Biochemical Molecular Machines
Can we magnify life to see splendid machinery at work?
Has humanity become so use to modern technologies that we fail to see the awesome and splendid intricacies of life's systems? And what does this machinery tell us?
What context or unique perspective can help us to see living cells as more than evolution's end product?
How might some quality, structure, function, or characteristic reveal that the cell is much more than simply a smaller component of a plant or animal's body?
Scientists today routinely report the incredible structural detail and the inner imperceptible functions of chemicals that give life a flow and productive character. How can we hope to capture the larger dimension of what is revealed from within all the detail?
If you can visualize a living cell's life systems in terms of a factory, production lines, processes directed by information, all working at maximum capacity and top speed ... then life becomes redefined in an entirely remarkable context. How could something called life appear so well coordinated and designed?
Only with the discovery of the molecular basis of life has science been able to address questions about life's basic mechanisms. Science has learned over the past four decades that the many cellular tasks required to sustain life are carried out by machines—literally, molecular machines. Behe (MC) Page 177
The WindowView now enlarges cell details to think with a bit of wonder about all the ultra-structures and inner workings of life. Take a really close look at the finer scale to life and to dimensions that make what's really small to have really huge implications! Every cell in your body exhibits something incredibly well designed ... now multiply that by the number of cells inside of you!
The human body, for example, has about 50 trillion cells. Spetner (NBC) Page 25
We are not talking about coordinating systems on any small scale. The number of cells in one organism speak to the number of places where a complete library of genetic information is stored. This number is also indicative of the number of compartments that are interlinked and structure into tissues and thereafter into organs that function in a specific set of high order tasks to keep the larger organisms on track, functioning, and alive to the next generation. Meanwhile, each little compartment is a veritable array of functions and a master work in its own right.
The machinelike parts and coordination of chemical production within cells requires a discerning look. Blow up the cell, crawl inside, take a close look ... then it becomes clear that these structures are wonderful and so far beyond a chance construction that evolution falls far short of explaining what we see. But, indeed, do take that look. With just a bit of imagination helps in visualizing what this is all about ... then you can see that many who study these cellular structures have missed how extraordinary life truly is.
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From the dawn of light microscopy's first glimpse into life, science had a general appreciation for the presence of cells within living forms. In the 1600's light microscopes were greatly enhanced by better lenses and greater magnifying power. But at no time in all of human history was there ever a greater biological epiphany than when electron microscopes began to reveal the incredible intricacy within cells—from single celled organisms to cells in complex beings such as in our own human bodies. In fact, it seems incredible that anyone looking at the diagrams in a scientific weekly—such as Science or Nature—wouldn't readily agree that cellular structures and associated biochemical pathways are phenomenally organized and intricate. Every aspect of these publications' illustrations suggests a sculpting and design on the smallest scale—functional components working at the smallest of all possible levels.
Protein molecules are the ultimate stuff of life. If we think of the cell as being analogous to a factory, then the proteins can be thought of as analogous to the machines on the factory floor which carry out individually or in groups of all the essential activities on which the life of the cell depends. Each protein is a sort of micro-miniaturized machine, so small that it must be magnified a million times before it is visible to the human eye. The structure and functioning of these fascinating work horses of the cell was a complete mystery until the 1950s. Denton (ETC) Page 234
Each enzyme is a single large protein molecule consisting of some several thousand atoms linked together to form a particular spatial configuration which confers upon the molecule the capacity to carry out a unique chemical operation. Denton (ETC) Page 334
But faced with what seems the entirely inconceivable, scientists treat such detail as a fact of the ordinary—but with a moment's deeper reflection—reveals the small cellular details take on immense meaning. They are not ordinary. They are entirely mechanical, but are well tailored to specific jobs, and perhaps engineered beyond the reach of evolutionary natural selection and the supposed gradualism that is implied to be the pathway of decent from ancestral life forms. In fact what we call primitive cells embody complexities that are found in the cells of more complex organisms.
Molecular biology has shown that even the simplest of all living systems on the earth today, bacterial cells, are exceedingly complex objects. Although the tiniest bacterial cells are incredibly small, weighing less than 10-12 gms, each is in effect a veritable micro-miniaturized factory containing thousands of exquisitely designed pieces of intricate molecular machinery, made up altogether of one hundred thousand million atoms, far more complicated than any machine built by man and absolutely without parallel in the nonliving world. Denton (ETC) Page 250
The complexity of life is routinely paraded across the pages and illustrations of technical weeklies entitled 'Science' and 'Nature.' Other periodicals—'Time,' 'Newsweek,' 'Scientific American,' et al. —make the same topics more approachable by wider audiences. Yet a basic appreciation for what we all see is lost in the technical descriptions. First, life is very complex and second explaining the level of complexity we now observe is no simple matter ... it begs questions concerning origin, design, and precision that exceeds chance. Could primitive forms of molecules easily lead to the more advanced?
The impossibility of gradual functional transformation is virtually self-evident in the case of proteins: mere causal observation reveals that a protein is an interacting whole, the function of every amino acid being more or less (like letters in a sentence or cogwheels is in a watch) essential to the function of the entire system. Denton (ETC) Page 321
How would one track evolution of molecules to the current working protein in a cell? The remarkable shape and specific site of activity on a protein (e.g., enzyme) doesn't allow much room for scenarios where a lineage of nonfunctional proteins would precede the functional entity. How does a life form function based on an array of nonfunctional components. That's like saying a sentence or meaning existed near it's origin with gibberish in place of intelligible language. When does the gibberish turn into fully functional words? Can a meaningful sentence exist as gibberish until the words are properly set in place? Can production of non-functional protein be sustained while it is transformed to its fully evolved state?
But amino acids in a protein are not the same as moving letters or words around! Moving amino acids into and out of a protein changes the entire scheme of bonds, the overall shape of the molecule, and thus destabilizing the molecule to the point of being useless. Meanwhile, proteins as enzymes do not work alone. In this regard a coordinated series of changes would be required to make life possible.
Life's Machines, the Details
We've included a diagram of a cell as it appears in a 1924 biology textbook (diagram A). This is about as much detail as Darwin could see in a light microscope available to him in his day. A living cell might display inner streaming motion, but the detail within revealed nothing more than randomness, globules, particles, or variations in indistinct shape and color.
With the advent of electron microscopes and more sophisticated light microscopy, the cell takes on an entirely different appearance. We can now magnify the cellular details a thousand million times ...
... until it is twenty kilometers in diameter and resembles a giant airship large enough to cover a great city like London or New York. What we would then see would be an object of unparalleled complexity and adaptive design. Denton (ETC) Page 328
Look to the right of the (Fig 3.) "Diagram of a cell" (diagram A) below and you'll find an image from an electron microscope (diagram B). This photo is not magnified nearly as much as an electron microscope can do. But look at the line drawing of the membrane below this photo image (diagram C). The two layers of molecules that make up the membrane sheet and the large protein or carbohydrate molecules that extend into or across the membrane are our current refined view of life's highly ordered appearance.
Give those molecules all their specific jobs and add the rates of speed at which they service the cell or tissues around them and this static picture just zooms with activity and remarkable efficiency. Darwin and science—until shortly after World War II—had no clue of life at the molecular level.
A: An artist's representation (above) of the cell from the turn of the
Twentieth Century. The amount of detail is limited, much like what
was available to scientists to scrutinize in Darwin's day.
B: An electron microscope (EM) image form a plant cell—many thousands of times beyond the magnification made possible by a light microscope.
C: Electron microscopy, along with advances in biochemical research, now makes it possible to understand a membrane of a cell, its structure down to single molecular components, and the function of each type of molecule.
However, take the images and science data that accompany the structural and functional aspects to what we see and add a bit of poetic license AND the whole picture consumes our imagination to describe a reality that is way beyond our daily perception. But this describes the inner workings of our material being. Let's take a look as Dr. Denton moves from the outer membrane of a cell to the inner parts of this compartment of life.
On the surface of the cell we would see millions of openings, like the portholes of a vast space ship, opening and closing to allow a continual stream of materials to flow in and out. If we were to enter one of these openings with find ourselves in a world of supreme technology and bewildering complexity. We would see endless highly organized corridors and conduits branching in every direction away from the perimeter of the cell, some leading to the central memory bank in the nucleus and others to assembly plants and processing units. The nucleus of itself would be a vast spherical chamber more than a kilometer in diameter, resembling a geodesic dome inside of which we would see, all neatly stacked together in ordered arrays, the miles of coiled chains of the DNA molecules. A huge range of products and raw materials would shuttle along all the manifold conduits in a highly ordered fashion to and from all the various assembly plants in the outer regions of the cell. Denton (ETC) Page 328
Proteins are key mechanical components in life. They are like the cell's engineered automatons—specific tooled machines—displaying astonishing complexity based on thousands of atoms that uniquely make specific functional three-dimensional configurations.
When a number of enzymes are necessary for the assembly of a particular compound, they are arranged adjacent to each other so that, after each step in the operation, the partially completed compound can be conveniently passed to the next enzyme which performs the next chemical operation and so on until the compound is finally assembled. The process is so efficient that some compounds can be assembled in less than a second, while in many cases the same synthetic operations carried out by chemists, even in a well-equipped lab, would take several hours or days or even weeks. Denton (ETC) Page 334
The cell, however, manufactures all its component structures, even the most complex, by fully automated assembly techniques which are perfectly regulated and controlled. Unlike our own a pseudo-automated assembly plants, where external controls are being continually applied, the cell's manufacturing capacity is entirely self-regulated. Denton (ETC) Page 335
Whoa ... hold on tight ... not only is the machinery intricate, the efficiency of the way these molecules work is at WARP speed. What goes on at the cell level can be mimicked but not be reproduced in a modern laboratory. And there is the sense that all this is directed. So, beyond the physical presence of all the cell components is the issue of the information that drives all processes to sustain life at all levels.
We would see that nearly every feature of our own advanced machines had its analogue in the cell: artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of pre-fabrication and modular construction. In fact, so deep would be the feeling of deja-vu, so persuasive the analogy, that much of the terminology we would use to describe this fascinating molecular reality would be borrowed from the world of late twentieth-century technology. Denton (ETC) Page 329
We can think of the cell as a marvelous factory, full of activity, speed, efficiency, and modular sub-unit of tissues and organs in the body. But there is one more remarkable feature that exceeds the likes of a typical factory. The cell is able to completely replicate itself within a matter of hours. What machine or factory is capable of that! The cell, as a factory, surpasses anything engineered by human material production platforms.
LET'S MAKE A MODEL!
Dr. Denton suggests we think in terms of constructing an atomic model of the cell. Take one atom at a time and simply put it into the model. How long would it take to build the model?
A typical cell contains some ten million million atoms.
Suppose we chose to build an exact replica to a scale of one thousand million times that of the cell so that each atom of the model would be the size of a tennis ball. Constructing such a model at the rate of one atom per minute, it would take fifty million years to finish, and the object we would end up with would be the giant factory, described above, some twenty kilometers in diameter, with a volume thousands of times that of the Great Pyramid. Denton (ETC) Page 330
Denton further elaborates on this model to show how construction of the cell might take less time. However, even with some advantages in model building the concludes: "Working continually day and night it would still be difficult to finish the model in the space of one million years."
Less we forget ... we can marvel at the complexity and construction of a cell, but there are staggering issues to comprehend when we move on to an organ such as a mammal's brain!
... The human brain consists of about ten thousand million nerve cells. Each nerve cell puts out somewhere in the region of between ten thousand and one hundred thousand connecting fibers by which it makes contact with other nerve cells in the brain. All together the total number of connections in the human brain approaches 1015 or a thousand million million. Numbers in the order of 1015 are of course completely beyond comprehension.
Despite the enormity of the number of connections, the ramifying forest of the fibers is not a chaotic random tangle but a highly organized network in which a high proportion of the fibers are unique adaptive communication channels following their own specially ordained pathway through the brain. Even if only one hundredth of the connections in the brain and were specifically organized, this would still represent a system containing a much greater number of specific connections than in the entire communications network on Earth. Denton (ETC) Page 330
Denton's quotation comes from the mid-1980's, so, perhaps it's only fair to say his estimate for human communication systems is in need of a slight adjustment due to the more recent advent of the Internet. Lets say two or three hundredths were specifically organized ... the brain still far exceeds our global connections.
Earlier in the WindowView Science Area narrative, there is the strong suggestion that the universe, chemical origin to life, evolution, and many other perspectives leave us hard pressed to conclude the cosmos and life within are by chance or random process. Add to this ... scientists marvel over the architecture and function of the brain. Science has yet to discover so much about the brain, yet the structure alone is a clear testimony to design!
Undoubtedly, the complexity of biological systems in terms of the sheer number of unique components is very impressive; and it raises the obvious question: could any sort of purely random process ever have assembled such systems in the time available? Denton (ETC) Page 331
Magnifying a cell—to allow our tour inside—is again a structural experience. The information housed inside speaks to yet another marvel.
In a separate feature article we illustrate the incredible nature of DNA to store, replicate, and transport information. The storage capacity alone for DNA ...
... is so efficient that all the information needed to specify an organism as complex as man weighs less than a few thousand millionths of a gram. The information necessary to specify the design of all the species of organisms which have ever existed on the planet, a number according to G. G. Simpson of approximately one thousand million, could be held in a teaspoon and there would still be room left for all the information in every book ever written. Denton (ETC) Page 334
Life is based on the inner workings of biochemical molecular machines. Embrace the material existence you live today and leave room to wonder, be awe struck, and consider that you are the object of what is in fact so remarkable! Life, indeed, is special!
Quotations from "Mere Creation"
(MC) edited by William A. Dembski are used by permission of InterVarsity Press,
P.O. Box 1400, Downers Grove, IL 60515. www.ivpress.com All rights reserved.
No portion of this material may be used without permission from InterVarsity
Quotations from "Not By
Chance" (NBC) written by L. Spetner, are used by permission granted by
Dr. Lee Spetner.
Quotations from Dr. Michael Denton's "Evolution: A Theory in Crisis" are used by permission of Adler and Adler Publishers Inc., 5530 Wisconsin Ave, Suite 1460, Chevy Chase, MD 20815
Writer / Editor: Dr. T. Peterson, Director, WindowView.org