Part 10 – A Closer Look at DNA and Closing Thoughts
Scientists have discovered that DNA has approximately 20,000 protein-coding genes which are used to yield the 70,000 – 87,000 protein variations which build our body's anatomy and drive our body's processes. Some proteins are assembled completely by following the gene encoding, while other variations are generated by splicing the protein-coding genes. Some variations are made by first assembling a protein from the instructions in the DNA, and then modifying the protein afterwards (post-translational modification). Scientists have identified approximately 400 ways the human body modifies generated proteins to yield variations of proteins that are needed in the body. The National Library of Medicine article, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5837046/, explains techniques of post-translational modification.
DNA not only stores the coding for proteins in our genes, but also has coding for the regulation of the reading of the coding for these proteins. Some molecules are generated from DNA which help to regulate which genes are expressed in which cells and at what times. These molecules can turn genes off and on and control the rate in which gene portions are copied. For more information on the controls over gene expression, see this article by Bouchard: https://medium.com/the-philipendium/is-dna-like-a-blueprint-a-computer-program-or-a-list-of-ingredients-1484b34a9121
Scientists see flexibility encoded in DNA; part of its coding allows for variation and reorganization as seen in the varied B-cell generation. DNA is fluid in certain ways, making changes suitable to environmental factors. The cell has molecular tools that are used to act upon the strands of DNA to cut, splice, activate, and deactivate portions of the DNA for its benefit. The cell has organelle systems and chemical cascades in place to manipulate the DNA and vary the genes or gene expression for the organism's survival. This article from the National Library of Medicine, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4280507/, delineates some of the molecular chemistry involved in DNA modifications.
DNA's epigenome consists of the chemical compounds that modify or mark a cell's genome to control gene expression. The epigenome can change which genes are expressed to promote the organism's survival. The epigenome can also be influenced in ways alter gene expression and cause a negative effect on the organism. Sometimes scientists have observed DNA change to secure the momentary survival of a species, but in the end the species is left with less variability in another feature. In other words, for a present-day benefit, a self-imposed DNA change is made that results in less variability in code, which later results in a reduced survival rate. An introduction to epigenetics can be found in this CDC article, https://www.cdc.gov/genomics/disease/epigenetics.htm, and this National Library of Medicine article, https://pubmed.ncbi.nlm.nih.gov/19127539/.
When a cell copies DNA, the cell has systems to check for and repair copy errors. But copy errors can still occur. When the error results in more than one or two amino acid changes, it almost always results in protein dysfunction. Occasionally a beneficial outcome is observed. But even when a beneficial outcome is observed, it most often results in loss of information and loss of system flexibility over time. This article by the National Library of Medicine explains the types of mutations and their results on proteins, cells, and organisms: https://www.ncbi.nlm.nih.gov/books/NBK21114/#:~:text=Mutations%20result%20either%20from%20errors,that%20occur%20(Section%2014.2).
If a mutation occurs in a switch to a master gene, then we can observe massive changes in the organism. But the changes we observe are the result of affecting a switch and a gene that are already in place. Different features can be turned on and off by master genes, but still the system encoding was already present in the DNA, and we are only seeing the effects of changing the switches.
All of these facets of DNA are quite amazing. DNA is not just a read-only recipe book; it is interactive with control loops and a multilayered control network of protein regulators distributed throughout the body. And as amazing as all the control and modification features are, the features are observed to continue or enhance survival within the framework of the system which is already built. The framework allows for modification, but stays within the bounds already built.
For example, the generation of varied B-cells in the human immune system involves very specific DNA splicing and alteration by molecular tools that identify specific genes to target for increasing the organism's survival. However, the result is still B-cell factories which have been more finely tuned for the present need. DNA appears to be able to adapt its instructions to yield survival outcomes, but this adaptation seems to be confined to specific variation within the operating framework.
Closing Thoughts
The human body is steeped in complexity. When I zoom into the molecular level, I see the chemical cascades that occur in literally every cell organelle, every body organ, and every system of the human body. The level of function observed, the resulting system achievements, and the coordinated anatomical and molecular multisystem interdependence is mind-blowing.
For example, looking into the human eye and visual cortex, we see the unique materials, the controls, and the chemistry are encoded across thousands of genes, and yet, are so intricately coordinated, that to me, it begs the question of the how likely is it that so many varied components could appear in proximity, in compatibility, in proper sequence of utility, and yield a result so astounding... human sight.
Human reproduction is incredibly intricate in coordination of details and timing, and dependent upon multiple systems for creating structures and supplies. The growing embryo/fetus is constantly changing, and the mother's organ systems respond in great orchestration to meet the baby's newly developing needs. Each varying step is steeped in chemistry; we saw there were eight pages of chemistry required to move the sperm and assist its union with an egg.
The interlocking cell types of our immune system are created in several different body systems and work in conjunction with the circulatory system to defend our body against invaders. The B-cells use a targeted replication technique that involves specific splicing and reorganization of genes to yield a more successful defense.
We have seen that each body system requires not only a vast and specific list of proteins, but also, each of these proteins must have a molecular address label for delivery, a maintenance crew for transport, enzymes for activation and regulation, and a by-product waste management system. And the DNA that encodes for these proteins and enzymes is far more than just a list of these protein codes. DNA also has coding for regulating the reading of its code and generating components for epigenetic control.
Whether evolution occurred through random mutations or unknown biological laws interacting with environmental and cellular conditions, I have to ask myself what does it really mean to say that the human body is the result of evolutionary changes.
Starting with mere atoms and molecules of chemical elements, some condition must have caused the first self-replicating organism to form. When we investigated one of the first fossilized organisms, bacteria, we learned that even bacteria are not a simple step from nonliving chemicals. Bacteria are complex and coordinated machines. Therefore, even the generation of the components of bacteria require complex and highly organized, sequential events.
Evolution must not only create the first DNA-like structure, but also must generate a method of its self-reproduction. As seen in one of the links about bacteria, self-replication in bacteria is complex and multifaceted. Then whenever code was altered and expanded in DNA, each new resulting protein must have been successfully integrated. Today we see this involves an accompaniment of transporters, regulators, waste managers, and even DNA copy regulators and often protein modifiers.
Each protein generated into DNA must fit into existing chemical cascades; new proteins must not only be able to combine with a precursor output, but also serve itself as a new input that can lead to a beneficial result. These changes must replace simpler precursor systems to build up to the complex, multilayered dependent systems we observe today.
When I look at the specifics of one of our body systems like the eye, or at the system-wide integration of our body systems with the circulation system, then these evolutionary requirements take real form. Even if the earth started with an enormous array of different bacteria with differing genes, each of today's organisms' organelles, cells, organs, chemical pathways, and systems must be stepwise generated, with every precursor being functional and reproducible.
Whether I consider the path of building the 20,000 protein-coding genes in our human DNA which results in anatomical marvels, intricate chemical cascades, and exquisite functions, or I consider the path from bacterial cell replication to a system of male and female organs, a placenta, and multisystem-wide dependence, the number of stepwise functional changes that must be conceived is astounding.
Because these changes are written in the language of amino acids, we can study the likelihood of various amino acid sequences resulting in functional proteins. The observed probability for copy changes to yield new sets of operational, compatible, and system-functional proteins is low. This low likelihood of success has to be considered every time a precursor organism encodes a new protein in DNA.
Furthermore, as precursor cell and organ types are developed, newly generated proteins must not only be operational, compatible, and functional, they also have to replace independent functionality with the systemwide dependence we see everywhere in cells and organs and organisms. Evolution of the human body requires the generated encoding to repetitively result in function, increasing complexity, and multilayered dependency. The brief investigation into uterine birth and the circulatory system gives a tangible example of how much function and multisystem dependence is required.
The human body has another feature which I find even more astounding than all the outcomes and functions we have looked at in this journey. We've already briefing seen that our brain controls and interprets many of our body organs. But our brain is also able to retrieve stored data. Retrieving stored data requires having a code for storage, hardware in which to store data, an operating system, a way to write code, and programs that retrieve and manipulate the data stored.
If we evolved, DNA alterations would have to not only yield the anatomical structure and chemical control of our brain, but also develop of a system of data storage, coding, retrieval, manipulation, and evaluation that interacts with our consciousness.
Today we observe changes caused by biological events. However, beneficial changes caused by biological events which result in an increase in complexity, information, and/or dependence, is extremely rare. And the quantity of iterations of beneficial changes needed to produce the human body would have to parallel the complexity and dependence present today. This would require a multitude of multiplications of very unlikely events.
When I study the results of copy changes in DNA which we observe in the body today, I see that it is highly probable that a change results in dysfunction. Personally, the effect of nature alone observed in the world today does not give me evidence to choose to believe that nature alone could result in the multiplied unlikely probabilities of encoding our DNA and yielding the outcomes we observe in the human body.
In Calculus, the limits of functions are studied. The limit of a function can be understood as the value or behavior the function tends to approach under certain conditions. For example, if a function continually approaches zero as the number of inputs increase, the limit of the function, as the inputs get increasingly large, is defined to equal zero.
After I have taken a closer look at the world around and within me, I can imagine sketching a graph of a function representing the probability that nature alone has caused the world I see. The more inputs I learn about, the closer that probability function approaches zero. After studying the molecular biology of our bodies, the possibility of nature alone resulting in the world around me, has to me, become a function whose limit is zero.
I see a world that is filled with astounding function, with beauty, with multisystem multilevel coordination, and with intricate coding that results in survival. I am aware of my being and see an astounding orchestration of design in my body. All these things together have convinced me that I am more than just the undirected result of molecular reactions in the vast test tube of the universe.
I then, therefore, must seek to find the Designer of the world of which I find myself to be a part.
Suzanne Dawson
In the preface of my book, What's It All About? I have written about part of my journey that led me to the One I have found is the Designer of our world. This book can be found under the Products and Services option above. This short book takes a narrative journey through the key events recorded in the Bible. It is my hope that this might help you on your search to understand our world and find the answers to its many questions.