Intelligent Design Undergraduate Research Center

Chemical evolutionary theory and its need for revision:

A Review Paper

By Holly Q. Bau

Published On-line June 16, 2005

Intelligent Design Undergraduate Research Center

www.idurc.org

Summary

Chemical evolution has grown out of the application of natural selection to chemicals in accounting for the origin of life. This paper examines the development of chemical evolution as a theory that has arisen in the past one hundred fifty years. The adequacy of chemical evolution as a theory is challenged in terms of historically important experimentations and its application of natural selection to chemicals. The probabilities of irreducible complexities are assessed, as well as chemical evolution's value as a scientific theory.

Initially, the Miller-Urey experiment performed by Stanley Miller in 1952 is examined. Miller was able to actually form amino acids in the lab. This experiment is highly regarded, even today, as a clear demonstration of chemical evolution and of the Oparin Scenario. However, several troubles within the Miller-Urey experiment, such as the composition of gases in the system and resulting amino acid structures have called these conclusions into question.

An experiment similar to Miller's was completed by Sidney Fox with his results being published whose results were published in 1958. Fox attempted to create life in the lab by simulating primordial conditions. While the findings are regularly cited as supporting chemical evolution, the this conclusion cannot be supported due to problems inherent in the results.

The probabilities of spontaneous formation of life are examined in regard to the simplest of cells and the complexity innate in their structures. Various chance values are presented that are connected related to basic units of life.

Lastly, chemical evolution is evaluated through the eyes of Karl Popper and Thomas Kuhn. The principles of falsification and paradigm shift are applied to chemical evolution. Looking at the difficulties with the experiments and the lack of progress physically testing the evolutionary theory , the reader is simply left with the quandary of whether it is time for a paradigm shift and a scientific revolution to arise.

Full text

It is necessary for an edifice to possess a sound foundation that can weather even the toughest of storms . Evolution, as a whole, encapsulates the groundwork upon which all of modern biology is constructed . Charles Darwin was completely unaware of the voyage on which science was also embarking when he set sail on the H.M.S . Beagle in December of 1831 . Twenty-eight years later , in 1859 the naturalist published the “book that shook the world,” officially known as On the Origin of Species (Allen) . This book immediately became immensely popular, while Darwin became a common, household name . However, little did Charles Robert Darwin know that, over time, he would become one of the most controversial names in history and in science.

Darwin established his theory of evolution based upon natural Darwin based his theory on natural selection for the level of the organism at the organismal level . Many scientists , since then , have made attempts attempted to apply this explanation to molecules at the chemical level . Darwin admitted that he did not understand the ultimate origin of life from non-living matter; however, he speculated in an 1871 letter to Joseph Hooker that life was created in “some warm little pond” ( Denton 249 Darwin 94, 188-9 ) . Hence, the chemical evolution world of research the world of chemical evolution research sprang into life . Many scientists seized upon Darwin 's suggestion and immediately began formulating hypotheses and experiments to explore the validity of Darwin 's original conjecture .

Since 1859, however, progress in this field has been disappointing . Students today ponder the question of whether the chemical evolutionary theories adequately account for the origin of life . Many pioneers in this field preceded the major biochemical discoveries of the century, such as the double-helical DNA structure published by Watson and Crick in 1953 ( Denton 233) . The initial chemical evolutionists who laid the groundwork theories were not even aware of the complexity present in DNA, a cell, a strand of protein . , etc. The established theories convey the scientific ignorance of the time-period in which they were formulated .

The field of chemical evolution has , itself , evolved over the past 150 years . Haeckel, well-known for his embryological embryo research, believed in the 1870s and 1880s that life was simply “protoplasm,” and that a cell consist s ed of a “homogeneous globule of plasm” (Meyer 115) . In the 1920s and the 1930s, Russian biochemist Alexander Oparin created another suggestion proposed an idea that was a bit more sophisticated in its implications . The Oparin Scenario, as it quickly became known, said hypothesized that life evolved from a series of chemical reactions; however, Oparin, l l ike Darwin , Oparin neglected to explain the initial processes (Meyer 115) .

Stanley Miller was curious about the Oparin Scenario and set out to prove its truth . . Miller performed the famous Miller-Urey experiment in Harold Urey's lab at the University of Chicago in December of 1952 . Miller needed to create an “ atmosphere ” that most likely existed in the prebiotic world . Therefore, he chose a mixture that resembles interstellar gas clouds (Wells 14) . Miller's “atmosphere” contained methane (CH4), ammonia (NH3), water vapor (H2O), and hydrogen (H2) (Wells 15) . These gases were placed in glass with an electrical discharge chamber running through the system (see Appendix). Miller then sent a high voltage through this chamber for one week to simulate lightning and the ultraviolet light effects of the sun . After the first experiment, this procedure only resulted in the formation two amino acids . However, through modifications of the system, nineteen out of the twenty known amino acids were eventually created . The twentieth amino acid was glycine (Meyer 116) .

Numerous scientific difficulties impediment are commonly associated with Miller's experiment . First of all, the mixture of gases that Miller used to imitate the atmosphere does not accurately reflect the early setting composition . No evidence exists supporting the assertion that the atmosphere contained many free ammonia molecules . Instead, ammonia absorbs the UV light rays, which in turn destroy the molecules (Wells 20) . Also, if methane were present in the prebiotic atmosphere, then geologists would find an abundance of organic compounds in early rock formations . However, this is definitely not the case (Wells 20) . Miller also neglected to remove the hydrogen from his system . By the end of the one trial week, hydrogen gas composed seventy-six percent of the mixture in the glass chamber (Wells 21) . In reality, the hydrogen would escape from the earth's atmosphere because of its relatively insignificant mass . In Miller's atmosphere, he assumed that oxygen was not present because it would have caused an explosion in the presence of the high-voltage discharge (Wells 12) . The common consensus today among scientists and geologists is that CO2, N2, and H2O were the main components of the early atmosphere (Meyer 118) . They also suspect that trace amounts of hydrogen atoms existed but would have escaped as already discussed (Wells 15) . Holland and Abelson suppose d that this atmosphere was believed to have been created by the Earth's volcanoes (Wells 15) . From these elements, oxygen would then have been present because of the photodissociation (splitting) of the water molecule into hydrogen and oxygen molecules (Wells 15) . The presence of oxygen is the root of a large debate among scientists . Generally, though, they accept that oxygen was indeed part of the atmosphere . For instance, oxygen is essential for the ozone layer to have been formed, which protects life on earth from the lethal UV rays of the sun ( Denton 261) . In 1996, Smithsonian Institution paleobiologist Kenneth Towe announced that “the early Earth very likely had an atmosphere that contained free oxygen” ( Wells 19 Towe (12)7-(12)15 ) . Researchers went back returned to the traditional Miller-Urey experiment in 1983 and substituted CO and CO2 for the methane in the gas mixture . This time, glycine was the only amino acid that they were able to form (Wells 21) . If one recalls Miller's original experiment t T his point is interesting because glycine was the sole amino acid that Miller was not able to create using the procedure with methane .

Another large significant dilemma dealing with the experiment pertains to is the structure of the amino acids . Nineteen of the twenty amino acids (except glycine again) have two different structures: the D form and the L form (Evolution) . These two different shapes are chemically known as enantiomers because the atoms are in the same positions, but the overall molecule is a mirror-image of the other . These differing types of amino acids are also known as left and right handed (Evolution) . The trouble with the experiment is that Miller's amino acids consist of an equal proportion of D and L forms . Biological life is incapable of using both these two different varieties in living tissue; instead, all L forms are essential (Parker 23) . Also, the amino acids procured from the experiment were beta, gamma, and delta amino acids, meaning that their structure was long; however, living tissues need alpha (short) amino acids (Parker 23) . Inserting just one beta, gamma, or delta amino acid into a chain of alphas affects both the secondary and tertiary structure of the protein and prevents it from folding in the necessary manner (Parker 23) .

Oparin and Miller, along with their fellow researchers, believe d that this prebiotic model for the “primordial soup” would have needed billions of years before it could create life . Science now faces a dilemma because the oldest rocks found on the planet date from 3.5 to possibly 3.85 billion years ago found on the planet , and they , indeed, contain single-celled organisms (Meyer 118) . This would require that life would have had to evolve rather quickly and not as the Oparin Scenario suggests . Plus, the supposed time between the birth of earth and the creation of life has been decreasing as more research is being performed in that field ( Denton 263) .

The Oparin model suggests that the amino acids formed proteins through a series of reactions . However, when amino acids combine, one water molecule is released (Behe 169) . This action then , in turn, inhibits other amino acids from forming proteins because of the concentration gradient that is formed . Even many leading scientists in chemical evolution are becoming skeptic s al o n f the Miller-Urey system . Because of today's knowledge, many researchers have disregarded the experiment . For instance, in 1995, Jon Cohen wrote in Science that “the early atmosphere looked nothing like the Miller-Urey simulation” ( Cohen 1925-1926) . in 1975 [something more current for “today's knowledge”?], Marcel Florkin, a Belgian biochemist, declare s that the experiment is “not now considered geologically accurate” (Wells 20). A prominent figure in the field of origin of life research named Klaus Dose commented in 1988 :

More than 30 years of experimentation on the origin of life in the fields of chemical and molecular evolution have led to a better perception of the immensity of the problem of the origin of life on Earth rather than to its solution . At present all discussions on principle theories and experiments in the field either end in stalemate or in a confession of ignorance. ( Johnson, Darwin 109, Behe 168, Meyer 118 Dose 348-356 ) .

Miller performed the experiment even before Watson and Crick had published their discovery about DNA . Science has not generated any new widely accepted theories on chemical evolution since the complexity of life at the molecular level has been was revealed . Taking into account today's knowledge, the Miller-Urey experiment possesses little reliability . This inadequacy of the experiment would not be a problem had the scientific world simply progressed past these conceptualizations . However, many textbooks including college biology texts and the International Baccalaureate Biology book still seem to esteem the work of Stanley Miller and Harold Urey as being absolute proof of chemical evolution (Weem 315) . Science needs to progress and begin informing students on of new knowledge instead of dwelling on outdated data.

Sidney Fox attemped t o create life in the l ab , in an experiment similar to Miller's . An experiment similar to Miller's by Sidney Fox was performed, again, attempting to create life in the lab. Fox heated pure, dry amino acids at temperatures ranging from 150 °C to 180 °C for approximately four to six hours . Fox designed his experiment in this manner in order to reproduce the environment and scenario around the edges of a volcano (Bliss 21) . His findings were published in Science in 1958 . His investigation produced microspheres (random groupings of protein-like molecules) and proteinoids (molecules that are similar to proteins) . Still, this test, like Miller's, proved to be problematic . Serine and threonine, two important amino acids in the formation of proteins, are were destroyed by brutal heat such as those in the brutal heat present in the experiment . Also, this heat convert s ed all of the starting L forms of the amino acids to , again , an equal proportion of L and D forms (Bliss 21) . As the readers recalls, these forms cannot form living tissues . The resulting proteinoids had interesting characteristics, such as modest catalytic abilities (Bliss 21) . However, they also lacked vital functions compared to the modern protein . In his book , assessing origin of life theories, Robert Shapiro remarks that “[the proteinoid theory] has attracted a number of vehement critics, ranging from chemist Stanley Miller…to Creationist Duane Gish . On perhaps no other point in origin-of-life theory could we find such harmony between evolutionists and Creationists as in opposing the relevance of the experiments of Sidney Fox” (Behe 170) . Fox's experiment comprises another argument that many scientists have basically relinquished .

Many scientists are now realizing the irreducible complexity within the most basic foundations of life . For instance, the cell is able to store, edit, and transmit information, while regulating its metabolic processes (Meyer 113) . Even the simplest of all cells are fantastically complex . Scientists have investigated the absolute minimum requirements for a completely self-replicating cell . Chemical evolutionists have had come face to face with the numerous interdependent cycles within the building blocks of life . For example, the simplest cell has many complex systems . The most primitive cell membrane is the bilayered lipid membrane . Five proteins are needed for the synthesis of these fats in the membrane . An energy metabolism system requires eight proteins . Ten proteins direct the synthesis of DNA and the nucleotides . Eighty separate proteins perform the ribosomal protein synthesis ( Denton 263) . These processes are dependent on each other and are necessary for the correct functions of the rest of the cell .

Even if these proteins could be assembled spontaneously, by themselves, they could not carry out the ir overall function . The cell membrane holds the entire cell together . The synthesis of the fats and lipids is required for the bilayered membrane. The energy metabolism system supplies power for the rest of the cell in all of its tasks . The DNA stores the information for the rest of the cell and provides the “blue print” for replication . The ribosomal protein synthesis performs replication and allows for new cells . An early cell would also have to perform the functions of replication nearly perfectly . It is necessary for the cell to translate accurately . Molecular biologist, medical doctor and author Michael Denton conveys the importance of precision when he states that “the function of a protein depends on it being very accurately manufactured and possessing exact highly specific configurations” ( Denton 265) . If the system possessed error prone translation machinery, then how would evolution ever move forward? Errors would simply create death within the protein . Proteins and cells that were speckled with faults would have created an entire chain of life whose functions were hindered by their inaccuracies .

Even some well known scientists and leaders in the field of chemical evolution are aware of the problems inherent in chemical evolution . For instance, minds such as Francis Crick are were baffled . Crick commented that “An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get if going” (Denton 268) . Today, even more knowledge exists in molecular biology than when Crick made this remark . Knowledge in this field during this past century has skyrocketed . Crick saw too many problems with modern molecular evolution and, therefore, chose to believe in directed panspermia . Panspermia is the concept that extraterrestrial organisms brought life to the planet earth at some point in ancient history . This theory, however, still does not explain the origin of life . It may answer the question of how life on earth came to be, but scientists are looking for the method that life, in itself, came to be . Even other authorities, such as the late British astronomer , Fred Hoyle , see too many problematic areas with the modern chemical evolutionary theories and turn to panspermia ( Denton 271) .

Bacteria, the most primitive organisms, exemplify an extremely complex structure . The probabilities associated with bacteria are amazing . The first bacteria are assumed to have had smaller and simpler enzymes than the present day bacteria ( Hayward 35) . The probability just for one of these enzymes to arise spontaneously is already 1 in 1020 ( Hayward 35) . However, this number does not acknowledge the 2,000 different enzymes that are necessary for the various jobs within the bacteria cell .

The origin of DNA also proposes a great challenge . The DNA, in its entirety, must have been created spontaneously along with the translation machinery (Meyer 121) . Without translation, DNA would be useless . Also, proteins would have had to be created to comprise the translation process . As was said before this point, the knowledge of molecular biology has grown incredibly since the discovery of the double-helical structure of DNA in 1953 . Nicholas Wade, a science writer for the New York Times wrote in June of 2000 that “everything about the origin of life on Earth is a mystery, and it seems the more that is known, the more acute the puzzles get” ( Wells 24 Wade ) . Scientists have been realizing this in private, but the general public is unaware of the weakness of current theories (Behe 172) .

The probabilities connected with DNA and amino acids also lend themselves towards the area of cause doubt within a student's mind . Peptide bonds are what transform the building blocks of proteins, amino acids, into a fully functioning strand . The probability of a peptide bond occurring independently of all other aspects of the protein strand is ½ . Then, if one considers the probability for one hundred amino acids peptide bond linkages to occur it would be (½)100 or a chance of 1 in 1030 (Meyer 125) . To add to the complexity of the problem, the synthesis of the protein also requires particular enzymes to produce the specific strand . Then, the student must remember that changing one amino acid results in the loss of the protein structure and sometime its function also . A well known example of the change in one amino acid is sickle cell anemia . The disease occurs through faulty hemoglobin when the amino acid valine is substituted for the glutamic acid (Bliss 28) . Now, consider that it is necessary for a protein strand to be composed of certain and specific amino acids in a designated order . The chances for the spontaneous appearance of this amino acid is 1 in 10130 for a typical protein (Meyer 125) .

However, scientists are able to ameliorate the probability by taking cassette mutagenesis into account . Cassette mutagenesis considers how many codon changes in the an amino acid sequence a protein is able to tolerate, while still retaining the majority of initial protein structure and function . The numerical value when scientists factor cassette mutagenesis into the problem is 1 in 1065 (Meyer 125) . As a whole, scientists do not wish to rest almost the entirety of evolution on the concept of chance . This is based on the fact that mathematicians consider any chance that is smaller than 1 in 1050 impossible ( Hayward 35) . Therefore, from the mathematical perspective, many of the figures given for the probability for just one protein to form are impossible . Then, this chance is only for the one protein . The probability of interdependent complex cycles arising is, of course, many orders of magnitude smaller . It is also valuable to point out that evolutionary theory rests upon these initial chances .

Two different methods of scientific epistemology can then be applied to the theory of chemical evolution . Karl Popper stresses the necessity for scientific theories to be falsifiable, meaning that they must be capable of being tested and experimented (Woolman 113) . Also, the possibility of evidence must exist that would disprove those theories . Popper believes that the only way in which science moves forward is if certain theories are falsified . Those old ideas are then disregarded and pushed aside to make room for the newer theories that fit today's evidence (Woolman 115) . Popper also states that “an hypothesis that cannot be falsified cannot be scientific…if you cannot, theoretically, falsify an hypothesis then it will not lead to new knowledge” (Woolman 115) . Falsification and, especially, falsifiability encourage the progress of science . Researchers cannot just become static in their findings . If one applies this to the concept of chemical evolution, he would be extremely surprised . The current, popular, scientific view of the origin of life postulates the inerrancy of chemical evolution . Under this paradigm, negative results are not seen as challenges to the theory . The question must be asked what evidence would suffice to upset chemical evolutionary theory . In other words, is it falsifiable? This important question is mostly ignored by mainstream science .

Thomas Kuhn is another important scientist who has had a great impact . Kuhn's foremost principle deals with paradigms . Scientists and humans, in general, are presented with an idea that originates in a certain set way of thinking . This concept is called a paradigm (Woolman 115) . Every aspect of human thought now stems from this point of view or perspective . “Eventually there comes a point when new observations are no longer compatible with the existing paradigm” (Woolman 115-116) . It is then time to switch to the new paradigm, which is the most accurate in relation to today's knowledge . The paradigm can shift whenever it becomes necessary and however frequently it is needed . This transfer then creates a scientific revolution (Woolman 115) . Kuhn's points are applicable to the field of chemical evolution . The theories that are still being presented are significantly discredited by the current knowledge that is available to mankind and science . Continual communication of the truth which supposedly lies in these theories seems to encourage scientific ignorance . Scientists defend chemical evolution so fiercely because huge complications would result, as Kuhn predicts from such a paradigm shift . A large scale scientific revolution, of the type Kuhn discusses, would occur from an awareness of the complete failure of chemical evolution (Johnson, Reason 70) .

The theories of chemical evolution seem to have reached their nemesis . Michael Denton declares that “the problem is to all intents and purposes insoluble in terms of modern biochemical knowledge” ( Denton 268) . Denton 's quotation implies that the theory is not falsifiable . These thoughts of falsifiability and falsification cannot be brushed off as mere opinions of the methods within science . For science, in itself, advocates these ideals . Science thinks that whatever theory lacks the ability to be falsified should not be regarded as a firm foundation on which to base scientific inquiry . However, how does the theory of chemical evolution measure up to this standard? Can it be investigated or falsified? Michael Behe is one of the prime scientific researchers and authors on the relations between biochemistry and evolution on the molecular level . Behe reveals that “in private many scientists admit that science has no explanation for the beginning of life” (Behe 172) .

After examining the Oparin Scenario, scientists such as Stanley Miller and Sidney Fox embarked on journeys to further progress scientific knowledge . Now, considering today's data, scientists understand the inadequacies of these past experiments . Also, bearing in mind the probabilities involved and the complexity apparent within DNA and the cell, researchers recognize the intense order within common structures . In light of all of this, the reader is only left to wonder why today's scientists have relatively halted the renewal of suitable theories . Research certainly is being conducted today but not nearly at the rate that it once was . The chemical evolutionary explanations presented in today's world fail to sufficiently account for the ultimate origins of life on planet earth Earth . Scientists need to light the spark in the origin of life research, kindle the passionate flame and bring molecular evolution into the twenty-first century.

Appendix:

Figure A—Miller-Urey Experiment (Wells 10) .

(a)Vacuum line; (b) high-voltage spark electrodes; (c) condenser with circulating cold water; (d) trap to prevent backflow; (e) flask for boiling water and collecting reaction products; (f) sealed tube, broken later to remove reaction products for analysis . In later experiments, the electrodes were moved up into the larger flask at the upper right, and a stopcock for withdrawing reaction products was added to the trap at the bottom . Most textbook drawings show these later modifications (Wells 11).

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