The Invisible City

Everything that is currently classified as “alive” possesses cells. Bacteria and their kin consist of a single cell, with more complex creatures, such as humans, being made up of trillions. Though the general design at its most basic form is similar amongst the many forms of cells, a great deal of varieties exist, differing not only between the five kingdoms of life, but also within any complex, multicellular organism. Human beings for instance possess some two-hundred types of cells within their bodies,(1) including nerve cells, bone cells, muscles cells, and others. Sidestepping the more derived variations for a moment, let us examine the structure of a basic cell.

Cells come in two basic forms: prokaryotic and eukaryotic. Differing primarily in the structure of their composition and in size, prokaryotic cells lack internal membranes and are a great deal smaller than eukaryotic cells. Additionally, prokaryotic cells are found only in bacteria and their kin, while all other forms of life possess eukaryotic cells. As such, we will focus our examination of cellular structure on that of a basic eukaryotic cell, specifically an animal cell.

Cells have long been referred to as “simple” in their design, with many classical researchers describing them as little more than protoplasmic blobs. With the advent of modern technologies, we now know this to be blatantly false. Upon microscopic examination, essentially any given cell can be seen possessing a great many internal structures, otherwise known as organelles. These organelles function much like the organs of a larger organism, with specific structures performing digestion, maintenance, construction, and a multitude of other molecular functions.

The exterior of our cell, the cell membrane, is more than a simple enclosing material. Known also as a cytoplasmic membrane, it is a selectively permeable barrier, providing ions, gases, nutrients, and other substances passage either into or out of the interior of the cell as needed. Structurally, the cell membrane is composed of quantities of proteins and a thin, self-assembling layer of polarized amphipathic phospholipids, that layer itself possessing various pores, channels, and gates through which ions and other molecules are transmitted. Beneath this can be found the cytoskeleton. Arranged by an organelle called the centrosome, the cytoskeleton is composed of actin-based microfilaments, tubulin-based microtubules, and intermediate filaments composed of as many as seventy other proteins, and it provides necessary support to the cellular superstructure, functioning as a molecular scaffold for proteins and various organelles to anchor too, and providing the foundation for specialized membrane extensions and organelles such as cilia, filopodia, and others. Critically, the centrosome at the apex of the cytoskeleton is itself composed of a pair of centrioles, which separate and engage various actions during cellular division. Thus the cell membrane is far more specialized structure than a simple sack meant to enclose the cytoplasm.

The cytoplasm itself, made up primarily of cytosol (a complicated matrix of cytoskeletal filaments, water, and other molecules), is a jelly-like fluid in which many of the cell’s actions take place as it swirls and flows within the cellular superstructure. Inclusions such as various crystals, starches, lipids, and others also can be found floating within the cytoplasm, being utilized by the cells for purposes of storing energy, fatty acids, etc. Critically however are the vastly important organelles found with the cytoplasm.

Among the most crucial of those organelles is the nucleus. This structure, encapsulated by the double nuclear envelope, is the processing center of the cell, housing the chromosomes and providing a safe place for essentially all DNA & RNA synthesis to occur. It is here where mRNA is synthesized from the DNA, and nearby, in a region of the nucleus known as the nucleous, the ribosomal subunits – which eventually will construct proteins from the mRNA produced in the nucleus – are assembled. The ribosomes produced here can later be found either bound to membranes or free floating in the cytoplasm.

Outside of the nucleus is a network of flattened, sac-like membranes known as the endoplasmic reticula (ER). The endoplasmic reticula (singular: endoplasmic reticulum) come in two forms: rough ER (studded with ribosomes) and smooth ER. Together they are responsible for folding and storing synthesized proteins, ensuring that they are structurally sound, and working in conjunction with another organelle – the golgi apparatus – packing those proteins within transport vesicles, delivering them via the cytoskeleton to other locales within the cellular superstructure, or even beyond, into the extracellular spaces past the cellular membrane.

The Golgi apparatus itself produces another type of organelle known as a lysosome. These spherical, membrane-bound organelles contain over fifty different hydrolytic enzymes, and are capable of digesting essentially any biomolecules within the cellular environment, from proteins and nucleic acids, to sugars, starches, oils, and other materials. Additionally, the lysosomes contribute to a number of cellular functions, including membrane repair, cellular communication, and various metabolic activities.(2) Similar in some regards to lysosomes are the peroxisomes. These are produced by the ER and are used not only for the oxidation of toxic peroxides within the cell, but also to breakdown long-chain fatty acids into a useable form for yet another organelle: the mitochondria.

The mitochondria are the power plants of the cell, providing the majority of the cell’s energy via the generation of the compound adenosine triphosphate (ATP). This of course is only a portion of their overall function, as they are typically involved in other functions as well, including – among others – chemical signaling, the production of cellular heat, the storage of calcium ions, and the regulation of the cell’s life cycle. Structurally, the mitochondria appear roughly bean-like, filled with a series of concentric, folded layers, possessing both outer and inner phospholipid membranes, and several associated matrixes. Interestingly, while the majority of a cell’s DNA is housed within the nucleus, the mitochondria possess their own unique genome, each being organized into circular-shaped chromosomes, and possessing genes encoding for the production of various ribosomal RNAs and a number of tRNAs necessary for the synthesis of specific proteins. In humans, this mitochondrial genome is some 16,000 base pairs in length and encodes 37 genes.(3)

3.07 Diagram of a Generalized Animal Cell.jpg
Figure 3:07- Diagram of a Generalized Animal Cell

While fundamentally similar to animal cells, plant cells differ in the possession of several unique organelles, including a cell wall, vacuoles, and chloroplasts. Cell walls, possessed also by bacteria and fungi, provide additional protection and support to the cellular superstructure. Vacuoles are large, membranous sacs that store water and other materials within the cell, or alternatively can be used as pumps to remove excess water from the interior of the cell. Finally, the chloroplasts are specialized disk-like structures in which solar energy is utilized, through photosynthesis, to produce carbohydrates.

Just from this brief look at the primary components of a generic cell, it should be obvious that complexity abounds. Not just compartmentalized complexity, but intricate, hardwired interdependence! In many cases, this level of reliance goes far beyond what any rational mind could attribute to the random, unguided whims of naturalism. Such requisite interdependence, where the whole cannot exist if even a single component is absent, is known as irreducible complexity.

As author Michael Behe put it, irreducible complexity is “a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.”(4) An amazing example of this phenomenon can be found in the specialized outgrowths of the cellular membrane, cilia.

The cilia are fantastic example of the vastly complex microcosm of interdependency found within a cell. At first glance, cilia appear as tiny, whipping hairs lining the surface of various cells, yet their function depends on the nature of the cells upon which they are found. Those on isolated cells or single-celled organisms beat rhythmically, driving the structure through the fluid environments in which they reside. Conversely, those cilia found upon cells which are bound together, including various tissues within the human body, through the same rhythmic beating that moves individual cells, here instead drives fluids – such as mucus – over the tissue surface.

Structurally, each cilium is a bundle of fibers, anchored within the body of the cell, bound by an extension of the cellular membrane. Individually, those fibers are composed of nine microtubules, each itself built of a pair of fused tubes – one inside the other (Subfiber A & Subfiber B) – of the protein tubulin. Along the inner surface of these outer, doublet tubules, running towards the core of the cilia like the radial spokes of a bike wheel, are a series of projections ending in a bulbous heads (Spoke Head). Each of the outer doublet tubules, connected to their neighboring bundles by the protein nexin, possess two additional arms (the Inner Arm & Outer Arm) composed of another protein – dynein – which functions as a tiny molecular motor, driving mechanical energy. Nearby, within the main, hollow core of the cilium itself, are two additional microtubule rods (Central Singlet Microtubules), each joined to the other near the center by a protein bridge (Central Bridge).

3.08 Cross-section Diagram of a Cilium.jpg
Figure 3:08- Cross-section Diagram of a Cilium

Functionally, the movement of these microscopic appendages is equally complex, starting with bridges of dynein connecting one microtubule to the next. As the ATP-driven process begins, the dynein motors force microtubules to slide past one another until the process is halted by loose bands of nexin, interwoven amongst the microtubules themselves. Though the original sliding process is then stopped by the nexin links, the dynein motors continue driving further movement, causing the microtubule to bend somewhat, shifting and twisting rhythmically. As this motion continues across each cilium, its characteristic beating action is produced, providing the cell or microorganism with the ability to move or otherwise interact with its local environment.

As should be clear, the cilial appendage is extremely complex, both in its construction and its movement, yet despite this complexity, their presence and ability is vastly important to untold microorganisms, cellular systems, and the larger multicellular organisms that possess them. That said, the irreducible complexity of the cilia is undeniable. Remove any portion of the cilia’s construction and the whole system fails. Without the dynein, the structure doesn’t move, lacking its molecular motor. Remove the nexin bridges and the individual microtubules would slide past one another like a load to loosely-bound pipes on the bed of a shaky truck. Even the very arrangement of the cilium’s internal structure cannot be ignored, as its design is critical to the moment of the structure as a whole.(5)

A similar and equally irreducible structure is found in the bacterial flagellum. While the driving force of the cilia can be found in the dynein arms throughout its composition, the flagellum instead possess a singular rotor drive near the base of its protein filament. Forgoing the molecular motors of other cellular structures, the bacterial flagellum instead is driven by a complex of proteins powered by energy produced as acid flows through the membrane of the bacterium. Like cilia however the flagellum is far more complex than casual observation would indicate, possessing:

  • A self-repairing, water-cooled rotary motor with a proton motive force drive system
  • That motor operates at speeds of up to 100,000 RPM
  • It also possesses both forward and reverse gears, and rapid direction-altering capabilities
  • Further, it has an intrinsic signaling system with internal memory

All told, the typical flagellum could not function without the precise interaction of approximately forty proteins!

Mainstreamists will insist that there is a naturalistic explanation for the existence of such structures, yet no adequate explanation has been forthcoming, as any attempt to justify such structures through purely natural, random assembly defies not only hundreds of years of true, scientific observation, but also good, common sense. The intrinsic complexity of these structures and their functions demonstrates that they could not have been happy accidents, built one upon another until the marvelous arrived. These structures are irreducible, and as such, to explain their existence naturally, mainstreamists must account for their complexity as a whole, of how they could arrive complete and functional within the cells that needed them at precisely the moment they needed them. For me, that all seems a bit much now; a bridge too far.

From the complexity of the brick-and-mortar compounds, to the irreducibly complex construction of the cell’s organelles required to maintain the functions of their molecular environment, the true starting point of actual life, the cell itself, is vastly and undeniably sophisticated. Earlier, I equated the mainstream naturalistic origin of life to placing all of the disparate components of a home in a vacant field and waiting for the structure to effectively build and maintain itself. That analogy of course may have been a bit too tongue-in-cheek, yet, in truth, it was far more generous a comparison than that reality demonstrates under observation. In fact, to compare the complexity of the cells and all their functional and structural components to a house is lenient by several orders of magnitude, as the volume of intricacy found in a “simple” cell is more in line with that of a city!

As one observer put it, “Although the tiniest bacterial cells are incredibly small, each is in effect a veritable microminiaturized factory containing thousands of exquisitely designed pieces of intricate molecular machinery, made up of 100,000,000,000 atoms, far more complicated than any machine built by man and absolutely without parallel in the nonliving world.”(6) Another commentator observed that a typical, “simple” cell houses an unimaginable array of incredibly complex and sophisticated features, including:

“…automated assembly plants and processing units featuring robot machines (protein molecules with as many as 3,000 atoms each in three-dimensional configurations) manufacturing hundreds of thousands of specific types of products. The system design exploits artificial languages and decoding systems, memory banks for information storage, elegant control systems regulating the automated assembly of components, error correction techniques and proofreading devices for quality control.”(7)

Say what you will about my comparing the naturalistic origin of life to waiting for a home to construct itself, yet, given the sophisticated construction of a “simple” cell, such an analogy is woefully insufficient as a comparison for the matter at hand, and indeed should give one cause to question what they may believe in regard to the formation of that cell simply by the random interactions of base chemicals and compounds. Even Sir Francis Crick, one of the co-discoverers of DNA and a firm evolutionist, admitted, “An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going.”(8)

Notes & References

  1. “The Cells in Your Body,” Science Net Links, The American Association for the Advancement of Science,, retrieved June 13th, 2015
  2. Settembre, Carmine; Fraldi, Alessandro; Medina, Dielo L.; Ballabio, Andrea “Signals from the lysosome: a control centre for cellular clearance and energy metabolism,” (2013). Nature Reviews Molecular Cell Biology 14 (5): 283–296
  3. Chan, DC, “Mitochondria: Dynamic Organelles in Disease, Aging, and Development,” (2006-06-30),  Cell 125 (7): 1241–1252
  4. Behe, Michael J., “Darwin’s Black Box, The Biochemical Challenge to Evolution,” Touchstone, Simon and Schuster, New York, New York, 1996, pg 45
  5. Behe, Michael J., “Darwin’s Black Box, The Biochemical Challenge to Evolution,” Touchstone, Simon and Schuster, New York, New York, 1996, pages 61-68)
  6. Denton, Michael, “Evolution: A Theory in Crisis,” Adler & Adler, Bethesda MD, 1986
  7. Missler, Chuck, “Elegance by Accident: Chance as the Master Architect,” Koinonia House, June 2000,, retrieved June 23rd, 2015
  8. Crick quoted from “Panspermia,”, retrieved December 31st, 2012

– This was an excerpt fromRemnants of Eden: Evolution, Deep-Time, & the Antediluvian World.” Get your copy here today. God bless! –

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