Perspectives on Evolution

In 1859, Charles Darwin published On the Origin of Species in which he put forth an explanation for how life could have diversified by natural processes from a simple, original organism to the variety and complexity of organisms we see today.  He believed that the mechanism for this diversification was natural variation operated on by natural selection.   Darwin’s proposed mechanism was an extrapolation of the evidence, but at the time, it seemed to be both plausible and elegant.  After all, variation within a species was well known, as was the fossil record, which showed a progression from simple to complex life over time.  In the early 20th century, the discovery of genes and mutations gave a possible mechanism for the variation seen by Darwin, giving rise to what is called neo-Darwinian evolution.  Since the middle of the 20th century, however, science has gained an amazing understanding of the molecular details of life. These details challenge the neo-Darwinian theory of evolution.

This branch of the originseducation.org web-site will provide you with information that challenges the neo-Darwinian theory of evolution and the theory of chemical evolution, which tries to explain biological origins.  But first, we need to discuss some definitions.  If evolution is defined as change over time in the plants and animals living on the earth, then evolution is certainly true.  The fossil record is good evidence for this.  If evolution is defined as small changes in a species due to variation or mutation operated on by natural selection, such as bacterial resistance to antibiotics, then evolution is also true.  If evolution is defined as the common descent of all living organisms from a single, or perhaps a very few, single celled organisms by a process of random mutation operated on by natural selection, then evolution has some serious problems, as you will see.

 

Outline

The information presented will divide neo-Darwinian evolution into two separate aspects: 1) common descent and 2) the mechanism of random mutation operated on by natural selection.  Neo-Darwinian evolution integrates both of these aspects; so our separation may seem awkward at first; but we believe that the two aspects should be evaluated independently to the extent possible.  You will see that evidence for common descent, though inconclusive, is much stronger than evidence for random mutation operated on by natural selection being the mechanism for common descent.  If common descent is true, but random mutation operated on by natural selection is inadequate to explain common descent, then what is the mechanism for common descent?  Michael Behe in The Edge of Evolution, suggested that nonrandom mutation might be considered.  If common descent is false while the mechanism of random mutation operated on by natural selection is true, this situation would describe micro-evolution.  In addition, both could be true or both could be false.  That is why we will separate them.  We will also address biological origins, also called chemical evolution.  So, the topics to keep in mind are:

            1) biological origins or chemical evolution;

            2) common descent; and

            3) the mechanism of random mutation operated on by natural selection.

Biological Origins--Chemical Evolution

Chemical evolution is the hypothesis that, when life started, chemicals combined through random natural processes to form the molecules of life.  Gases in the earth’s early atmosphere, with the help of lightning, combined to form amino acids, sugars, phosphates, bases, and other molecules.  These were washed into lakes and ponds where the amino acids combined into chains to make proteins, the sugars, phosphates and bases combined to form RNA and DNA, and fat molecules organized to form membranes.  Ultimately, the proteins, RNA or DNA and membranes “cooperated” to form the first, living one-celled organisms. 

In 1953, the Miller-Urey experiment synthesized some amino acids (the building blocks of proteins) from a atmospheric gases that could have existed at the time life began.  Since then, other amino acids and molecules used in DNA and RNA have been synthesized in similar experiments.

At the time, the Miller-Urey results seemed to be strong evidence for the theory of evolution since it demonstrated that amino acids, the building blocks of proteins (which are the building blocks of life), can be produced by natural processes.  Following this success, it was believed that amino acids could then assemble into functional proteins by natural processes.  To date, this has not been realized.  Amino acids have not been found to assemble into functional proteins in natural environments.  There are some rather serious problems with the chemical evolution theory.

Problem 1:  The Miller and subsequent experiments used an “atmosphere” without oxygen, and oxygen would disrupt the formation of amino acids and other molecules needed for life.  Today, scientists believe that the early atmosphere contained oxygen.  Also, the experiments assumed that the early atmosphere contained methane and ammonia, but there is no evidence to support that assumption.

Problem 2:  Amino acids link to each other by peptide bonds, but these bonds do not form spontaneously.  Peptide bonds require the addition of energy and a mechanism for using the energy to assemble the molecules (Thaxton, Bradley & Olson; The Mystery of Life’s Origin).  In a living cell, amino acids are linked together by a molecular machine (itself made of proteins) called a ribosome, and ATP is used as an energy source.  The peptide bond reaction liberates water and requires a drying environment.  At the same time, a wet environment loaded with amino acids is required to bring different amino acids together.  Besides needing a mechanism to form the peptide bonds, one would need alternating wet and dry cycles for a chain of amino acids to form.

Problem 3:  The processes that form amino acids and other basic life molecules (assuming these processes are possible) also form contaminants including amino acids that are not used in proteins.  There are 20 amino acids used in proteins.  If a nonprotein amino acid or other contaminant links with an amino acid chain, the chain will be useless as a protein.

Problem 4:  Nineteen of the twenty amino acids used in proteins come in both left- and right-handed symmetries.  Roughly equal numbers of each are produced in origin-of-life experiments.  Proteins can use only left-handed amino acids.  If a right-handed amino acid is included in the amino acid chain, the chain will be useless as a protein.  This is called the chirality problem.

Problem 5:  Not all amino acid strings, even if there are no right-handed amino acids in the string, will fold into a functioning protein.   Doug Axe; (Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds; J. Molecular Biology, 341, 2004.) estimates 1 in 1077 amino acid chains will fold to produce a functioning protein for amino acid chains that are 150 amino acids long.  This is rather short for a functioning protein, and even so, the odds are not very good.  However, we can make a lot of amino acids with the carbon in the earth’s oceans, crust, and atmosphere. 

It is estimated (on the high side) that there are 1020 kg of carbon in the earth’s crust, oceans, and atmosphere—that is 5x1045 carbon atoms.   With about 4 carbon atoms per amino acid, a 150 amino acid string will require 600 carbon atoms, and we can make 8.3x1042 of these amino acid strings at a time using all of the earth’s carbon.  Let’s assume that we can make 8.3x1042 amino acid strings every second in the 500 million years between the time the earth cooled sufficiently and the first identified living cells.  I use one second as the assembly time because that is roughly the time it takes a ribosome to assemble a small protein.  There are 1.6x1016 seconds in this 500 million year period.  Thus, we can conceivably assemble 8.3x1042 x 1.6x1016 = 1.3x1059 amino acid strings.  According to Axe’s estimate, the probability that we can get one functioning protein by a natural process is 1.3x1059 x 10-77 = 1.3x10-18 or about one in a quintillion.

Problem 6:  A living, reproducing cell requires a minimum number of proteins.  Estimates say at least 100 (and probably 200 to 400) average sized proteins are required for the simplest living cell (Denton; Evolution, A Theory in Crisis, p264).  Proteins consist of between 50 and 3000 amino acids (Behe; Darwin’s Black Box, p 262), and the median length for bacterial proteins is roughly 400 amino acids.  If getting a single functioning protein is improbable, getting 100 proteins that work together is far beyond the reach of natural processes.

Problem 7:  The first living cell would also require DNA, RNA, and a cell wall.  This cell would require DNA with at least 120,000 base pairs (Denton; Nature’s Destiny, p 309). The problems associated with assembling sugars, phosphates and bases into DNA or RNA is a more difficult problem that assembling amino acids into proteins.

In a living cell, the assembly of a protein requires carefully controlled environments, molecular machinery, and the information provided by RNA, not just matter, energy, and amino acids.  RNA formation and DNA replication require the action of protein machines.  These form an integrated, interdependent system in a living cell.  Assembly of the first living cell is out of reach of natural processes.

A variety of theories that attempt to overcome these problems have all failed, including the “RNA world” theory.  In conclusion, chemical evolution has serious problems and defies rational belief.  For more information see the books The Mystery of Life’s Origin, Signature in the Cell Chapter 9, and Icons of Evolution Chapter 2.

Common Descent

The idea of common descent is that present plants and animals descended from a single, or a very small number of, one celled ancestor(s).  Evidence for common descent is generally based on the following areas of evidence:

            Paleontological evidence--suggestive fossil sequences in the fossil record;

            Morphological evidence--similarities in structure;

            Vestigial evidence--useless organs or structures that functioned in ancestors;

            Embryological evidence--features in the embryo that recapitulate those of ancestors; and

            Molecular evidence--similarities in DNA and protein sequences.

Paleontological evidence--The fossil record shows a progression from simple to complex animals over time.  According to macro-evolution theory, the progression went from single celled organisms, to invertebrates (several phyla), to fish, to amphibians, to reptiles, to birds and mammals, and mammals to man.  The fossil record may be interpreted as evidence in favor of common descent; however, basic types of animals suddenly appear in the record, stay almost unchanged for millions of years, and become extinct.  There are very few, if any, intermediates between basic types of animals and they are all controversial.

The Cambrian explosion refers to a 5-10 million year period 530 million years ago when most of the complex, multi-celled animal phyla (basic classification) came into existence.  Before that time the earth was populated with single celled organisms (bacteria), and, toward the beginning of the Cambrian, some jellyfish.  Intermediates between one-celled organisms and complex animals are missing.  This troubled Darwin, but he guessed that the fossil record was incomplete.  Today, the intermediates are still missing even though extensive samples of the fossil record have been found.  The fossil record has preserved jellyfish embryos and evidence of bacteria, so it is unlikely that the intermediates were “too soft to be recorded.”

for more information see Icons of Evolution, Chapters 3, 6, 10, and 11, Stephen Meyer’s Darwin’s Doubt and https://www.youtube.com/watch?v=4DkbmuRhXRY and https://www.youtube.com/watch?v=iZFM48XIXnk.

Morphological evidence—Animals (and also plants) have been organized and classified based on the similarity of their features, including morphology.  Macro-evolution assumes that these features are similar because the animals that possess them are genetically related.  That is one possibility, but the homologous features among animals come from different areas of the animals’ genomes, which is inconsistent with common descent.  For more information, see Icons of Evolution, Chapter 4 and https://www.youtube.com/watch?v=XgXT9sU6y18.

Vestigial evidence—Some animals have nonfunctioning organs that were functioning in their presumed ancestors.  Examples are mammae in male mammals, wings on non-flying birds, gills in mountain salamander embryos, and rudimentary pelves in boa constrictors and whales.  Common descent could explain these organs; however, the list of vestigial organs is shrinking as useful functions are identified for some organs or structures previously thought to be vestigial.  Also, common descent does not explain why some snakes and whales have a pelvis but others have little to no trace of a pelvis.

Embryological evidence—At one time scientists thought that the development of embryos recapitulates evolution.  In the mid 19th century, a biologist named Ernst Haeckel produced drawings showing the similarity among vertebrate embryos during the early stages of development.  These drawings appear in modern textbooks.  It has been known for over 100 years that Haeckel faked the drawings.  He modified them to look like he thought they should look.  In fact, the embryos are quite different during the earliest stages of development.  For more information, see Icons of Evolution Chapter 5 and https://www.youtube.com/watch?v=ByMn-_QD3P0.

Molecular evidence—An evolutionary tree, based on anatomical similarities and differences, purports to show the path over which animals evolved from a common ancestor to all the animals seen today.  One would expect that molecular evidence from comparing the amino acid sequences of proteins in different animals and sequences of base-pairs in DNA would support the existence of an evolutionary tree.  In general, similar animals have similar sequences in some proteins, but not others.  Base-pair sequence comparisons typically give a variety of trees depending on where in the genome one looks.  The trees do not give a consistent picture of common descent; and therefore, the tree model for evolution is almost certainly not a good model.  For more information, see Icons of Evolution Chapter 3 and Evolution, A Theory in Crisis Chapter 12.

The evidence for common descent is mixed and inconclusive.

 

The Mechanism of Random Mutation Operated on by Natural Selection

The theory of neo-Darwinian evolution, by random mutation and natural selection, is described by the following process:

1. It begins with a single celled organism with a few hundred genes, and progresses to highly complex organisms, with many thousands of genes, requiring increasing numbers of genes over time.

2. Genes in a DNA strand are sometimes duplicated (evidence for this is claimed to be found in “pseudo-genes.”), and strands of DNA may be transferred from other organisms like viruses. 

3. Sometimes chromosomes duplicate.  (Polyploids in plants give some evidence for this.)

4. Genes and chromosomes change by random mutation to produce new proteins without destroying the function of the original proteins.

5. Advantageous new genes (and their proteins) are selected by natural selection.

6. Advantageous genes spread in subsequent generations of a population.

7. Combinations of new, interacting proteins provide new innovations.

8. Changes in regulatory and developmental “genes” produce new body plans.


There are three key questions that arise from this process:

1. Is random mutation and natural selection an adequate explanation for development of the new proteins and protein interactions necessary for the innovations seen in the fossil record?

2. Can random mutation and natural selection explain the evolution of new body plans?

3. Would this process result in the DNA structure that we see today?

The adequacy of random mutation and natural selection—Behe deals with this question in his two books Darwin’s Black Box and The Edge of EvolutionEvolution from a single celled organism to the complex organisms in existence today requires the development of new innovations using thousands of new proteins and thousands of new multi-protein interactions.  Most multi-protein interactions involve six or more proteins with some involving several tens of proteins. According to Behe, no new protein interactions have been seen in 1020 P. falciparum (malaria parasite), 1020 HIV, or 1013 E. Coli cell divisions.  He calculated that if 1020 cell divisions are required for an interaction between 2 proteins, 1040 cell divisions would be required for an interaction among 3 proteins.  There have been a total of 1040 cell divisions since the beginning of life; therefore, interactions among 3 proteins are marginally possible and interactions among more than 3 proteins are out of reach of life’s resources.

The argument against the neo-Darwinian mechanism being capable of developing new biological systems through new protein interactions depends on probabilistic analysis.  In his analysis Behe assumed that developing new binding interactions between different sets of proteins are independent and that the probability for developing multiple, coordinated binding interactions is the product of the probabilities for developing the individual binding interactions.  Evolutionists challenge this assumption.  Their argument is that if each new binding interaction, which occurs in 1020cells, provides a protein complex that is beneficial to the organism, then the binding interaction will be conserved and a second coordinated beneficial binding interaction would require another 1020 cells. This would be much more likely than two coordinated binding interactions occurring in 1040 cells as calculated by Behe.  Kenneth Miller in his article “The Flagellum Unspun: The Collapse of ‘Irreducible Complexity’” (See Debating Design) argues that proteins analogous to the motor proteins in the flagellum’s motor are found in other molecular machines.  In fact, he suggests that all of the proteins found in a system might have independently developed in other beneficial systems.  When they are all present, they will assemble into a new beneficial system.  This argument is called co-option.  There are some problems with this argument:

1. The co-opted proteins Miller talks about are analogous to but not identical to those needed for the new system.  They must undergo at least a few mutations to interact with the other proteins in the system.

2. In recent experiments, Axe and Gauger started with functional proteins that are very similar in structure but have different functions.  They attempted to mutate one protein to obtain the function of the other.   They determined that more than seven mutations were necessary and ran a population genetics model finding that seven mutations would require far longer than 15 billion years and is thus out of reach for a random mutation-natural selection process.  (Gauger & Axe; The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway; Biocomplexity, 4/11/2011)

3. If co-option is true, we would expect to find all bacterial flagellum proteins used in different beneficial functions in the cell, but we don’t.

4. There must also be a protein system for the assembly process and another system for the maintenance process for the flagellum.  The machine, its assembly process, and its maintenance process would have to come about at the same time.  But how can an assembly system develop with nothing to assemble, and how can a maintenance system develop with nothing to maintain?  We would expect to find proteins for assembly, repair, regulation, and control of the flagellum that came together from other systems, but we don’t.

5. The idea that all of the pieces of a multi-protein complex, its assembly process, and its maintenance process developed independently and then came together to form a new biological system defies the imagination and has never been demonstrated.

6. Many systems contain “orphan” genes and proteins.  These are genes and proteins that are unique in structure.  The number of mutations needed to develop these proteins is far beyond the capability of random mutation and natural selection. 

Evolution of new body plans—Recent experiments are beginning to show that body plans are not determined by DNA.  It would appear that some epigenetic characteristic in the egg is responsible for determining body plan or architecture.  If this is true, then DNA and mutations to DNA may not have anything to do with new body plans.  See Signature in the Cell’s Epilogue for more information.

Random mutation and DNA structure—Roughly 2-3% of DNA codes for proteins in humans.

Until the mid 1990s, scientists thought the other 97-98% was junk--meaningless repetitive sequences and broken genes left over from the random mutation process.  It makes perfect sense that such a process would leave debris.  Recently, however, the ENCODE project has shown that most (at least 90%) “junk” DNA is transcribed and much of it provides gene expression, developmental processes, and regulatory networks that are functionally similar to those in engineered, logic-based systems.  In addition the information in DNA, including “junk,” is highly organized with efficient data retrieval, cross references, and a sophisticated hierarchical structure.  The organization in DNA is inconsistent with random processes, even those operated on by natural selection.  See Signature in the Cell’s Epilogue and The Myth of Junk DNA for more information.

The evidence from these three areas—new protein interactions, new body plans, and highly organized DNA—suggests that they cannot be explained by the mechanism of random mutation and natural selection.

Summary

1. The probability that chemical evolution could produce the first functional protein, much less a living cell, is infinitesimally small.

2. The evidence does not favor common descent, but cannot conclusively rule it out.

3. Random mutation operated on by natural selection cannot explain the innovations found in the fossil record.  In fact, DNA, and therefore mutations, may have little to do with producing new body plans.  The highly organized information in DNA argues against a neo-Darwinian process.

Neo-Darwinian evolution is a theory in crisis.

 

Bibliography

Darwin’s Doubt; Stephen Meyer; Harper One, 2013.

The Myth of Junk DNA; Jonathan Wells; Discovery Institute, 2011.

Signature in the Cell; Stephen Meyer; Harper One, 2009.

The Edge of Evolution; Michael Behe; Free Press, 2007.

Icons of Evolution; Jonathan Wells; Regnery, 2000.

Darwin’s Black Box; Michael J. Behe; Simon&Schuster, New York, 1996.

Evolution, a Theory in Crisis; Michael Denton; Adler & Adler, Bathesda, MD, 1985.

The Mystery of Life’s Origin; Thaxton, Bradley, Olsen; Philosophical Library, 1984.