Cellular Biology as Evidence for God.

Cell biology fascinates me. Understanding this aspect of life leads one to conclude on many other aspects of life. This includes purpose, plan, and providence of the human race.

One of the very first lessons in biology is the ‘cell theory.’ It states that all living things are composed of a functional unit of life known as the cell; a microscopic biochemical entity composed of all the necessary systems required to carry out the functions of life. Cells are defined in a number of ways. It is called the smallest unit of life capable of replicating itself.  Also, the building blocks of life.

Human skin cells stained for contrast.

 

Actual surface view of individual cells that make up your skin.

No such simple description is sufficient to describe the incredible complexity and sophistication of the cells regulatory “intelligence” in managing the affairs of life. Minimally, cells are capable of feeding, defending, moving, removing wastes, communicating, repairing, duplicating, often hibernating, attacking, performing thousands of chemical reactions and sensing the environment around them.

A free living amoeba – a single celled animal that moves, feeds, and reproduces.

Some cells are autonomous units; functioning as independent living beings like bacteria and protozoa (animals) and the protophyta (single celled plants like algae). Even in the multicellular animals like ourselves, composed of some 12 trillion cells, there are many autonomous cells programmed to function for the health of the individual. These move about the body sensing invasion of infective cells or damage to healthy tissue or they knit the body back together after injury.

Blood smear. Red blood cells contain no nucleus. The larger cells are neutrophils, one of many kinds of white blood cells.

This is in contrast to the cells that take up residence in the construction of tissues, organs and organ systems such as bone, muscle and brain. The human body is composed of at least 200 cell types with specialized abilities to secrete, stretch, conduct electronic impulses, insulate, store food, and detoxify the body; just to name a few of these abilities.

A single celled plant. Free living, mobile and green.

 

A nerve cell, the neuron. Note the central body that houses the nucleus. Projections are the filaments or axons that conduct impulses to other nerves.

At the subcellular level cells house the chemical reactions that govern these and many other ‘life’ functions. These chemical reactions are term biochemistry as they are unique to life and not found outside the biology of living cells. The biochemistry of cells include the information and regulatory chemistry that controls all other processes and governs such functions as reproduction (cell duplication).This information is stored in the chemistry of the DNA molecule. Proteins facilitate the growth, repair, and manufacture of all cellular features. Proteins are most accurately described as the molecules that translate the information of DNA into the activities we recognize as ‘living.’ DNA is localized in the nucleus of eukaryotic cell types like those that make up our bodies.

The cell is made of many specialized features. The nucleus contains the DNA. The nucleolus inside the nucleus assembles ribosomes for protein synthesis.

The code for assembling proteins is embedded in the DNA itself and must be transcribed into an intermediate molecule in order to communicate to the cell what is to be translated into chemical activity. The intermediate is much like the DNA molecule in that it too is a nucleic acid composed of similar and complementary subunits of nucleotides. This ribonucleic acid or RNA functions as a copy of the DNA code that can be read by specific cellular machines in a way that translates the code into the functional entity of a protein. Both the transcription of the DNA code into RNA molecules and the translation of those molecules into functional proteins occur due to the activity of a multitude of proteins. All of these proteins are coded for in the massive storage library of the DNA molecule.

Tiny molecular machines: the ribosome has two subunits. It reads the code of RNA and translates the code into functional proteins.

The biochemistry of the reactions that proteins carry out is complex as are the proteins themselves. One of the most complex of biochemical activities is found in the creation of the molecular machines responsible for the process of translating the RNA code into proteins. The ribosome is responsible for this process. The components of this giant biomolecular machine are encoded for by the DNA molecule as well. The ribosome is composed of both RNA and protein. RNA in this case does not function as a code for protein but rather as a framework for the assembly of nearly 100 other proteins and protein factors that cooperate in a coordinated fashion for this assembly. In this article, we look at the current knowledge of how the cell assembles the ribosome. This knowledge though incomplete at this time reveals a highly regulated and very specialized process of biogenesis for ribosome assembly. The details of this manufacturing process are fascinating and placed in the context of cellular life makes one ponder the origin of such an ingenious machine let alone the impressive regulatory process by which it comes into being.

Top to bottom. Double strands of DNA hold the code for the production of the RNA molecules that make up the ribosome backbone. Notice a single strand of RNA is made from the large ribosomal gene and then it is cleaved into smaller RNA strands. These create the backbone for the large and small ribosomal units.

The ribosome is one of many thousands of such machines distributed in specific locations within the cell. It is a complex machine made of two major units; the small subunit and the large subunit. When RNA is made available for translating protein the two subunits combine to facilitate the process of protein manufacturing. The smaller of the two subunits is made of an RNA molecule and 33 different proteins. The larger of the two is composes of three different sized RNA molecules and at least 46 other unique proteins.

Illustration of the copying of DNA into RNA by an RNA polymerizing enzyme.

 

 

Example of the complex folding of the ribosomal RNA molecules into predetermined three dimensional configurations. Many proteins will attach to the backbone of RNA to create a subunit for the ribosome.

One of many things we know little about is what drives the cell to make more ribosomes. Cell division, growth and signals such as hormones trigger the DNA inside the nucleus to begin to make more ribosomes. But the details of this process is not well known.
What is known is the incredible coordinated regulation of the production of each of the components that make up the subunits of the ribosome. When biogenesis begins, a flurry of activity occurs in a localized area called the nucleosome. This specialized region houses the genetic instructions of the DNA sequence for the RNA molecules inside the nucleus of a cell. Here the nucleosome coordinates the processing of the RNA from transcribing it from the DNA template to modifying the RNA to form its correct structure. It does this in collaboration with the entry and attachment of the ribosomal proteins into the nucleus in a coordinated fashion for proper assembly of the ribosomal subunits.

This is not a cell. It is a diagram of the nucleus within a cell and within the nucleus is the nucleolus that assembles ribosomes.

Remarkably, there are a number of specific enzymes which create the RNA molecules of different types; some RNA is transcribed for protein production by one type of RNA polymerase protein and several other RNA enzymes transcribe only the DNA sequences that code for ribosome RNA. These specialized proteins recognize the DNA sequences for the RNA molecules that will eventually become the backbone of the two ribosome subunits. The read the sequence and polymerize the RNA molecules into existence from nucleic acids manufactured by other protein enzymes in the cell. As the ribosomal RNA (rRNA) is made, a multitude of small RNA-protein complexes (up to 75 unique complexes) and more than 200 other protein molecules coordinate the modification of new RNA strands; making chemical changes, folding the strands, exposing regions for proper ribosomal protein binding and facilitating the three dimensional structure of what will become one of two subunits of the functional ribosome.

Cut away diagram of the RNA polymerase enzyme and its many cofactor proteins that collectively recognize the RNA gene and create a copy of the gene from the DNA code into RNA.
The double stranded DNA molecule is seen in the center of this complex of proteins.

As this activity occurs in the nucleolus of the nucleus many proteins and assembly factors are transported through pores in the nucleus to the sight of ribosome synthesis. The protein fractions of these factors are formed of course by functional ribosomes in the regions of the cell outside the nucleus. They are made precisely and in numbers that are exactly required for the number of ribosomal units being made and must be transported to the nucleolus for incorporation into the subunits or to facilitate the coordinated assembly of the many and varied associations with the rRNA backbone. For this reasons there must be many feedback mechanisms regulating the gene activity for the nearly 300 proteins involved in actually assembling into the ribosome or coordinating proper folding and configuring of the giant molecular machine.

From the time of ribosomal RNA transcription to mature ribosomal subunit the assembly of the various protein constituents of the ribosome is coordinated as the maturing unit is moved through the nucleolus to the nucleus and finally pushed through the nuclear pore into the cell’s cytoplasm. Once outside the nucleus the subunits shed their various assembly collaborators and float freely waiting for the hint of RNA transcripts which call for protein translation. As RNA transcripts are release from the nucleus the small subunit migrates through as yet unknown mechanisms to the site of the RNA which now acts as the messenger of the DNA molecule. Contact of the RNA transcript with the small subunit aligns the message with the translation start site and this calls for the merging of the large subunit with the small unit. Like hands in gloves the ribosome begins to read the transcript three nucleotides at a time which aligns much smaller carrier RNA molecules called transfer RNA molecules into a sequence of alignments; each transfer RNA (tRNA) carrying with it a specific amino acid. As the tRNAs align along the messenger the amino acids they carry are put into proper sequence as the coded message calls for.

Assembly and maturation of ribosomal subunits as they move from the nucleolus through the nucleus and to the cytoplasm of the cell.

This allows the ribosome to act as an enzymatic conveyor belt connecting each amino acid in proper sequence as the messenger RNA (mRNA) is fed through the two subunits like film strip; each frame specifying a particular amino acid with which to connect to the growing chain of amino acids. When the code is translated the ribosome stops adding amino acids to the growing protein, releasing it to the cell where it will take up residence in some particular reaction or possibly become part of some large molecular device involved in transporting nutrients into the cell or degrading sugars to creating useable energy molecules or neutralizing some toxic chemical.

The ribosome is so complex that it becomes difficult even for a diagram to show how the many proteins are bound to specific sites on the ribosomal RNA backbone. ES = the specific binding site for a protein.  The numbering of proteins indicates the order each protein binds to the RNA backbone. If the order is not followed the ribosome is rejected and then degraded… it fails the quality control measures of the cell’s nucleus.

How the nucleolus is able to control the entry of ribosomal proteins into the processing steps of ribosomal biogenesis is not known. What is known is that the addition of each of the nearly 100 proteins making up the ribosomal subunits must be done in a specified sequence in order to produce a functional translation unit. Consider how a computer is built. With prefabricated parts like memory chips, central processors, microphone, camera, and ports for USB, landlines, Fire Wires or fiber optic cables, each part must be added in a sequence of events for the unit to work as a whole. The computer will translate radio waves or electrical signals into sound and video. It translates one signal into other kinds of signals.

Computer parts.

 

Intelligent assembly of computer parts into a functional unit.This is the role of the ribosomes which number in the thousands in a mature cell. They will take a molecular signal and translate it into a completely different form of chemistry. And just as the computer is governed by the rules of assembly and has a quality control inspector to determine if the final unit is fully functional, so too the ribosome is govern by rules of assembly and before it is released into the cell for the task of genetic translation, certain protein factors will release only those matured and properly assembled ribosomes to the cell. If the ribosome is defective, it is dismantled and its components recycled. Literally, each ribosome is put through a dry run by assembly factors before being licensed for use by the cell.

 

Once commissioned ribosomes are able to function at breakneck speeds with extremely high fidelity. Tens of thousands of proteins can be made in minutes once a cell has been signaled to begin protein synthesis. This is accomplished by the 2000 ribosomes generally available at any one time to translate the RNA code into protein.
To summarize, ribosomes are assembled from their genetic blueprints in an intricate and tightly regulated way. Specialized regions of the nucleus exist to coordinate the assembly of the two units of the ribosome and when finally matured, the quality of the particle, as well as the amount of active ribosomes, is checked. There is much molecular cross-talk and genetic feedback with the ongoing protein synthesis for the components of the ribosome. The ribosomal components are produced and their synthesis is regulated according to growth rate, nutritional status, and signals from hormones, foods, or nervous signals.

All of these activities are regulated autonomously by the genetic material of the cell. Quite remarkable is the fact that DNA by itself is only a library of information. Without proteins, cell membranes, RNA, and a thousand control biological reactions, the DNA is just stored information; a blueprint in a filing cabinet.
The idea that such a molecule exists which governs the existence of other molecules like RNA and protein which in turn govern the biochemistry of the DNA molecule is beyond physical explanation. The elaborate mechanisms for precise coordinated regulation of the genesis of molecular machines like the ribosome, a particle that can read genetic information and translate it into functional protein molecules, each having specified roles to perform in the myriad reactions we know of as life, is beyond fascinating; it is phenomenal. Such activities cannot arise from the chemistry of physical science. Such precision and complexity demonstrates the existence of deliberation and forethought. Such a system does not function unless the whole of the biological chemistry exists at once.

The phenomenon of life!

 

There is nothing evolutionary about the biochemistry of life. Instead, the understanding of such information demands any honest mind to admit in the existence of an intelligence or intelligence’s not of this universe. This is because the fundamental laws of this universe do nothing to explain the miracle of life. We can understand how a protein enzyme breaks down starch to sugar molecules or how hydrogen bonds hold the double strand of DNA together. But nothing in this universe explains how the information for creating a living being came into existence in the molecule of DNA. Nothing in the universe explains how the uniqueness of biochemical reactions came to be compacted into the microscopic unit of life we call the cell. Nothing in the universe explains how a single cell can grow into a human being of 12 trillion cells or 200 cell types and house the existence of personality.

 

We are special.

 

These things are beyond science. They are beyond nature. They are the product of something super natural. If such things exist which have no conceivable explanation by the governing laws of the universe, to be honest and remain sensible we must accept that we are not alone and we never have been; that there is a metaphysical answer to our questions. There is something far more than just material existence. There must be deliberation. There must have been planning. There must have been therefore a cognition not of this world. Whatever was, must still be, and that means there is a plan for that which is.

 

For me the greatest quest in life has not been to understand biology but to understand the meaning of biology. Life is the proof that a creator exists. And if this exist then what is the plan, what is the purpose? Suddenly morality has meaning. Ethics become important. Life has a goal. Human existence has pleasure and more; it has joy. There is hope in the darkest of our days. There is a freedom to grasp life to the full and to revel in existence; to seek that which is good and to know the difference from evil. There is a light that shines in the darkness and the darkness cannot overcome the light.

 

 

Love becomes the all in all and the purpose for our self-awareness. Such an awakening allows one to have gratitude in daily living and a honest expectation that the future is filled with goodness. Even when this life gives out, we will not end. It makes no sense otherwise. Any other conclusion is a denial of reality or must be an ignorance of the facts of life.

 

Design demands a designer.

 

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