A ribosome is a cellular machine that makes proteins. Proteins have many different functions in a cell, ranging from forming structures to controlling chemical reactions.  A human being uses tens of thousands of different kinds of proteins in his body, all made by ribosomes. According to evolutionary theory, a source of energy such as ultra-violet rays from sunlight shining on raw chemicals can eventually turn them into living cells.

         Ribosomes are extremely complicated. A glance at the following animations shows just how this is so. The animations have great value in showing the impossibility for life to appear spontaneously from natural sources, as we shall see.

         There is a fundamental, basic issue of contention between evolutionists and creationists. The very possibility of a natural origin of life depends on who is correct about this issue. On the one hand evolutionists propose that a structure such as a ribosome gradually acquired its current level of complexity through a series of very small changes, with each change providing increasingly effective performance. The idea is that each step of the series would become simple enough that it would be reasonably likely to occur within a reasonable period of time. Creationists on the other hand believe that a structure such as a ribosome needs to have a single-step first appearance. I.e., it needs to be fully functional from its first appearance. Creationists also believe that scientific observation has clearly uncovered a number of problems that work against any possibility of a gradual appearance of a ribosome.  The only reason this evidence is rejected by evolutionists is because of their philosophical bias against the implications of the observations.  

         There are four major problems that a ribosome presents to evolution:

         1) A ribosome is composed of over 50 individual kinds of proteins, all precisely defined with precise functions. Yet, the only known way for a specific protein to form is from an already working ribosome. So, how can a ribosome gradually emerge on the basis of specific, step-by-step modifications of the proteins used to make it when specific proteins can’t be made until a ribosome already exists? Observed science provides no known alternative for making proteins in accordance with a sequence defined in the DNA than the ribosome and supporting components. Any claims to the contrary are purely speculative. They would appear to be more in the category of science fiction than true science.

        

         2) Scientists have never been able to form even a 50-amino acid protein in a laboratory using processes that would be reasonably available in a pre-life scenario. This is despite having complete control over conditions and chemicals used in the experiment. One must assume that the wildly fluctuating conditions of a natural setting, particularly over hypothetical, geological time spans would give only worse results. So, proposed processes available in pre-life conditions have never been able to make a protein, not even one composed with a random sequence of amino acids. However, many experiments have been performed in an attempt to do this. They have all failed. The reasons for the failures are the outcome of the normal laws of physics and chemistry. There is no scientific basis to expect success, ever. Incidentally, 38 of the proteins used in a ribosome are made from 100 or more amino acids. The largest uses 557. There is currently no observable basis to demonstrate how natural processes could provide even a single 100-amino acid protein for a single ribosome to appear under natural pre-life conditions. So, where do proteins sufficiently large to make a ribosome come from?

         3) We will show that the proteins in a ribosome have very specific properties. This in turn requires that they have a very specific sequence of amino acids. How difficult would it be for a specifically needed protein of 100 randomly selected amino acids to provide a required sequence? It is unlikely for a single, isolated copy of it to appear in a single step on any hypothetical planet in the observable universe for just one hour in over 10,000,000,000,000,000,000,000,000,000 years. Even this would take conditions so favoring its appearance as to be extremely unrealistic and not applicable to real life. A trillion  years is only 1,000,000,000,000 years. It is dwarfed by this number. This demonstrates how difficult it would be to get only a single isolated protein of 100 amino acids to appear anywhere in the universe for an just one hour. Is one hour too short? If you prefer to have available for 100 times as long (i. e., one hundred hours), then the time for it appear just increased by 100 times.

        The problems against a  natural appearance of a ribosome do not stop here. Eight of the proteins used in a ribosome are over 200 amino acids in length. We estimate that for every amino acid added to a chain, the odds against it being usable are about 1 in 10. The reasons for this are discussed in another article. This means that it would take about about an additional ten times as long for the required amino acid sequence to appear for each additional amino acid required.  A 200-amino acid protein has an additional 100 amino acids. This would increase the time for a suitable amino acid to appear by a factor of 10100. This number is commonly called a “Googol.” In other words the odds against an isolated protein appearing on any planet in the observable universe for one hour would normally take over a Googol years. Of course, this is only for a brief, isolated instance of the required protein.

         In truth, if single-step selection is required, then life as we see it here on earth can not have been formed by means of the normal laws of physics and chemistry. This has nothing to do with a person’s philosophical prejudices and biases. It has everything to do with the natural conclusions of scientific observation. If single-step first appearance of a ribosome and other cellular components are required, then the observations of science favor special creation and not chemical evolution.

         4) Currently, scientists cannot even make a single RNA nucleotide in a laboratory using plausibly pre-life processes without human intervention. Yet, a ribosome uses over 4,000 nucleotides distributed among three strings in an exact sequence. At one point, an RNA-world was viewed as a solution to this problem. However, RNA has such a short lifetime (typically half of messenger RNA molecules in a solution will decay in well under one day) that a proposed “pre-RNA world” was hypothesized. This has its own problems, including how to transition from pre-RNA to RNA, including what pre-RNA might be, and how components in it could spontaneously appear in the quantities and species needed. The reality is that experimental evidence available to date teaches against the expectation that the components required to fabricate a ribosome would ever be available as the product of natural processes.

   

         As one looks at the following animations, it would be well to keep in mind that the big issue concerns whether the observed data reasonably allows the possibility of gradual step-by-step processes or whether a single-step, full-formed first appearance is required. How much wiggle room does the observed evidence reasonably allow for gradual processes, if any?

Three Ribosome Animations That Debunk a Natural Origin of Life

By Timothy R. Stout

Ribosome Small Subunit

         This is an animation of the small subunit of the ribosome used in e. coli bacteria. The animation demonstrates its 3-dimensional complexity. The light orange color represents the RNA strand. There are 1,542 nucleotides in this strand, with four possible choices of nucleotide at every position. The green shading is like a shadow; it varies according to the angle of view.  The blue shading represents the proteins used in the subunit. There are 21 proteins among them, formed from 3,116 amino acids.  

As the subunit turns, notice the groove running across its width, about 1/3 down from the top. This groove provides the bottom portion of a channel through which a long molecule called messenger RNA travels as a new protein is fabricated. The information specifying the amino acid sequence of the protein being built is provided by messenger RNA. The messenger RNA conveys the information on how to build the protein stored in the DNA.

Notice the extreme complexity. A large number of proteins are used as structural elements to get the RNA to fold into its proper shape. Every single protein must have the exactly required shape and the exactly required selection of amino acids to bond properly to the RNA molecule at the correct location; otherwise, the entire assembly fails. The entire combination needs to make a single-step first appearance. Here is why:

The small subunit independently self assembles within a cell. The various individual RNA molecules and proteins to be used are “dumped” into a cell unassembled. Then, when a certain, specific protein out of the group randomly comes into contact with the RNA molecule, it identifies a certain location on it and then attaches to that point. The electrical and chemical characteristics for this to happen need to be built into the construction of both the RNA molecule and the protein. Also, no other proteins in the cell and no other nucleotide sequences of the RNA can be allowed to have similar identification characteristics. Otherwise, false self assembly will occur. Once the protein has attached properly, the RNA/protein combination reconfigures into a new shape. The second ribosome protein is only able to attach to the newly acquired shape. Then, after the second protein has attached, the emerging ribosome takes on a yet new shape. This process repeats until all of the proteins have self assembled.

Self-assembly precludes the possibility of gradual, step by step modifications forming the cell. From the very beginning, all of the amino acids and RNA need to be in a form that provides for a fully functioning ribosome.

Evolutionists frequently talk as though emergence and self-assembly allow complicated structures to appear out of random components. Scientific observation teaches otherwise. It is observed that In a cell, self-assembly mechanisms are defined by the information describing how to build the various components. This does not simplify the requirements of making a proper component, it adds an entirely new level of complexity. This complexity must be part of the protein’s structure from the beginning and could easily be the most difficult part of protein definition. The same applies to ribosomal RNA. Each individual component needs this additional information built into to it from the beginning and the the assembly of all of the various components used must be designed so wrong assemblies are inhibited. This is probably the most important restriction imposed on a system by self assembly.  

Therefore, self assembly adds yet another layer of complexity to the specification of a protein. Each protein not only needs to know where to assemble and what bond characteristics to exhibit to bond properly with the assembly at the appropriate time, it also needs to have the proper shape and bonding potential to preclude bonding improperly to any other potential structure that it comes in contact with. This includes not only the other components of the small subunit, but also of the large subunit, of the various synthetases, transfer RNAs, elongation factors, golgi body components, cellular spindle components, and a long list of other potential components. This, in truth, requires not only for the complete ribosome to be properly defined from the beginning, but also an entire “laundry list” of other components get included. In effect, the entire cell needs to make a single-step first appearance.  This is about a strong a case for single-step first appearance that is is possible to get.

To keep this in the proper perspective, remember that it is unlikely to discover by chance a specifically required, 200-amino acid protein on any planet in the universe in over a Googol years of opportunity. This degree of dilution makes self-assembly of a group of components rather difficult.

Ribosome Large Subunit

         This is an animation of the large subunit of a ribosome of an e. coli bacterium. The orange, coiled strand is a single strand of RNA composed of a string of 2,906 nucleotides arranged in a specific order. The green is shadow. The yellow strand at the top is a second RNA strand composed of 120 nucleotides. The blue structures are proteins. A large subunit uses 4,223 amino acids spread among 36 different proteins. This is even more complex than the small subunit. However, it takes this degree of complexity for the ribosome to accomplish its task. The large subunit also self assembles.

  

         The large subunit is much more complicated than the small one in that it has many more channels for various components to pass through. These channels must be precise in their individual shapes and locations and need to interconnect with each other in a precise manner. There is no room for experimenting with various possibilities until a suitable one appears. Either the ribosome works or it doesn’t. Natural selection cannot choose between the better of two failures. If a certain assembly fails to work, it is irrelevant to natural selection as to how close it might have been to working. There is no selection advantage to a failure.

Assembled Ribosome

         This is an illustration of how a small subunit and large subunit appear when assembled together. When a small subunit has a messenger RNA properly located within its groove and the proper transfer RNA molecule attached to the messenger RNA, as shown in the next animation, the large subunit attaches to the lower subunit.

       The attachment is a self-assembly process. The lower subunit is slightly flexible. It does not attach to the large subunit under normal conditions. However, it changes shape when the messenger RNA and first transfer RNA molecule are attached. The new shape allows the two subunits to combine properly.

         Once fabrication of the new protein has been completed, the messenger RNA and the finished protein leave the ribosome , the lower subunit returns to its original shape, and the two subunits split apart.  The capability of the small subunit to change shape in accordance with the status of the ribosome adds to the difficulties of getting a suitable assembly of nucleotides to fabricate it. The capability for the assembled ribosome to change its shape as necessary is a critical function which needs to be present from its beginning.

         So, the various proteins of the ribosome not only need to be configured in such a way that they can self-assemble, but also they need to be able to generate specific configurations depending on the state of the ribosome. This is yet more complexity which is designed into the ribosomal components from the beginning.

 How a Ribosome Works

          In the animation to the right, the lower yellow structure is a ribosome small subunit. The black thread extending across the page is a strand of messenger RNA. It will function as a template containing the information to specify the choice of amino acids in fabricating through protein to be built. When a messenger RNA molecule and a small subunit of a ribosome cross paths, the messenger RNA will attach to the small subunit in its groove. There is a mechanism  to get everything aligned properly.

The components with the bright blue structures are called transfer RNA. A transfer RNA molecule  has an amino acid attached to it at its tip. At its base it has identifier “codons” which determine whether it represents the kind of amino acid needed at this spot in the emerging protein. The amino acid attached to the tip will ultimately be transferred from the transfer RNA to the proper location in the emerging protein.  A protein is composed of an assortment of 20 different amino acids. Therefore, a cell has at least 20 different kinds of transfer RNAs, one for each kind of amino acid.

 Only the  kind of tRNA specified by the messenger RNA will bond to it at any given bonding site. The light blue attachment to the tRNA is called a synthetase. All the different kinds of transfer RNA have the same basic structure where the amino acid is attached. A separate molecule called a synthetase actually joins the proper amino acid to the proper transfer RNA.  There is a channel between the small subunit and the large subunit for a transfer RNA to enter a ribosome. If the code information at the bottom of the transfer RNA matches the information in the messenger RNA telling what kind of amino acid is needed, the transfer RNA bonds to the messenger RNA and the synthetase is released. Otherwise (not shown in the animation) the transfer RNA is rejected, leaves the ribosome, and a new one enters. Rejection is the normal outcome. With twenty choices of amino acids and only one correct one, most of the time the wrong amino acid will appear.

A ribosome can hold three transfer RNAs at a time. The center one attaches its amino acid to the emerging string of amino acids forming the new protein. The one entering the ribosome with its synthetase attached will supply the next amino acid of the protein.

Once the synthetase has been released from the ribosome, indicating that the proper transfer RNA has bonded to the messenger RNA, a large protein called an “elongation factor” attaches to the ribosome and pushes the entire messenger RNA/transfer RNA assembly forward. In a human being, the elongation factor is composed of 578 amino acids. How many multiple Googles of years should it take to get a single, momentary appearance of this protein from random processes?

The animation above shows the transfer RNA changing shape as it advances from the first to the middle position. This shape change pushes the emerging protein through a small channel until it exits out the top of the ribosome. This shape change is a tricky process.  The transfer RNA molecule needs to rise the proper amount to advance the protein the exactly required amount so that the next amino acid to be attached will line up properly. The amino acid sequence of the transfer RNA needs to change its shape in accordance with its progress through the ribosome. This is another characteristic which needs to appear correctly at its first time; otherwise, the amino acids do not get properly joined to each other.

The remaining steps shown in the animation concern activities related to protein processing subsequent to the actual protein assembly and will not be discussed here. However, it is obvious that the structures are much more complicated than an elongation factor and that is composed of well over five hundred amino acids.

There is another difficulty. ATP (adenosine tri-phospate) supplies the energy for most of the assembly process. There needs to be an abundant source of ATP molecules for the entire process to work. ATP molecules are made in the Krebs cycle.  9 proteins are associated with it, having lengths of 136, 437, 136, 413, 868, 708, 1117, 510, 617, 466 amino acids. Most of these are extremely large and would take multiple Googol times Googols of years to appear briefly one time by random processes. This would  make a rather dilute concentration. The problem is that to make these proteins, a working ribosome is needed, along with the proper information in the DNA. Yet, the proteins are needed to make ATP energy units use to operate ribosome. The ribosome and Krebs cycle components together form an irreducibly complex system which needs to have a single-step first appearance

It is difficult to believe that sunlight or some equivalent unconstrained source of energy could convert raw materials such as methane, ammmonia, carbon dioxide, hydrogen, water, etc. into a system with this degree of complexity. Also, the things we have looked at give strong evidence that the entire first cell needed to make a single-step first appearance. Sunlight shining on raw chemicals most definitely cannot create a ribosome and all of the other cellular components that work with it in a single step.

Ribosome Small Subunit

Ribosome Large Subunit

Assembled Ribosome

How a Ribosome Works

Concluding Remarks

If one works through everything required to build properly a ribosome, it seems clear that it needs to make a single-step first appearance. However, the ribosome is so complex that natural processes cannot reasonably be expected to make it in the required first step, particularly at the time and place the rest of the cell needs it to appear. This has strong religious and philosophical connotations.

Natural processes naturally go one way. By contrast, a  living cell needs specific chemicals at specific times and locations. There is nothing to constrain or restrain what is produced to what is needed. As a result, the wrong things are produced and a natural origin of life cannot appear. This is the hypothesis of Abiogenetic Disconnects talked about elsewhere on this website.

Evolutionists talk as if the use of RNA in a ribosome is evidence of an earlier instance of what is called an “RNA World.” It makes more sense to view the combination of RNA and protein as the most efficient way to effect the self-assembly of the ribosome. It is also possible that the phosphate backbone of RNA may provide a “smoother” surface for the messenger RNA to glide along than would a structure made purely of amino acids.  In other words, a ribosome uses both RNA and protein because that is the most effective way to build it and has nothing to do with a hypothesized RNA-world.

Ultra-violet rays from the sun do not turn random raw chemicals into something this complex. They destroy it if it already exists. Scientific observation clearly teaches against the possibility of natural, unguided processes creating a ribosome. The entire notion of abiogenesis appears to be a fairy-tale.

Since the preceding discussion gives strong, observable evidence favoring a single-step first appearance of a ribosome, as well as various other cellular components, and since it is beyond the capability of natural energy sources such as sunlight to produce this degree of complexity in a single step, then it appears that natural processes are incapable of creating a living cell. This would indicate that supernatural processes are required. Science cannot speak directly about the existence of God one way or the other, since God cannot be constrained to be studied in an experiment. However, it appears us that science gives us tools for two things: 1) The tools show us the kinds of things that are needed to produce life. 2) The tools show us that natural processes are incapable of making these things.

If natural processes are all that are available, according to what we have learned from science we shouldn’t exist.  However, we do. Hence, we need to have an origin outside of natural processes. Thus, an honest appraisal of the observations of science provide strong evidence favoring special creation and not chemical evolution as the source of life.

The above animations were taken from the wikipedia.org article on “Ribosome.”

The animations are used in accordance with the

It is recommended that our article   Random Sequence Difficulties be read together with this one, as the two supplement each other in providing a single argument about the difficulty and significance of life emerging from random sequences. The “Difficulties” article goes through calculations showing just how unlikely it would be for natural processes to make the chemicals of life.  The results are staggering. For most chemicals, the entire universe is very unlikely to form just one instance of only one of them in a Googol years. It takes an already living cell to make these chemicals. This article shows single-step initial appearance is required. Together, these articles form a powerful argument for special creation.