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Handy Dandy Evolution Refuter

Handy Dandy Evolution Refuter

Chapter 6 - Molecular Biology and Evolutionary Theory

The frontier of biological science is molecular biology and molecular genetics. The fundamental assumption is that all biodesign information is contained in the genes and that changes in genes produce evolutionary change in species. Therefore, molecular biology should explain how evolution occurs.

1. Has molecular biology explained development of the embryo?

Answer: In 1984 Nobel Laureate biologist Paul Berg of Stanford University said No:

At present, there is no general theory that can be formulated to explain development; for example, the progress from a fertilized cell to an adult organism...

Another aspect of development that intrigues many people is trying to translate cell phenomenology or organ morphology into molecular terms. For instance, what governs the liver's growth and shape? What regulates the growth of cells? What triggers a cell into the division cycle? All of these questions require molecular explanation. Ultimately they will be defined in molecular and chemical terms.1

Take note of Prof. Berg's faith for the future.

Ten years later in of 1994 much progress has been made in understanding the genetic control of embryonic development. However, the location of designs for complex biological structures is still shrouded in much mystery. As we shall see, neither the embryonic development nor the evolutionary origin of complex structures and organs has yet been adequately explained.

Below under Question 6 we have quoted from an authority on embryonic development and evolutionary theory, Prof. Lewis Wolpert. Take note of the fact that in 1994 Lewis Wolpert affirmed the same faith in the future that Paul Berg did in 1984. We are still waiting for them to prove their case. They are still seeking their holy grail, the origin of life without God the Creator.

2. Has molecular biology explained speciation?

Answer: No, the process by which new species form is not well understood.

Prof. Richard C. Lewontin of Harvard University wrote in 1974, "...we know virtually nothing about the genetic changes that occur in species formation."2 Eight years later Prof. Edward O. Wilson, also of Harvard, said, "It [molecular biology] doesn't have much to say about speciation, about macroevolution or about rates of evolution."3

3. Has molecular biology explained embryonic development and evolution?

Answer: Although much has been learned about this subject, the big questions are still unanswered.

In Section 7 below we have quoted at some length from Lewis Wolpert's 1994 survey of recent progress in the study of embryonic development. He makes it clear that, at the level of molecular genetics, it is still not known why an egg becomes a chicken in 21 days. If this be so, it is certain that evolutionary science cannot explain how a microbe became a university professor in three billion years.

4. Has molecular biology explained the evolution of new complex organs or structures?

Answer: No, only limited variation has been partially explained.

Two internationally respected biologists, G. Ledyard Stebbins and Francisco J. Ayala, said No:

The most dramatic changes in thinking about evolution stem from new knowledge about genetic processes at a molecular level, and yet the implications of that knowledge for evolutionary theory remain obscure. The molecular pathways that lead from genes to visible characteristics are long, complex, and as yet largely unexplored. Until the relation of genes to development is better understood at a molecular level the full impact of molecular biology on evolutionary theory cannot be assessed.4

A family of genes, homeobox genes, are found in many different organisms to have important influence in the embryonic development of basic body plans. In 1992 Jean Marx surveyed recent progress in the coordination of two fields of evolutionary biology, embryonic development and molecular genetics. She observed that homeobox gene research,

...is starting to bring together developmental and evolutionary biologists, a merger that is badly needed, considering the intractability of certain evolutionary puzzles, such as the long-standing quandary of how the body plan of multi-celled organisms arose. ...While the final marriage of developmental biology and evolutonary theory is clearly some way off, perhaps one day it will produce an offspring that can explain in satisfying molecular detail, how new species evolved.5

By the term "new species" Marx actually refers to new organisms characterized by new complex biological structures.

5. Does molecular biology explain the origin of complex new biochemical systems?

Answer: No, such an explanation has yet to be published. Biochemist Michael Behe has dealt with this question very effectively in his 1996 book, Darwin's Black Box.6 He shows that the crucial issue at the molecular level is that of "irreducible complexity." This is logically related to the principle of a complex combination of complex interdependent parts that was outlined in Chapter 2 in our consideration of the molecular rotary motors that power the flagellae of the microbe E. coli.

For example, the step-by-step sequence of many biochemical reactions needed to synthesize one important molecule, adenosine monophosphate (AMP), in a living cell is amazingly complex (pp. 142-161). The process starts with a foundation molecule, ribose-6-phosphate. This foundation molecule is then modified in a series of reaction steps that leads finally to the product, AMP. Could such a complex biochemical system evolve step-by-step by a random process of mutations and natural selection (M&NS)? Evolution is defined as a blind process that does not know what its goal is. So what is NS selecting for? Each new intermediate step that is added by evolution must make a product molecule that has some value to the organism that causes it to be selected. Furthermore it presumably carries the process nearer to the AMP molecule that is the unknown goal. Therefore, an evolutionary theorist trying to explain the evolution of this chain of reactions leading to the desired amino acid must dream up some benefit offered to the organism by each reaction step and its product molecule that M&NS adds to the evolving series of reactions. And finally this unguided process stumbles on the final product, AMP. Has such an explanation ever been published in the biochemical literature? NO, not yet. And the principal reason for this failure is the fact that the existing system of chemical reactions that produces AMP is useless if any one of the reactions and its intermediate product is missing. If the complexity of the biochemical system is reduced by deleting just a single step, the system is non-functioning. The system as it exists for producing AMP is irreducibly complex.

Other irreducibly complex biochemical systems treated in Prof. Behe's book include the chemistry of vision (pp. 18-25), Bombardier beetle's artillery (pp. 31-36), cilia (pp. 59-69), bacterial flagellae (pp. 69-73), and the human immune system(pp. 74-97). Prof. Behe made a thorough survey of the scientific literature of molecular biology. He reports that the Journal of Molecular Biology in the past 25 years published about 100 papers per year on molecular evolution. Not a single paper attempted to explain in any detailed scientific manner the evolution of any complex biochemical system. The many hundreds of papers on this subject in the Proceedings of the National Academy of Sciences yield the same zero result (pp. 165-179).

6. Does not molecular biology prove that protein molecules have evolved?

Answer: The comparison of amino acid sequences of corresponding proteins in different species has been interpreted in terms of homology. It has been assumed, for example, that the cytochrome c molecule has evolved with time as new species have evolved from pre-existing species. However, a series of proteins with systematic differences and similarities no more proves evolution than does a series of fossil skeletons or of living creatures. (See Chapter 10, sections 1 & 2)

The fundamental protein chain of cytochrome c contains 101 amino acid residues, and the amino acid sequence (the order of the different amino acids along the chain) has been determined for about a hundred species of plants, bacteria and animals. The differences have been analyzed in terms of the assumption that the cytochrome c molecules have evolved by mutations at a constant rate for years. If this were the case, then the number of differences in the cytochrome c molecules from two different species should be proportional to the length of time back to the separation of their two lines of descent from a common ancestor. These times are obtained from the theory of evolution and the time table of historical geology. Graphs of this relationship have been published which show a fair straightline relationship, reflecting that the number of differences is proportional to the time.7 This may be taken as circumstantial evidence for the theory of molecular evolution.

On the other hand, :Michael Denton in his 1985 book, Evolution: A Theory In Crisis, shows that the data can be interpreted in accord with the creation model of origins.7 The essential structure of the enzyme is the same for all of the hundred or so species studied. For example, thirty-five of the 101 positions in the chain are invariant, being filled by the same amino acids in all of the species. Also, eleven of these unchangeable positions are together at the vital action center of the molecule where its enzyme function is performed. All of the cytochrome c molecules from the different species fold up into the same basic three-dimensional shape so that they can do the same job in cell chemistry. This accords with the view that the design was created, not evolved.

The differences in the amino acid sequences of the cytochrome c molecules of different species may be understood as either the result of mutations, or created differences, or a combination of these. The fewer differences generally observed between similar species is in agreement with the creation model. Denton has shown that the differences in the sequences, when arranged in a matrix, reveal that groups of similar species are separated from other such groups.7 There are no intermediates between the groups. These groups distinguished by the similarities of their cytochrome c molecules correspond precisely to their traditional biological classifications based on their bodily forms. And, finally, the molecular separations between these groups correspond numerically to the degree of their differences. For example, the difference between horse and dog (two mammals) is six percent, between horse and turtle (2 vertebrates) is 11 percent, and between horse and fruit fly (vertebrate and insect) 22 percent. The differences in cytochrome c molecules may in some cases be necessary or advantageous in certain species.

Finally, the theory and the graphs mentioned earlier were sharply criticized by prominent evolutionary scientists. It was charged that the time periods used in making the graphs were not really in line with current geological theory.8 It has been pointed out that, in order to interpret the protein sequence data and get results in line with current evolutionary theory, considerable computer "massaging" of data is practiced.10

Christian Schwabe of the Department of Biochemistry, Medical University of South Carolina, has raised serious questions about this theory. In 1986 he wrote an article entitled, "On the validity of molecular evolution," in which he said:

...many exceptions exist to the orderly progression of species as determined by molecular homologies; so many in fact that I think the exception, the quirks, may carry the more important message.11

For example the data of different molecular homologies often, in the same set of species, suggest different rates for the evolutionary "clock." It is not uncommon for the data from the same protein studied in different species to lead to ridiculous conclusions concerning the supposed evolutionary relationships of the species.

7. What bold assertions can we make about the failure of evolutionary biology?

Answer: We can assert that at the level of the molecular biology of the genes, where final explanations are supposed to be found, there are today still no testable theories or demonstrable mechanisms for biological inheritance, embryonic development, speciation, or the evolution of anything new.

Let us explain this sweeping claim. From the above quotations from leading evolutionary scientists we see that it is not known how or where in the DNA the design information is stored for the structures of organisms. Further, it is not known how any such stored information is translated into biostructures as the embryo develops from egg to adult. Biologists are struggling to solve this riddle. Humanly speaking, they might succeed someday. But as long as we are ignorant of this basic information, it is clear that we do not know how any new structures could be produced by evolution.

It is pretty well understood how genes are inherited, but just what the genes mean with respect to the structures of the organism is not known. Most genes apparently code for particular protein molecules, but it is not known what the proteins mean with respect to biostructures of the organism. Therefore, when chromosomes and their genes are inherited, we actually do not know what biostructures are being inherited. In other words, we really have only a very incomplete theory of biological inheritance! The complexity ot he situation is rendered almost infinite by the fact that most structural features of an organism are influenced by many genes (called pleotropy), and many genes influence many different structures in the organism.

Lewis Wolpert of the Department of Anatomy and Developmental Biology, University College London, is a leading authority on molecular biology and developmental biology, and their relation to evolutionary theory. In a brief survey of recent research published in 1994 he discussed findings in studies of the embryonic development of the fruitfly, Drosophila, raising serious questions:

...How, for example, does the change in just one gene change the antenna of the fly into a leg? It may well be that no general principles are involved in the control of morphogenesis and cell differentiation. Even so, we do not yet have an example where we understand in detail the development of a single adult organ. We remain largely ignorant of timing mechanisms and how the size of different structures is controlled.

How many genes control development -- as distinct from providing the housekeeping functions of the cell? The answer is not known, but one can guess. ...If one thinks of, say, 100 genes for each multicellular structure in the adult, then 50 different structures in Drosophila would require 5000 genes. For mammals, for which there are some 350 distinct cell types, tens of thousands of genes might be needed. Understanding the function of so many genes is made even more difficult by cases of apparent redundancy. that is, it is possible to knock out certain genes in mice without there being any obvious effect on the phenotype. It is likely that true redundancy is illusory and merely reflects the failure to provide the correct test for an altered phenotype. It may thus be very difficult to work out the true function of such genes.

Will the egg be computable? That is, given a total description of the fertilized egg -- the total DNA sequence and the location of all proteins and RNA -- could one predict how the embryo will develop? This is a formidable task, for it implies that in computing the embryo, it may be necessary to compute the behavior of all the constituent cells. ...

What will the next 20 years bring? ....We can also look forward to great progress in the area of evolution and development. We may then see the solution to grand problems like how basic body plans emerged, how they are conserved, and the origin of developmental novelty. We will thus come to understand how development constrains and directs the form of all multicellular organisms.12 (Developmental novelty refers to new, complex biostructures.)

It is clear from Wolpert's discussion that biologists cannot explain why an egg becomes a chicken in 21 days. He also makes it clear that the evolutionary origin of neither general body plans nor of new complex organs(developmental novelty) has been explained theoretically. But these are the primary, the most crucial problems for evolutionary theory. If secularistic science cannot explain how an egg becomes a chicken in 21 days, in it certain that a scientific explanation of how an amoeba could become a university professor in 3 billion years is far from achievement. Why is it then that the public is continually propagandized to believe that evolution is a fact and that science has it all explained? Could it be that science and education is now dominated by unbelievers who are falsely using science as a weapon against the God of creation?

8. Can we even be sure that all biological inheritance and all cellular activities are determined by the DNA of the genes in cells?

Answer: No, until it can be proved just where and how inherited information is stored in the genes, we cannot be positive that the genes do determine all inheritance.

To begin with, it is definitely known that some important biological information is transmitted in the structure of the plasma and outer cortex of the cell, not in DNA. This is the case both in fertilized egg cells and in protozoans which produce new generations by cell division.13 And so long as we remain ignorant of where and how the bulk of inherited information is stored in the genes, there is a possibility that important biological information is not stored in physical structures of the cell at all. In fact, it has been suggested that perhaps the genes cannot store enough information to describe and construct an organism.14

Let us indulge in a far-out speculation. Perhaps the information which determines the distinctive structures of the created kinds is provided through an immaterial channel, by special divine providence! In the current state of scientific knowledge and ignorance, it is not possible to prove that this speculation is false. Under this model for genetics, the information carried in the chromosomes and their genes provides for fundamental housekeeping in the cells and in the whole organism. This information would also provide for limited genetic variation and adaptation to changing environments.

In Chapter 2, Section 3-d, we described at length the mysterious construction of the Venus flowerbasket sponge by disconnected, blind, brainless single cells. Then we described the mysterious ability of blind, brainless amoeba-like arenacious foraminifera cells to build little houses from sponge spicules found in the dark ooze on the sea floor. Scientists are helpless to explain how DNA in genes can empower and direct these cells to accomplish their tasks. It is certain, therefore, that scientists are also helpless to explain how these tiny creatures evolved with their mysterious powers.

We conclude that Christians cannot be faulted on scientific grounds if they believe that some aspects of living organisms are actively directed by special divine Providence. The Scriptures suggest that God is actively involved in the lives of all of His creatures.

...These all wait for You, that You may give them their food in due season. What You give them they gather in; You open Your hand, they are filled with good. You hide Your face, they are troubled; You take away their breath, they die and return to their dust. You send forth Your Spirit, they are created; and You renew the face of the earth. (Psalm 104: 27-30)

...If He should set His heart on it, if He should gather to Himself His Spirit and His breath, all flesh would perish together, and man would return to dust. (Job 34:14-15)

As we said. we are offering a far-out speculation. But there is no law against speculation in science. This idea is not a testable scientific hypothesis, because it involves a supernatural element. But the definition of science does not prohibit a scientist from believing in divine special creation and in a supernaturally imparted aspect of living matter. These ideas can also be a part of his conceptual framework for his scientific work. We have proposed here a type of divine "vitalism." Vitalism is the idea that living matter possesses some character radically different from non-living matter, something beyond the laws of physics and chemistry. This concept was repudiated by most scientists after the mid-19th century, for two reasons. First, they had begun to have some success in showing how living organisms function according to the laws of physics and chemistry. Second, following Darwin, they were moving toward the belief that everything in the universe has a completely materialistic cause and effect explanation. But this view of the world has yet to be validated by science. A scientist who believes in a created, divinely directed world is entirely free to do so, and the data of science afford him much support for this belief.

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1 Berg, Paul in Chemical & Engineering News, 62, 13 Aug. 1984, p. 62.

2 Lewontin, Richard C., The Genetic Basis of Evolutionary Change (Columbia Univ. Press, New York, 1974), p. 159.

3 Wilson, Edward O. in Lewin, Roger, "Molecules Come to Darwin's Aid," Science, 216, 4 June 1982, p. 1092.

4 Stebbins, G. Ledyard, and Ayala, Francisco J., Scientific American, 253, July 1985, p. 72.

5 Marx, Jean, "Homeobox Genes Go Evolutionary," Science, 255, 24 Jan. 1992, pp. 309, 401.

6 Behe, Michael J., Darwin's Black Box the Biochemical Challenge to Evolution (Free Press, Simon & Schuster Inc., New York, 1996)

7 Dickerson, Richard E., ibid., 226, April 1972, pp. 58-72.

8 Denton, Michael, Evolution: A Theory in Crisis (Adler & Adler, Bethesda, MD, 1986), pp. 274-307; see also Kofahl, Robert E. and Kelly L. Segraves, The Creation Explanation (Harold Shaw Publishers, Wheaton, IL, 1975, pp. 165-169.

9 Crowson, R.A., Nature, 254, 3 April 1975, p. 464.

10 Dwinell, Mark, Origins Research, 8, No. 2, Fall/Winter 1985, p. 10.

11 Schwabe, Christian, Trends in Biochemical Sciences, 11, July 1986, p. 280.

12 Wolpert, Lewis, "Do We Understand Development," Science, 266, 28 October 1994, pp. 571-572.

13 Sonnenborn, T.M., "Gene Action in Development," Proc. Royal Soc. London. B. 176, 1970, pp.347-366; Jones, A.J., Creation Research Soc. Quarterly, 19, June 1982, pp. 13-18.

14 Bremmerman, Hans, Progress in Theor. Biol., 1, 1967, pp. 70-72.

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