Random Chance

There is still a strong acceptance of the concept that if you have water, the “right stuff” and slosh it around for a few million years life happens. We see a stagnant pool of water and come back several weeks later and there is pond scum. The images of primordial soup do not go away. If stagnant water can create pond scum isn't that kind of what happen a million years ago - give or take a million years?

No! Pond scum harks back to the abiogenesis problem. Remember the experiment that Louis Pasteur conducted. If he left beef broth exposed to air it was quickly contaminated with a bacterial growth. However if he bent the neck of the flask and microorganisms were unable to reach the broth it remained sterile. Pond scum is little more than a large-scale example of water being a collection point for microorganisms in the air. As one researcher explained the situation if you took a beaker of sterile water and placed a cell in it and then used a probe to puncture the cell you would not get life. The cell will not reassemble. Even in a situation in which you have exactly all the right elements to produce life it does not self- assemble. Or more bluntly put if you take a bucket of water, throw in the “right stuff” and stirring it you’ll get well-stirred water but not life.

There was no primordial soup that sloshed the right stuff into a rich broth of macromolecules. The Late Heavy Bombardment sterilized the Earth. There seems to be no way to naturally produce the left-handed molecules that are needed to form amino acids. Without amino acids there will be no proteins, without proteins there is no means for the cell to synthesize energy, create new proteins, build a cell membrane or function. Consider what you need for a protein molecule to form by chance. First, you need the right bonds between the amino acids. Second, amino acids come in right-handed and left-handed versions, and you've got to get only left-handed ones. Third, the amino acids must link up in a specified sequence, like letters in a sentence. The primary structure is a specific sequence of amino acids. Changes in the order or the substitution of a different amino acid will create a different protein or render the chain a non-functional blob. Since the early 1960’s biologists have known that the ability of cells to build functional proteins depended on the precise sequential arrangement of the bases in DNA.

In 1971 the French biologist Jacques Monod wrote a book entitled Chance and Necessity in which he outlined the process of evolution in modern terminology. Monod wrote that random mutations in the genetic makeup of organisms explains how variations in populations arise and generate evolution. His book was restating the fundamental principle that chance and random happenstance are the prime elements of evolution.

While Monod was writing that “chance” was a fundamental element of evolution other scientists, mathematicians, physicists and engineers were questioning the proposal of chance as a fundamental agent of creation. Chief among their questions was that natural selection can only select what random mutation produces. The skeptics noted that it is extremely difficult to assemble a protein by chance because of the large number of amino acid sequences. For every sequence that produces a functional protein a vastly larger number of possibilities exist that will generate a nonfunctional blob. As the length of the chain of amino acids needed to generate a protein increases the “chance” of randomly meeting the specific requirement rapidly diminishes.

In the 1990’s scientists began to formally address these issues by seeking to determine the minimal complexity of a living cell. According to the chance hypothesis the molecular building blocks of DNA, RNA and proteins were assembled from a prebiotic environment in which the subunits attached randomly. Amino acids attached to other amino acids to form polypeptide chains. Sugar and phosphate molecules attached to each other and then nucleotide bases attached to the sugar phosphate backbones. Millions upon millions of chance encounters would have been required to form even one fully functional protein. Since the requirements for assembling a fully functional cell (DNA, RNA and the requisite proteins) seemed an impossibility, at a single stroke scientists sought to determine the odds of randomly assembling a single functional protein of 150 amino acids.

To begin to understand what is required in creating a 150 chain protein it is essential to look at the probabilities. Since you have twenty different amino acids that can build proteins a two-chain amino acid would derive a chance of 20² or 400 possibilities. Obviously as the chain became longer the chances would increase (i.e., 20³ would have 8,000 possible combinations; 20⁴ would generate 160,000 sequences). The possibility of generating a specific 150 amino acid sequence is approximately 10¹⁹⁵ . However within the hypothesized primordial soup there are several hurdles that must be overcome. The first is that of chemical bonding. Amino acids form both peptide and nonpeptide bonds in equal proportions. Therefore in any random mixture the possibility of building a 150 amino acid linkage in which all peptide links is (1/2)150 or one chance in 10^45.

Secondly, amino acids used in protein formation must be a left handed version. Within the realm of nature right handed and left handed versions of amino acids are equally balanced. A mathematical notation of a possible scenario in which only left handed isomers were used to construct the 150 amino acids sequence is (1/2)150 or one chance in 10⁴⁵ . The final requirement is perhaps the most important as it requires that the letters of the amino acids linkage are in the specified sequential order. The obvious probability would be (1/20)150 or roughly 1 chance in 10¹⁹⁵ . This final probability has been challenged because it is known that a limited number of sites along the amino chain can tolerate some variance or substitution without destroying the function of the protein. Douglas Axe conducted mutagenesis experiments to determine the amount of flexibility within amino acid linkages. On the basis of his experiments he was able to determine (a) the number of 150 amino acid sequences that can perform a particular function and (b) the whole set of possible amino acid sequences of this length. Axe estimated the ratio as 1 in 10⁷⁴ . Having acquired a more precise number for the final evaluation on the possibility of randomly arriving at a specific functional 150-amino-acid chain the math is actually quite straight forward. The calculation only requires adding the exponents of the previous calculations (i.e., 45 + 45 + 74) which yields the answer of 10¹⁶⁴ ( Signature in the Cell pgs. 205-208, 212). By adding the possibility of an amino acids formed from all peptide linkages, plus the probability of using all L- form ( left handed) amino acids to the probability of a specific 150 amino acid linkage the result is 10 with 164 zeros behind it.

Many people such as myself are math dazzled - 10¹⁶⁴ is a truly enormous number but how can I begin to understand its significance. Perhaps this will help. There are only 10⁸⁰ protons, neutrons and electrons in the observable universe. You would have a significantly better chance of finding one marked proton in the entire universe than having a specifically sequenced 150 amino acid form randomly. The gamblers fallacy still grabs us. Well there is one chance. Surely some lucky protein will win. There is NO lottery commission that assures the “lucky” protein will be awarded the prize of functionality. In nature there are not always winners. It’s not a Disney movie. Undirected nature is not a laboratory that is carefully monitored. A lab tech doesn’t precisely measure several chemicals then gently mix them in a clean beaker, heat the mixture to a perfect temperature and then quickly remove the result. Chemical processes quickly move from one state to another and chemical mixtures may be overcooked, undercooked or another molecular process might interfere with the desired result.

Dr. Bill Dembski analyzed what is called probabilistic resources. There are 10⁸⁰ elementary particles in the universe. Due to the properties of gravity, matter and electromagnetic radiation physicists have determined that there is a limit to the number of physical events that can occur. Physically speaking an event occurs when an elementary particle interacts with other elementary particles. Bounded by the speed of light it has been determined that particles can interact with each other only so many times per second (10⁴³) . Since there has been a limited amount of time since the beginning of the universe 10¹⁷ seconds it is possible to calculate the limited number of opportunities for any given event to occur in the entire history of the universe.

Dembski calculated the amount of probabilistic resources by simply multiplying the three relevant factors. The number of elementary particles (10⁸⁰) times the number of seconds since creation 10¹⁷ times the number of possible interactions per second (10⁴³ ). His calculations determined the total number of events that could have taken place in the observable universe since its creation as 10¹⁴⁰ . In another words if the entire resources of the universe had only done one thing, attempt to assemble a single functional 150 –amino-acid sequence, it could not have happened randomly. The entire resources of the universe are represented by the number 10¹⁴⁰ while requirements of chance assembly are 10¹⁶⁴ .

Some things are beyond the possible, beyond reason, and in this case beyond the resources of the entire universe. If you still hold out hope for the lightning strike this should push you over the edge of disbelief. We have focused on the attempt to assemble, by chance, a single protein of 150 amino acids. The minimal requirement for any living cell is 250 proteins. Therefore for the first living cell to appear by random chance we would have to multiple the chance possibility of 10¹⁶⁴ by 250 which generates the probability of 10^41,000 . It didn’t happen! Dr. Fred Hoyle an avowed atheist, after analyzing the probabilities that life might randomly assemble issued the following statement.

"The chance that higher life forms might have emerged in this way (random chance) is comparable to the chance that a tornado sweeping though a junkyard might assemble a Boeing 747 from the materials therein."

Self-Ordering

Mathematicians and physicists were not the only ones able to do the math. As the complexity of life became more apparent researchers began to seek alternatives to random chance. Dean Kenyon as a young biophysicist wrote the following “… there would not be enough mass in the entire earth, assuming it was composed exclusively of amino acids, to make even one molecule of . . . a low-molecular- weight protein.” ( Signature in the Cell p. 229) Kenyon later co-authored a textbook with Gary Steinman entitled Biochemical Predestination. Self-ordering was seen as an alternative to the dimming hopes of chance and natural selection. The theory stated that the development of life was inevitable because the amino acids in proteins and the bases in DNA had self-ordering capacities.

The theory was based, in part, on the self-ordering as seen in such things as salt crystals. Chemical forces attract sodium and chloride ions to form highly ordered patterns. The figure below shows the tightly linked NA +CL+NA+CL forming an ordered structure. Knowing that there were other instances of chemical affinities Kenyon believed this same property would occur in proteins and DNA.

Since proteins are composed of long strands of amino acid the idea was that there would be some form of attraction between the amino acids that would cause them to line up and then fold to form functional proteins. The self-organizational theorists knew they needed to do more than simply assert that life arose because of chemical necessity. They needed to identify a specific law like process that could generate the critical components of living cells. The Kenyon and Steinman had noted the affinity of specific amino acids in “di-mer” bonding experiments. The results indicated that alanine formed linkages with glycine twice as frequently as with valine. Additionally these differences in chemical affinity seemed to relate to differences in the chemical structure of amino acids. Amino acids with longer side chains bond less frequently with a given amino acid than do those with shorter chains. ( Signature in the Cell p. 233) The two scientists proposed that these differences in affinity imposed certain tendencies and/or constraints on the sequencing of amino acids. “It would appear that the unique nature of each type of amino acid as determined by its side chain could introduce nonrandom constraints into the sequencing process.” ( Signature in the Cell p. 233.) Using this as a foundation the two scientists proposed that the difference in affinity might correlate with the specific sequences that were typical in proteins.

Like many theories the concept met with a rather bleak reality. Experiments quickly indicated that while there were slight affinities among amino acids none of them corresponded to any of the known patterns for creating proteins. Scientists might have been willing to spend more time seeking alternate routes and other variables if it had not been for the question of Hubert Yockey (information theorist) and Michael Polanyi (chemist). Their question was “What would happen if we could explain the sequencing in DNA and proteins as a result of self-organizing properties?” (Creator and the Cosmos p. 233)

Remember that in salt the crystalline structure organizes around a repeating pattern. If this were extrapolated to DNA A (Adenine) would always attract G (Guanine) and you would create A-G-A-G-A-G-A-G. This is not a message that will build proteins. This is where Yockey's Information Theory comes into play. To convey information you need irregularity that yields uniquely discernible patterns that function according to rules. A book does not have a single word that is repeated page after page. A useful and informative sentence does not have only one word or even words that are all four letters.

If all you had were repeating characters in DNA, then the instructions would merely tell amino acids to assemble over and over in the same manner. The biological complexity of life requires the flexibility to form different kinds of proteins and assign them differing functionality. Irregularity that is specified by a set of functional requirements is called “specified complexity” which is recognized as information. DNA's structure depends on certain bonds that are formed by chemical attractions. The hydrogen bonds between the sugar and phosphate molecules form the backbone of DNA molecules. However, there are no chemical bonds between the nucleotide bases, which are the DNA's assembly instructions. The letters that spell out the text in the DNA message do not interact chemically with each other in any significant way. “The point is - there is no attraction or bonding between the individual letters themselves. So there's nothing chemically that forces them into any particular sequence. . . . Neither chemistry nor physics arranges the letters (DNA) into the assembly instructions for proteins.” (Creator and the Cosmos, p. 235.)

The following clip "Intelligent Design" provides a commentary by Dr. Dean Kenyon on his theory of Biochemical Predestination. Dr. Stephen Meyer points to the growing information on the intricacy of protein formation ; which ultimately led to Dr. Kenyon repudiating the idea of self-assembly of proteins.

Dr. Stephen Meyer uses the example of letters adhering to a magnetic blackboard. The letters adhere in any arrangement much like the nucleotides adhering to the hydrogen phosphate backbone of DNA. However if we dropped letters onto the blackboard we might get a random two or three letter word. But the possibility of spelling “molecular,” “biological,” or “complexity” approaches none existent. It greatly exceeds any possibility that a sentence would randomly assemble. The molecular and biological world that is life is an elaborately complex assemblage.

Within an evolutionary scheme it is necessary to postulate simpler or more primitive systems. Dr. Michael Denton talks about the impossibility of having a less perfect translation system. How would it be possible to have a crude system - one that did not copy the gene information properly? According to the evolutionary mantra, the gene would select advantageous changes - however since the system copied only crudely any advantage would be destroyed in the next mistranslation. Each cycle of misinformation would increase the “noise” and erase crucial information - rather like a poor photocopier - each image would become fuzzier and fuzzier until the original is no longer recognized. In the case of transcribing the code of life, high mutational rates would flood the proto-cell with junk proteins swamping vital information - with an Alzheimer like effect.

The cat sat on the mat. Normal code

Mat the on sat cat the Inversion

He at at n he at Deletion

The hcat zsat jon the kmat Insertion

The cat cat satsat on the matmat Duplication

Take any one of the mutational forms and you can see how quickly a cell would be rendered nonfunctional. DNA consists of a complex code formed of four “letters” that are arranged into three letter “words.” Each word codes for a sub-unit of a protein, an amino acid. The proteins are analogous to complex machines, in that they have moving parts that repetitively perform a task. Several classes of mutations are shown above, but even in this simple illustration it is obvious that random changes in code do not increase the information content, making it unlikely that DNA mutations are responsible for the complex specificity of life.

Scientists have spent years trying to fashion pathways and find ways for DNA or RNA worlds to gradually aggregate into a living cell. The complexity of life has continued to elevate the problem.

Evolutionary Problems:

Oxygen-Ultraviolet Paradox:

The atmospheric presence of oxygen (via photodisocciation) would destroy or stop all prebiotic molecular development. An atmosphere devoid of oxygen would make it impossible for Earth to have a protective ozone layer and ultraviolet radiation would kill all prebiotic and/or organic molecules that did form.

STOP

Earth’s early atmosphere:

With the presence of a neutral atmosphere, no known terrestrial means is available to assemble biomolecules to form a primordial soup. The appeal to extra-terrestrial sources as the cupboard to create and deliver prebiotic material to the Earth has also proven to be a dead end. Additionally, any prebiotic material delivered prior to the Late Heavy Bombardment would have been sterilized by this catastrophe.

STOP

Primordial Soup:

Geochemists’ measurement of the ratios of both carbon and nitrogen in ancient deposits indicate that ALL such carbonaceous deposits were formed from the remains of living organisms. NONE of the deposits formed from prebiotic material. There is direct evidence that the mythic primordial soup is indeed a myth.

STOP

Formation of amino acids:

Chirality - Nineteen of the twenty amino acids necessary for life exhibit a specific handedness which has no natural means of formation. There is no naturalistic pathway to form the basic functionality of amino acids. Without amino acids, there can be no proteins.

STOP

DNA and RNA Co-Dependency:

DNA requires RNA to act as messengers to form proteins, create energy and replicate however RNA cannot function unless DNA provides information or instructions. If only DNA existed it could not replicate itself and would die. If only RNA existed it would have no function.

STOP

Cell membrane:

The cell is not just a bag of amorphous glop surrounded by saran wrap. The cell membrane is an integral part of the cell. The cell membrane provides protection from oxygen radicals and to contain DNA and ribosomes. Because of its integral function with DNA it is difficult to image a cell membrane or enclosed cellular body without a functionality.

STOP

Sudden Appearance of Life:

Life appeared suddenly and it was complete and whole. Cyanobacteria contains some of the most complex machinery of life. Prior to biomolecular research it was thought that life was only a matter of chemistry (i.e., water and the right elements). This theory has failed in light of the complex machinery of all living cells.

STOP

Summary:

All of these problems apply directly to the appearance of life. Life appeared suddenly and at its inception it was chemically and biologically complex. The slow gradual chemical pathway that was proposed by Darwin and assumed by many has proven to require a miracle - if not impossible. The chemical resources postulated as necessary for forming the fabled primordial soup were not available on early Earth. A neutral atmosphere does not provide the right stuff for the “chemical soup.” Additionally oxygen was present in at least limited amounts which would have stopped the production of prebiotic chemistry. Recent research into the presence of prebiotics on early Earth indicate that all of the carbonaceous substances were formed from biological or living matter. There was NO primordial soup kitchen.

Nor was there an extended time period to randomize and percolate this hypothetical chemistry. Life appears as soon as the rocks form. This first life may not have been as tall as you and me but cyanobacteria and the other microorganisms were responsible for the oxygenation of Earth. This first life required protein synthesis. The key to the conversation is that life requires information. Cyanobacteria and all subsequent life contains specified complexity, a blue print for the replication and construction of itself. Ink on paper makes a book. But if you pour ink on a piece of paper it would not form words and certainly not an entire play. The appearance of specified complexity will be dealt with more extensively in the next section (Behe's Nail).