Presuppositions of Science
 as Related to Origins

GORDON C. MILLS 
Dept. of Human Biological Chemistry & Genetics  
University of Texas Medical Branch Galveston, TX 77550 

From: PSCF 42 (September 1990): 155-161.

 The author begins with quotations from Hans Krebs: "hypotheses must not move very far from the facts" and "evolution is based upon acceptance by faith of fundamental presuppositions"; then proceeds to examine the validity of the presupposition "that everything can be explained in terms of natural processes." He argues that this latter mechanistic presupposition is clearly inadequate in the light of our present biochemical knowledge. The complexity at the molecular level of even the simplest life forms leads the author to propose: "An intelligent cause was involved in cosmological and biological origins; nearly everything else may be explained in terms of natural processes."

In this paper, I will consider some underlying principles important for scientific research and some of the presuppositions that undergird our scientific endeavor. In June 1988, I attended an interdisciplinary conference in Tacoma, Washington, entitled "Information Content of DNA," which dealt with many of the topics that I am concerned with in this paper. I will discuss subsequently some of the contributions of these individuals to my current thinking. I will also refer to other prominent scientists whose research and writings have helped to mold my views. One of the latter is Dr. Roger Williams of The University of Texas who made the following comment in a lecture; he thought it may have come originally from one of the Wright brothers:

If everyone accepted as true what is generally believed to be true, there would be no room for advances.

I believe this statement is one that every scientist should consider seriously. A scientist should always have a questioning attitude! I will come back to this thought repeatedly in the course of this paper.

I also have several quotations from Dr. Hans Krebs, a Nobel prize recipient. Dr. Krebs is certainly one of the most outstanding biochemists, with a research career extending from the 1930s to the 1980s. He spent about a month on our campus in the 1960s, and I had the opportunity to interact with him and listen to his lectures. Hans Krebs, in a lecture which was mostly philosophical in nature, made the following statements:

Specific axioms are needed as guides to hypotheses, which in turn serve as a stimulus for experimental  verification.¹

This of course, is generally recognized. Krebs went on to say, however:

Hypotheses must not move very far from the facts.¹

The history of biochemistry, particularly in regard to metabolic pathways, is littered with proposals that were later shown to be incorrect, primarily because the hypotheses proceeded too far beyond the facts. If you build hypotheses upon hypotheses, you will nearly always be wrong, and the result will be worth little or nothing. Scientific research must always be solidly anchored with experimental verification of initial hypotheses. It seems to me that this principle has often been forgotten in the pressures to obtain research funding. When a set of basic experiments is proposed in a grant application, the applicant is expected to go on to propose a second set of experiments and then a third set of experiments without knowing the results of the first experiments. This type of pressure is always a danger in our present system of grant supported research. The applicant is forced to proceed from valid hypotheses to hypotheses that are very tenuous.

Let's consider another statement by Dr. Krebs which relates to evolution:

Although supported by a body of evidence, it cannot be rigidly proved or disproved; it is based upon acceptance by faith of fundamental presuppositions.¹

Let us examine now some of the basic presuppositions of science, and see whether we agree with them, or whether they need to be challenged. The following resolution comes from the National Academy of Science:

Religion and science are separate and mutually exclusive realms of human thought whose presentation in the same context leads to misunderstanding of both scientific theory and religious beliefs.²

In general I would agree with this statement, and certainly in practice I would agree with it. However, when you deal with presuppositions, you cannot really separate religion and science, nor can you separate philosophy and science. All of these are intertwined in some manner or another when we consider the basic presuppositions of science.

Let me now examine some of the basic presuppositions as expressed by others. These are some that are cited by Dr. Charles Hummel in his book The Galileo Connection.³

 1. "There is order in nature. Nature has an underlying order that can be discovered."This is so fundamental that if it were not valid, most of us would not be doing research.

2. "There is uniformity in nature. What happens in one laboratory can be repeated elsewhere. "This last portion may need to be qualified somewhat by adding "under the same conditions." Achieving the same conditions is what causes lots of problems for scientists. If someone else cannot repeat our work, we hope we can attribute it to not having the same conditions. Uniformity has also been used in geology; not that events are happening necessarily with the same intensity, but that the same types of events have been happening throughout the various geological ages, whether they be catastrophic in nature or not.

3. "Validity of sense perception, or of sense extenders. "We have all sorts of instruments whereby we may extend our various senses, whether they be microscopes to extend the capacity that we have to see, or whether they be other instruments utilized to detect various other phenomena.

These are three of the major presuppositions of science, and I believe they would be accepted by nearly all scientists. If we start pressing them too far, we might find some problems. For example, with the validity of sense perception, there is always the problem of artifacts. Simply because data comes out of a machine does not necessarily mean that it is correct. We have to constantly be alert for the possibility of artifacts by carrying out appropriate control studies. Nevertheless, the presupposition regarding the validity of sense perception would be generally accepted by most of us.

The following is one basic presupposition where one might challenge a portion of the statement: "That everything (including origins) can be explained in terms of natural processes."⁴ The part that bothers me is that the word "everything" permits no exceptions. If it were "nearly everything," I would not object.

Jacque Monod, in his book Chance and Necessity, expresses the same thought in somewhat more flowery language: "...that chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, is at the very root of the stupendous edifice of evolution."⁵ 

When you deal with presuppositions, you cannot really separate
 religion and science, nor can you separate philosophy and science.

All of these are intertwined in some manner or another when we consider the basic presuppositions of science. George Gaylord Simpson, in The Meaning of Evolution,says: "Man was certainly not the goal of evolution, which evidently had no goal. He was not planned, in an operation wholly planless."⁶

Henry Margenau, Professor of Physics and Natural Philosophy at Yale University, makes the following comment: "Darwin's theory of evolution relies heavily on chance, unmitigated chance."⁷

In regard to the role of chance events, Margenau notes: "There are...important differences between the role of probability in quantum mechanics and in Darwinism. One difference is that quantum mechanical probabilities can be computed in an a priorimanner, and their values have been verified through innumerable measurements. This is not true in the theory of evolution, where the probabilities involved are related to certain conjectured chemical processes..."⁸

Margenau, in his book, The Miracle of Existence,provides an excellent critique of the views of origins that may be referred to as materialistic or mechanistic, i.e., that everything may be explained in terms of natural processes.⁹ The emphasis in the rest of my paper will relate to challenging that word "everything"in the above presupposition. Can we qualify that word, or at least modify it? I believe we can.

Let me come back now to the word "evolution"that has been used in my previous quotations. I like to be somewhat more precise in defining the word "evolution."I believe there is a great need for properly defining the terms that we use. Basically, there are three different types of evolution.

1. Chemical evolution,which refers to the origin of life; the origin of living cells from nonliving matter. It is really quite distinct. Charles Darwin, in his On The Origin of Species, had nothing to say about chemical evolution.

2. Microevolution,which is the divergence of species. This is really the primary contribution of Darwin's research; the tremendous divergence and development of new species. He provided a considerable body of evidence for this type of evolution.

3. Macroevolution,a term which is generally applied to the development of new phyla, or possibly to new orders or classes. Sometimes, the term macroevolution has been used in regard to the development of the eye, or the development of hearing, etc.

There is no sharp dividing line between macroevolution and microevolution. Since we have these three distinct types of evolution: chemical evolution, microevolution, and macroevolution, I will try to be precise in my terminology when I deal with these types. 

"Pure chance, absolutely free but blind, 
is at the very root of the stupendous edifice of evolution."

"G.A. Kerkut, in his book Implications of Evolution,includes the following assumptions as involved in theories of evolution:

1. Non-living things gave rise to living material, i.e., spontaneous generation occurred. 2. Spontaneous generation occurred only once. 3. Viruses, bacteria, plants and animals are all interrelated. 4. The protozoa gave rise to the metazoa. 5. The various invertebrate phyla are interrelated. 6. The invertebrates gave rise to the vertebrates. 7. Within the vertebrates the fish gave rise to the amphibia, the amphibia to the reptiles, and the reptiles to the birds and mammals.¹⁰

Kerkut evaluates each of these assumptions critically, noting arguments both for and against each of them. He also indicates certain alternate assumptions for some of these that may be equally plausible. Kerkut then notes: "...that these seven assumptions by their very nature are not capable of experimental verification."¹⁰ 

Our understanding of the complexities of cellular processes has
 increased by orders of magnitude, not just by doubling or tripling. 

The first assumption of Kerkut would correspond to chemical evolution. The second assumption, which is sometimes referred to as a monophyletic origin (as opposed to polyphyletic origins), is related more to universal similarities of organisms. More recently, many have suggested that the universality of the genetic code makes more sense if life originated only once. It should be noted that if this second assumption is correct, chemical evolution would not qualify for scientific study since repeatability is an essential prerequisite for experimental studies. Without a more specific indication of the evolutionary change involved, it will suffice at this point to note that both macroevolutionary and microevolutionary changes would be included in assumptions three through seven. These seven basic assumptions are related very closely to the one presupposition previously mentioned; i.e., that everything can be explained on the basis of natural processes.

There have been several books published in recent years that relate to the topic of chemical evolution. The Mystery of Life's Originsby Charles Thaxton, Walter Bradley and Roger Olsen, and Origins: A Skeptic's Viewby Robert Shapiro, both carefully evaluate the experimental evidence for chemical evolution. The authors of both books agree that experimental studies thus far provide no real evidence in support of chemical evolution. The third book is one written by Michael Denton of Australia, Evolution: A Theory in Crisis.Denton is a molecular biologist, but one who has a very broad understanding of all areas of biology. In regard to chemical evolution, Dr. Denton asks this question: 

Is it really credible that random processes would 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?¹¹

 I don't believe we should have any argument regarding the validity of this statement. The intelligence of man, in the forty years that I have been involved in scientific research, has advanced our understanding of science tremendously, particularly in regard to molecular biology. This is very evident when I compare the concepts current when I was in graduate school forty years ago with those of today. For example, the knowledge that a specific protein has a specific sequence of amino acids in a linear chain was unknown then. We considered then that the plasma protein, albumin, might be a group of closely related molecules with similar properties; but the idea that a particular protein might have a specific amino acid sequence was unknown at that time. Our understanding of the complexities of cellular processes has increased by orders of magnitude, not just by doubling or tripling. This illustrates the type of scientific advance that led Michael Denton to make the statement I quoted above. 

"Hypotheses must not move very far from the facts."

"Let me come back briefly to the issues of chemical evolution. For a number of years, school textbooks have included the experiments of Miller and Urey involving the production of amino acids from so-called primordial gases in a sparking chamber. This was hailed by many as a real breakthrough in chemical evolution studies. Both of the books noted above (Shapiro, and Thaxton, et al) have pointed out that the major presupposition for this experiment was that a reducing atmosphere surrounded the earth at the time that life began. Yet they also note that most scientists today doubt that a reducing atmosphere ever surrounded the earth. This, of course, means that all of the experiments utilizing a reducing atmosphere have no significance to origin of life studies. All workers in this field agree that if there were no reducing atmosphere, those experiments make no sense as origin of life experiments. But even if these experiments did make sense, the amino acids produced were a mixture of D- and L-amino acids, and many of the amino acids formed are not found in protein molecules. I must note again the quotation cited earlier from Dr. Krebs: "hypotheses must not move very far from the facts."¹ Yet advocates of chemical evolution, postulate that by chance you would get the kind of genetic information that we see in DNA and in protein molecules.

One of the other individuals present at the "Information Content of DNA"conference, was mathematician Dr. Hubert Yockey. He has calculated the probability that one might obtain by chance the sequence of amino acids found in cytochrome c, if the appropriate twenty L-amino acids were in solution.¹²> Cytochrome c is a protein of ca. 100 amino acids linked end to end by peptide bonds (C1 carboxyl group to alpha amino group). It is found in living cells, from the simplest organisms to the most complex. In making his calculations, Dr. Yockey assumes that the amino acids would react together in appropriate peptide bonds. Actually, they would not react without prior activation. He also considers, based on all the known amino acid sequences of cytochrome c in a wide variety of organisms, that any of the different possible sequences would be functional. With these assumptions, he found a probability of finding a functional cytochrome c by chance to be 2 x 10^-65. Others have calculated that if you filled all the oceans on earth with protein molecules you would require 10⁴² molecules. Is one to propose that by chance you would have not only a cytochrome c molecule, but enough other catalytically active protein molecules in close proximity to one another at the same time to have a living cell? Note that the probability of 2 x 10^-65 for the  formation of a single protein would be for the most favorable  circumstances. If the starting materials were racemic mixtures of D- and L-amino acids, as one would expect them to be, the probability of obtaining a cytochrome c molecule with the correct sequence of 101 L-amino acids would appear to decrease from 2 x  10^-65 to 2 x 10^-94.¹² 

"A belief that proteins basic for life as we know it appeared 
simultaneously in the primitive milieu on earth is based on faith."

If we considered the possibility of obtaining a cytochrome c molecule in a solution of a hypothetical primordial soup, the presence of nonfunctional amino acids and other reacting compounds in the solution would decrease the probability even further. These probability calculations prompted Yockey to conclude: "A belief that proteins basic for life as we know it appeared simultaneously in the primitive milieu on earth is based on faith."¹³ Surely, any hypothesis that has a probability of 2 x 10^-65 or 2 x 10^-94 or even lower, cannot be considered as scientific.

Any suggestion that chemical selectivity might greatly increase the mathematical probabilities for formation of a specific protein in non-enzymatic reactions is not valid. Depending upon the conditions, there might be slightly different degrees of incorporation of the different amino acids into a protein molecule. However, with a protein molecule of ca. 100 amino acids including all twenty amino acids, any preferential incorporation would tend to balance out; i.e., in many cases, incorrect amino acids might be preferentially incorporated. There would seem to be no reason to postulate that this could affect the overall incorporation of correct amino acids by more than a factor of ten in either direction. A ten-fold change would be minimal when related to a probability value of 2 x 10^-65. For calculation of this probability value by Yockey, it was assumed that only L-forms of amino acids would be available.¹² Consequently, another type of selectivity would relate to incorrect peptide bonding involving either the epsilon amino group of lysine or the C₄ and C₅ carboxyl groups of aspartate and glutamate. 

Any suggestion that chemical selectivity might greatly increase the 
mathematical probabilities for formation of a specific protein
in non-enzymatic reactions is not valid.

 If possible peptide linkages involving these groups were considered, probability values would be reduced even further. For the probability value of 2 x 10^-94, with the assumed starting mixture of D- and L-amino acids, peptide bonds would be as readily formed by the D-amino acids as the L-amino acids. There might be some slight differences in degrees of incorporation for the L- and D-forms, but it is unlikely that these would affect relative amounts incorporated by more than two- or three-fold. In any case, chemical selectivity would be just as likely to favor the incorrect D-form as the L-form of the amino acid. As noted by Yockey, the listed probability values would give the most favorable values, with actual probabilities probably being much lower.¹³

My particular contribution to the conference in Tacoma dealt with the translation system.¹⁴ This system involves the transfer of genetic information from a nucleic acid molecule, messenger RNA, to a specific sequence of amino acids in a protein molecule. The primary enzyme molecules in this process, the aminoacyl-tRNA synthetases are very complicated and extremely specific. For example, in the aminoacyl synthetase of a bacteria (Bacillus stearothermophilus) which utilizes tyrosine, fourteen different amino acids of the enzyme molecule make up the three-dimensional site on the enzyme that binds the different substrates, and initiates catalysis of the reaction sequence. The amino acids in this three-dimensional active site on the enzyme range from position 34 to position 233 of the linear chain.¹⁵ In the initial reactions of translation, the correct amino acids are attached to the corresponding transfer RNA molecules and not to incorrect ones. There are approximately 200 different protein molecules involved in the entire process of translation. The translation system is extremely specific and one obtains the newly formed protein molecules with amino acids in exactly the right sequence. Experimental evidence at this time indicates that this entire translation system is an absolute requirement of a living cell. You see in this case an example of a very high degree of specificity, and this specificity is an absolute requirement in obtaining a protein with the correct amino acid sequence. This translation system provides an excellent illustration of why many different protein molecules are required for a living cell, and why any suggestion that there might be life without a large number of these specific proteins is untenable.

I have cited for you only a few of the reasons why some scientists have concluded that the presupposition that life originated by chance is simply not a tenable position any more. Dr. Henry Margenau notes:

Many of these biologists, in trying to understand evolution, are still wedded to the old-fashioned but highly enigmatic notion of chance. Almost all of them feel however, that the original Darwinian concept needs some qualification, needs an invocation of some directedness, perhaps even goal-directedness, but they are embarrassed and unwilling to call it purpose or design.¹⁶

Michael Denton, who also participated in the Tacoma conference, makes the following comments:

The Darwinian claim that all the adaptive design of nature has resulted from a random search...is one of the most daring claims in the history of science. But it is also one of the least substantiated. No evolutionary biologist has ever produced any quantitative proof that the designs of nature are within the reach of chance.¹⁷

Whatever the reason for the extreme complexity of living things, there is no doubt that the level of complexity realized simply transcends all analogy and is without parallel outside the phenomenon of life itself.¹⁸

Dr. Peter Rust, another Tacoma participant, makes similar comments: "We have to conclude that the origin of the information contained in DNA is still a mystery...This brings us close to stating that the Creator designed it from the beginning."¹⁹

This translation system provides an excellent illustration of why 
many different protein molecules are required for a living cell, 
and why any suggestion that there might be life without a large number 
of these specific proteins is untenable.

 Denton also deals with problems of macroevolution; let me add that he accepts microevolution. I might note that many other workers in the field, Stephen Jay Gould of Harvard, for example, feel that macroevolution must have involved big jumps. Many of them feel that Darwinian natural selection cannot explain macroevolution, although natural selection may still have a role in microevolution. Denton chooses to use the term "discontinuities" to refer to these gaps or jumps in the evolutionary record. Whereas Gould still feels that the Darwinian hypothesis can be modified to accommodate these jumps or discontinuities, Denton feels that we have to take a whole new look and make major revisions in the theory. He comments as follows: "I have tried to show why I believe the problems are too severe and too intractable to offer any hope of resolution in terms of the orthodox Darwinian framework."²⁰

At this time, Denton is not too specific about what revisions are needed, but he argues strongly that the current theory is seriously flawed. He points out the inadequacies of phylogenetic trees. He feels that the protein sequence data fit far better into what he calls a circumferential arrangement rather than the traditional "tree."²¹ This departs from the presupposition that all living organisms were derived from some archetypal cell. He notes four different phylogenetic trees in the recent literature that differ so markedly in branching points that you would hardly recognize them. From the evidence he has cited, it is apparent that there are definitely some problems in explaining macroevolution as well as chemical evolution, and it is hoped that scientists will once again look at the evidence and evaluate carefully before accepting everything that is presented in textbooks, and especially in the popular science magazines.

I wish to propose to you that the basic presupposition presented previously be modified. I want to introduce the term "intelligent cause"which was suggested by several of the philosophers of science at the Tacoma Conference. One of these was Dr. Robert Augros, who expresses this thought as follows: "Either there is a mind behind this universe or there is not. If not, we should find no evidence of purpose or representation in natural things. But if there is a God, nature will necessarily show signs of the Divine intelligence since every effect reflects something of its cause."²²

The other scientist proposing the term "intelligent cause"was Dr. Charles Thaxton, to whom I have referred previously. The basic presuppositions that I am proposing are:

1. An intelligent cause was involved in cosmological and biological origins.Cosmological, because my understanding is that most astrophysicists agree that there is no way they can ever understand the origin of the universe. They speak of the first 10^-35 second after the Big Bang as being totally out of the reach of scientific understanding. As astrophysicist Robert Jastro has stated: "The latest astronomical results indicate that at some point in the past the chain of cause and effect terminated abruptly. An important event occurred-the origin of the world-for which there is no known cause or explanation within the realm of science. The Universe flashed into being, and we cannot find out what caused that to happen."²³

I feel that in regard to chemical evolution, we are dealing with probabilities that place this in the same category as the origin of the universe. This is why I include the term "biological" in the presupposition. Consequently, I am suggesting that scientists accept as reasonable the presupposition outlined above. I then suggest that the previous major presupposition be appended with a second statement as follows:

2. Nearly everything else can be explained in terms of natural processes.Both presuppositions are written in terms that should be acceptable to nearly all scientists.

In conclusion, I hope I have conveyed to the reader why I believe the original presupposition-i.e., that everything can be explained in terms of natural processes-is no longer tenable. I believe the evidence, if examined closely, will necessitate modification of it as I have in my second presupposition. If one wishes to argue that my first presupposition lies in the realm of religion or philosophy, I will agree, but also will note that all presuppositions are philosophical in nature. As Hans Krebs noted, all presuppositions are accepted by faith. If they prove to be contradicted by the scientific evidence, they may need to be replaced, but they should not be rejected "by definition" by claiming they are not science.

As a Christian and a scientist, I would personally modify these presuppositions further by saying that for me, the "intelligent cause" is the God of the Bible, and noting that the same God is sovereign over all of the natural processes included in my second presupposition. I would not necessarily expect those of other persuasions to agree with these latter statements. 

©1990

NOTES

¹Quotations from a lecture given by H.A. Krebs at the University of Texas Medical Branch, Galveston in December, 1966. 
²BSCS Newsletter, No. 49, 1972, p. 17. 
³C. Hummel. The Galileo Connection.Downers Grove, IL: InterVarsity Press, 1986, p. 158. 
⁴R. Nisbet. Origins Research,Vol. 11, No. 2, 1988, p. 1.
⁵J. Monod. Chance and Necessity.New York, NY: Alfred A. Knopf, 1971, Vintage Books edition, 1972, p. 112. 
⁶G.G. Simpson. The Meaning of Evolution.Yale Univ. Press, 2nd ed., 1967, p. 293. 
⁷H. Margenau. The Miracle of Existence.Ox Bow Press, 1984, p. 19. 
⁸H. Margenau. op. cit., p. 24. 
⁹H. Margenau. op. cit., chapter 2. 
¹⁰G.A. Kerkut. Implications of Evolution.Pergamon Press, 1960, pp. 6,7. 
¹¹M. Denton. Evolution: A Theory in Crisis.Bethesda, MD: Adler and Adler, 1986, p. 342. 
¹²H.P. Yockey. J. Theor. Biol., 67, 377 (1977). 
¹³H.P. Yockey. op. cit., p. 387. 
¹⁴G.C. Mills. Proceedings of the conference Information Content of DNA,"The Role of the 
¹⁵A.R. Fersht. Proceedings of the Robert A. Welch Foundation Conference on Chemical Research XXXI. "Design of Enzymes and Enzyme Models", 1987, p. 159. 
¹⁶H. Margenau. op. cit., p. 32. 
¹⁷M. Denton. op. cit., p. 324. 
¹⁸M. Denton. Proceedings of the conference, Information Content of DNA,"The Functional Integrity of Biological Systems: Implications for Genetic Engineering and Evolutionary Biology,"to be published. ^1
19P. Rust. Proceedings of the conference, Information Content of DNA,"The Unbelievable Belief That Almost Any DNA Sequence Will Specify Life,"to be published. 
²⁰M. Denton. Evolution: A Theory in Crisis,p. 16. 
²¹M. Denton. op. cit., chapter 12. 
²²R. Augros. Proceedings of the conference, Information Content of DNA,"The Significance of the DNA Code,"to be published. 
²³R. Jastrow. Truth: An International Inter-disciplinary Journal of Christian Thought,Vol. 1, 1985, p. 65.