteins control the overall process of replication. Very quickly, the two strands of DNA become four strands of DNA; a single double helix becomes two double helices-two identical blueprints for cellular life. One chromosome becomes two chromosomes.  When each helix of DNA becomes two double helices of DNA, the cell divides. When the cell divides each cell gets a copy of the DNA; the cell “inherits” a copy of DNA.  This molecule was found to be the master code; able to control the functions of life through a molecular blueprint encoded in the subunits contained on the complementary copies of molecule.

Each new cell formed under the control of DNA will have a copy of this “coded” information. In reproduction, each new cell formed under the control of DNA “inherits” the genetics of the parent(s). This is true of bacteria. This is true of moths and of oak trees and of human beings. The master code of DNA controls the development of a living being through a complex blueprint of instructions.  In sexual reproduction, the DNA from sperm and egg “recombine” the information from each of the two parents.  This creates molecular variations in the DNA.  This is one of the genetic mechanism that give rise to visible differences like eye color or invisible traits like the ability to digest milk sugar.  There are a fixed number of genetic variations within a type of organism. Though the variation in facial features in humans seems endless, humans always give birth to humans. This fixity in reproduction of specie is known as the Law of Biogenesis; that life only proceeds from life.

Among a number of known and fixed genetic events, when sperm or an egg are formed (these are called the gamete cells) DNA may be exchanged between chromosomes creating variation, but not new information. The picture shows a "cross-over" event leading to DNA recombination.

Among a number of known and fixed genetic events, when sperm or an egg are formed (these are called the gamete cells) DNA may be exchanged between chromosomes creating variation, but not new information. The picture above shows a “cross-over” event leading to DNA recombination event in the chromosomes that will be carried by sperm to egg.

The DNA molecule that holds a blueprint for each type of living thing is filled with enough information to fill a large library. This is quite remarkable. Not that just one master code exists to produce a human being, but that there are blueprints to produce a dog, a chimpanzee, a red oak, and an earthworm, a cardinal, a blue whale, the now extinct Tyrannosaurus rex and the dodo bird, a clam, a house fly, a horse, a chicken, a salmon and an octopus.

The variation that I spoke of earlier, the differences between my brother and myself and my two sisters are due to control processes in the cell during the formation of sperm and egg. None of this normally has to do with mutations. Mutations are either detrimental to genetic information or they are neutral to genetic information. In the 160 years since Darwin first proposed evolution, no one has ever found a mutation of any plant, bacteria, human being, or any other living organism on the planet that has added new useful information to that organism. Such new information would be called “a gain of function”. That is, the mutation if it is to be useful for natural selection to occur, must have added to the information content of the DNA molecule. This is what is required for evolution to occur.

Now remember, when I speak of evolution I do not speak of the variation between my sisters, my brother and myself. I speak of the process that was supposed to have taken molecules and through millions of years of some naturally occurring selection process to produce a human being. This process of evolution, often called macroevolution, has never been seen to occur. Most scientists who have an objective opinion understand this, even though that opinion may remain silent.

 

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