Chapter 5: The Cell: How it works
Why is there life on earth? Why does it exist? Why are there bacteria and archaea? How complex are they? How does the cell work? What have other workers found out about this now? - Michael Denton is a Molecular Biologist. He states in his book Evolution: A Theory in Crisis, about the cell and its different parts and functions:
"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 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." (1985:234).
"The linear sequence of amino acids in a protein can be thought of as a sentence made up of a long combination of the twenty amino acid letters. Just as different sentences are made up of different sequences of letters, so different proteins are made up of different sequences of amino acids. In most proteins the amino acid chain is between one hundred and five hundred amino acids long." (1985:235).
"Apart from structural and catalytic functions, proteins also carry out transport and logistic functions and, because of the enormous number of different protein functions, the variety of different sorts and shapes of proteins is correspondingly very great.
"Also proteins are amazingly versatile and carry out all manner of diverse biochemical functions. They are incapable of assembling themselves without the assistance of another very important class of molecules - the nucleic acids. To return again to the analogy of a factory, while the proteins can be thought of as the working elements of a factory, the nucleic acid molecules can be thought of as playing the role of the library or memory bank containing all the information necessary for the construction of all the various machines (proteins) on the factory floor. More specifically we can think of the nucleic acids as a series of blueprints, each one containing the specification for the construction of a particular protein in the cell.
"There are two types of nucleic acids, DNA and RNA. DNA is only found in the nucleus of the cell, equivalent to the head office of the factory, and containing the master blueprints. RNA molecules perform the fundamental task of carrying the information stored in DNA to all the various parts of the cell where the manufacture of a particular protein is proceeding. In terms of analogy we can think of RNA molecules as photocopies of the master blueprint (DNA) which are carried to the factory floor where the technicians and engineers convert the abstract information of the blueprint (RNA) into the concrete form of the machine protein." Denton, M. (1985:238, 239).
"Just as in the factory, the information in the blueprint flows via the photocopy and into the manufactured article on the factory floor. In terms of their actual structure, of course, nucleic acid molecules do not resemble blueprints but are long chain-like molecules. If we wish to continue thinking in terms of the factory/cell analogy a better picture of the nucleic acids would be to think of them as analogous to magnetic tapes, which are often used nowadays to programme automatic lathes or jigborers in the production of machine tools. ... The linear sequence of subunits of the DNA molecule contains a series of encoded messages, genes, each of which is decoded by the cell and translated into the linear sequence of amino acids of the protein." (1985:239, 240).
"The sequence of nucleotides in the mRNA is translated by the conventions of the genetic code into the amino sequence of a protein in the same way as a message in Morse code can be translated into a sequence of letters by applying the translational conventions of Morse. ... After its translation the mRNA moves from the nucleus into the cytoplasm to the actual site of translation where the decoding of the message takes place. The translation of the mRNA molecule is carried out by a complex set of molecules, which together comprise the translational apparatus. An important component of the translational apparatus is a complex globular organelle, known as the ribosome, composed of an aggregate of some 50 proteins and three chains of RNA. ...
"During the process of translation the mRNA passes through the ribosome just as the magnetic tape passes the recording head on a tape recorder. As each triplet reached the reading head, it associates loosely with its appropriate RNA, which is also carrying the appropriate amino acid. ... The synthesis of proteins by the cell is thus achieved as a result of a remarkable and intimate relationship between one class of molecules - the proteins - and another quite different class of molecules - the nucleic acids. The nucleic acids contain the information for the construction of proteins, but it is the proteins which extract and utilize the information at all stages as it flows through this intricate series of transformations." Denton, M. (1985:243-245).
Why is there life on earth? Why does it exist? How has it arisen? How complex is the living cell? Could it have arisen by itself from inorganic matter, through some primordial chemical evolution?
Molecular biologist Michael Denton: "We now know not only of the existence of a break between the living and non-living world, but also that it represents the most dramatic and fundamental of all the discontinuities of nature. Between the living cell and the most highly ordered non-biological system, such as a crystal or a snowflake, there is a chasm as vast and absolute, as it is possible to conceive. ... Molecular biology has shown that even the simplest of all living systems on 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.
"Molecular biology has also shown that the basic design of the cell system is essentially the same in all living systems on earth from bacteria to mammals. In all organisms the roles of DNA, mRNA and proteins are identical. The meaning of the genetic code is also virtually identical in all cells. The size, structure and component design of the protein synthetic machinery is practically the same in all cells. In terms of their basic biochemical design, therefore, no living system can be thought of as being primitive or ancestral with respect to any other system, nor is there the slightest empirical hint of any evolutionary sequence among all the incredibly diverse cells on earth. For those who hoped that molecular biology might bridge the gulf between chemistry and biochemistry, the revelation was profoundly disappointing." Denton, M. (1985:249, 250).
"The complexity of the simplest known type of cell is so great that it is impossible to accept that such an object could have been thrown together suddenly by some kind of freakish, vastly improbable, event. Such an occurrence would be indistinguishable from a miracle."
Why must also the smallest cell, which is able to live as a non-parasite, still have a certain size?
Michael Denton: "The protein synthetic system of all modern cells requires the integrated activities of nearly one hundred different proteins, all carrying out different, very specific steps in the assembly of a new protein molecule. If only a small proportion of these were 'crudely made' or 'statistical' it is practically impossible to accept that any protein would ever be manufactured, let alone one with a specific molecular configuration capable of performing a specific function in the cell. ... It is precisely because the translation system is critically dependent on accurately made proteins that an imperfect protein synthetic system is so difficult to envision."
Why?
Michael Denton: "If translation is inaccurate, this leads in turn to a more inaccurate translational apparatus which leads inevitably to further inaccuracies, and so forth. Each imperfect cycle introduces further errors. To improve itself, such a system would have to overcome its fundamental tendency to accumulate errors in exponential fashion. The very cyclical nature of cellular replication guarantees that imperfections inexorably lead to autodestruction. It is difficult enough to see how an imperfect translational system could ever have existed and achieved the synthesis of one single protein let alone the many necessary for the life of the cell. That such a cell might undergo further evolution, improving itself by 'selecting' advantageous changes would be inevitably lost in the next cycle of replication, seems contradictory in the extreme.
"Modern organisms get by despite mutations because the rate of mutation is low. ... However, if the mutation rate is raised, say, irradiation, then certainly this leads to an accumulation of errors down a chain of replication which is ultimately lethal to the clone of irradiated individuals (this can be experimentally demonstrated with micro-organisms). When the mutation rate is very high, no living system can avoid the path of autodestruction. Each cycle increases the 'noise' and erases crucial information, like a series of increasingly poor photocopies; ultimately, the text becomes illegible. That an error-prone translation system would lead inevitably to self-destruction is not only a theoretical prediction but also a well-established empirical observation. ... Just as a bird feathered with the frayed scales of pro-avis would plummet to the ground, so a cell burdened with inefficient proteins, an error-prone code, and choked with junk would grind instantly to a halt." Denton, M. (1985:264-268).
"The origin of life is actually far more difficult to envisage than the above discussion implies. There is much more to the cell than the 'mere' origin of the protein synthetic apparatus. In fact, the protein synthetic mechanism cannot function in isolation but only in conjunction with other complex subsystems of the cell.
"Without a cell membrane the components of the protein synthetic apparatus would not be held together. The integrity of the cell membrane, however, depends on the existence of a protein synthetic apparatus capable of synthesizing the protein components of the membranes and the enzymes required for the synthesis of its fat components. However, the protein synthetic apparatus consists of a number of different components and can only function if these are held together by a membrane: two seemingly unbreakable interdependent systems. To continue, the protein synthetic apparatus also requires energy. The provision of energy depends on the coherent activity of a number of specific proteins capable of synthesizing the energy-rich phosphate compounds - proteins which are themselves manufactured by the protein apparatus. A further couple of interdependent cycles!
"As we have seen, the information for the specification of all the protein components of the cell, including those of the protein synthetic apparatus, is stored in the DNA. However, the extraction of this information is dependent on the proteins of the protein synthetic apparatus - yet again another set of interdependent cycles." (1985:268, 269).
What have other scientists concluded about the design of a simple self-replicating system, about the parts, which the smallest possible cell would at least need?
Michael Denton: "It is not only biochemists who have difficulty in envisaging the design of a simple, self-replicating system. Eminent engineers and mathematicians, such as von Neuman (1966), who have considered theoretically the general design of self-replicating automata have shown that any automaton sufficiently complex to reproduce itself would necessarily possess certain component systems which are strictly analogous to those found in a cell. One component would be an automatic factory capable of collecting raw materials and processing them into an output specified by a written instruction. This is the analogue of the ribosome. Another component would be a duplicator, an automaton, which takes the written instruction and copies it. This is the analogue of the DNA replicating system. Another component would be a written instruction containing the specification of the complete system, which is the analogue of the DNA.
"The fact that artificial automata and living organisms both have to conform to the same general design to meet the criteria for selfreplication tends to reinforce the feeling that perhaps no system simpler than the basic cell can exist which could undergo genuine autonomous selfduplication." (1985:269).
Some evolutionists still do believe that the first cell has evolved by itself from inorganic matter through chance, through some lucky coincidence. Is such a belief reasonable? Is it scientific?
Michael Denton: "Living organisms are complex systems, analogous in many ways to non-living systems. Their design is stored and specified in a linear sequence of symbols, analogous to coded information in a computer programme. Like any other system, organisms consist of a number of subsystems, which are all coadapted to interact together in a coherent manner: molecules are assembled into multimolecular systems, multimolecular assemblies are combined into cells, cells into organs and organ systems finally into the complete organism.
"If complex computer programs cannot be changed by random mechanisms, then surely the same must apply to the genetic programs of living organisms. The fact that systems in every way analogous to living organisms cannot undergo evolution by pure trial and error and that their functional distribution invariably conforms to an improbable discontinuum comes, in my opinion, very close to a formal disproof of the whole Darwinian paradigma of nature.
"The impossibility of gradual functional transformation is virtually self-evident in the case of proteins: mere casual 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 in a watch) essential to the function of the entire system. To change, for example, the shape and function of the active site (like changing the verb in a sentence or an important cogwheel in a watch) in isolation would be bound to disrupt all the complex intramolecular bonds throughout the molecule, destabilizing the whole system and rendering it useless.
"Recent experimental studies of enzyme evolution largely support this view, revealing that proteins are indeed like sentences, and are only capable of undergoing limited degrees of functional change through a succession of individual amino acid replacements. The general consensus of opinion in this field is that significant functional modification of a protein would require several simultaneous amino acid replacements of a relatively improbable nature." Denton, M. (1985:316, 321).
Even in the simplest living cell we do find proof for planning, for design, and for intelligence. - Why?
Michael Denton: "We would notice that the simplest of the functional components of the cell, the protein molecule, were astonishingly, complex pieces of molecular machinery, each one consisting of about three thousand atoms arranged in highly organized 3-D (dimensional) spatial conformation. We would wonder even more as we watched the strangely purposeful activities of these weird molecular machines, particularly when we realized that, despite of all our accumulated knowledge of physics and chemistry, the task of designing one such molecular machine - that is one single functional protein molecule - would be completely beyond our capacities at present and will probably not be achieved until at least the beginning of the next century. Yet the life of the cell depends on the integrated activities of thousands, certainly tens, and probably hundreds of thousands of different protein molecules.
"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 prefabrication and molecular construction. In fact, so deep would be the feeling of deja-vu (= we have seen it all before), 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." (1985:329).
Where do we find ingenuity in the design of the living cell? And why does it exist? Who or what caused it to arise?
Michael Denton: "But it is not just the complexity of living systems which is so profoundly challenging, there is also the incredible ingenuity that is so often manifest in their design. Ingenuity in biological design is particularly striking when it is manifest in solutions to problems analogous to those met in our own technology. Without the existence of the camera and the telescope, much of the ingenuity of the design of the eye would not have been perceived.
"But it is at a molecular level where the analogy between the mechanical and biological worlds are so striking, and the genius of biological design and the perfection of the goals achieved are most pronounced. Take, for example, the problem of information storage, various solutions of which have been utilized in human societies: for thousands of years, information has been stored in written symbols on clay tablets, paper scrolls, and in books.
"A chemical solution to the problem of information storage has, of course, been solved in living things by exploiting the properties of the long chain-like DNA polymers in which cells store their hereditary information. It is a superbly economical solution. The capacity of DNA to store information vastly exceeds that of any other known system; it 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 (1960) of approximately a thousand million, could be held in a teaspoon and there would still be room left for all the information in every book ever written." (1985:333, 334).
"The genius of biological design is also seen in the cell's capacity to synthesize organic compounds. Living things are capable of synthesizing exactly the same sorts of organic compounds as those synthesized by organic chemists. Each of the chemical operations necessary to construct a particular compound is carried out by a specific molecular machine known as an enzyme. 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.
"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 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.
"Automated assembly is another feature which has reached its epitome in living systems. Except for relatively simple pieces of machinery - parts of television sets, ball bearings, milk bottles - fully automated production has not yet been achieved in our technology. 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 pseudo-automated assembly plants, where external controls are being continually applied, the cell's manufacturing capacity is entirely self-regulated.
"Every living cell is a veritable automated factory depending on the functioning of up to one hundred thousand unique proteins each of which can be considered to be a basic working component... Each protein is itself a very complex object, ... consisting of several thousand atoms, all of which are specifically oriented in space." Denton, M. (1985:334, 335).
"A solution of the problem of extracting solar energy was solved three and a half thousand million years ago when life began on Earth. The solution is the chloroplast, which is a micro-miniature solar energy plant, which converts the light of the sun into sugar - the hydrocarbon fuel, which ultimately energizes every cell on Earth. It was also the chloroplast that was the original source of all the fossil fuels upon which our technology is so crucially dependent, and without which the process of industrialization could never have begun." (1985:335).
The DNA consists of genes. - Only of genes?
Michael Denton: "DNA does not consist entirely of genes containing encoded messages for the specification of proteins; a considerable proportion is involved in control purposes, switching off and on different genes at different times and in different cells. This was considered, again by analogy with human information retrieval systems such as might be used in a library filing system or computer, to be positioned adjacent to, but separate from, the genes under its control.
"There was some empirical support for this very logical view but, once more, as in the case of the overlapping genes, biological design turned out to be far more clever than was expected, for it has now been found that many sequences of DNA which perform the crucial control functions related to information retrieval are situated not adjacent to the genes which they control but actually embedded within the genes themselves." (1985:336, 337).
The living cell is able to double itself. What must it know and be able to do, to double itself?
Michael Denton: "As Von Neuman pointed out, the construction of any sort of self-replicating automaton would necessitate the solution to three functional problems: that of storing information, that of duplicating information, and that of designing an automatic factory which could be programmed from the information store to construct all the other components of the machine as well as duplicating itself. The solution to all three problems is found in living things and their elucidation has been one of the triumphs of modern biology.
"So efficient is the mechanism of information storage and so elegant the mechanism of duplication of this remarkable molecule that it is hard to escape the feeling that the DNA molecule may be the one and only perfect solution to the twin problems of information storage and duplication for self-replicating automata." (1985: 337, 338).
How has this problem with the automatic factory been solved in the living cell?
Michael Denton: "The solution to the problem of the automatic factory lies in the ribosome. Basically, the ribosome is a collection of some fifty or so large molecules, mainly proteins, which fit tightly together. Altogether the ribosome consists of a highly organized structure of more than one million atoms which can synthesize any protein that it is instructed to make by the DNA, including the particular proteins which comprise its own structure - so the ribosome can construct itself.
"The protein synthetic apparatus is also, however, the solution to an even deeper problem than that of self-replication. Proteins can be designed to perform structural, logical, and catalytic functions. For instance, they form the impervious materials of the skin, the contractile elements of muscles, the transparent substance of the lens of the eye: and, because of their particularly unlimited potential, almost any conceivable biochemical object can be ultimately constructed using these remarkable molecules as basic constructional and functional units.
"The choice of the protein synthetic apparatus as the solution to the problem of the automatic factory has deep implications. Not only does it represent a solution to one of the problems of designing a self-duplicating machine but it also represents a solution to an even deeper problem, that of constructing a universal automaton. The protein synthetic apparatus cannot only replicate itself but, in addition, if given the correct information it can also construct any other biochemical machine, however great its complexity, which, because of the near infinite number of uses, to which it can be put, gives it almost limitless potential.
"It is astonishing to think that this remarkable piece of machinery, which possesses the ultimate capacity to construct every living thing that ever existed on Earth, from a giant redwood to the human brain, can construct all of its own components in a matter of minutes and weighs less than 10-16 grams. It is of the order of several thousand million million times smaller than the smallest piece of functional machinery ever constructed by man." (1985:348).
Why is there life on Earth? Why are there living cells? Why do they exist? Could they have evolved through chance, through some lucky coincidence? What do you conclude now as a molecular biologist from your own work?
Michael Denton: "It is the sheer universality of perfection, the fact that everywhere we look, to whatever depth we look, we find an elegance and ingenuity of an absolutely transcending quality, which so mitigates against the idea of chance. Is it really credible that random processes could have constructed a reality, the smallest element of which - a functional protein or gene - is complex beyond our own creative capacities, a reality which is the very antithesis of chance, which excels in every sense anything produced by the intelligence of man? Alongside the level of ingenuity and complexity exhibited by the molecular machinery of life, even our most advanced artifacts appear clumsy. We feel humbled, as neolithic man would in the presence of twentieth-century technology.
"It would be an illusion to think that what we are aware of at present is any more than a fraction of the full extent of biological design. In practically every field of fundamental biological research ever-increasing levels of design and complexity are being revealed at an ever-accelerating rate. The credibility of natural selection is weakened, therefore, not only by the perfection we have already glimpsed but by the expectation of further as yet undreamed of depths of ingenuity and complexity." (1985:342).