In addendum #3 we discussed developmental phenotypic plasticity and saw how it provides observable phenotypic change in organisms within relatively short periods of time.  We saw this change to occur as a result of non-random genetic response.  This response is non-random in so much as it is generated by environmental triggers and so does not occur fortuitously. 

       Phenotypic plasticity provides us with an observable alternative to the non-observable neo-Darwinian concept of random genetic mutation being responsible for the evolution of life forms over millions of years.  As already discussed in this series, genetic mutation is seldom advantages to an organism and therefore it is highly problematic that it could be the primary mechanism whereby organisms have evolved. Not only are mutations disadvantages to an organism, they are in most cases outright destructive.  They do not increase useful genetic information but are often seem to diminish useful genetic information. I use the word “useful” as it could be argued that any change in genetic information results in there being information that was not there before and therefore it is new information.   


       Genetic mutation involves changes in the arrangement of the letters of the genetic code. These letters are called nucleotides or nucleotide bases and are represented by the letters A, T, C and G. It is the various combination's of these letters that make up the genetic code found in the DNA.  It is the various arrangements of these four nucleotides that carry all the information necessary to build cellular machinery. The nucleotides are not the information but are the carriers of the information.  This is analogous to a fax.  Information is typed unto a piece of paper and sent via a fax machine to another person. The paper, ink, fax machine, etc. is not the information.  It is what carries the information from one place to another. Similarly, when human thought generates information and such information is transferred to an audio tape, the tape is not the information but the carrier of the information.  Likewise, the nucleotide is not the message but the medium carrying the message.

       The great debate currently raging in the scientific community revolves around the question of where DNA information comes from. Is such information simply the fortuitous arrangement of physical chemicals that make up the nucleotides or is there a non-material component involved?  At what point can a distinction be made between the physical and the non-physical. We know that all humanly constructed information systems result from the application of human intelligence.  It would logically follow that intelligence is also behind the information system found in the genome. Most evolutionary biologists, however, reject this conclusion.  While often admitting that biological organisms have the appearance of intelligent design, it’s concluded that such design is only illusory. They conclude life only looks designed but really results from fortuitous arrangements of chemicals.   

       This conclusion, of course, rests on the foundation of Darwinian and modern Neo-Darwinian belief that natural selection acting on random variation (classical Darwinism) or random mutations (Neo-Darwinism) can mimic the effects of intelligence and produce replicating living organisms devoid of  conscious intelligent design. Man, using his intelligence, has been able to breed faster horses by simply mating faster males with faster females. The same thing can happen naturally in nature without intelligent direction.  Faster horses can out run predators while slower horses cannot.  Therefore, slower horses diminish in number while faster horses increase in number.  It’s called survival of the fittest and seemingly has nothing to do with intelligent direction or design.  Darwin taught that given enough time, all life forms gradually came to be through this process. Darwin saw environment naturally selecting variations in organisms and therefore being the driving force behind the occurrence (evolution) of the great diversification of life forms. Upon discovery of genetics, evolutionists concluded genetic mutation is responsible for the random variation postulated by Darwin and it is this mutation produced variation that is acted upon by natural selection.  Thus Darwinism became known as Neo-Darwinism.

       Darwin readily admitted to not knowing how life began.  His focus was on how life developed after having begun.  Many early evolutionists believed life began through intelligent design with there being a variety of perspectives as to who/what was the source of such intelligent design.  It was believed that mind or intelligence proceeded matter.  However, with the advancement of chemistry and the discovery that organic chemical compounds found in living organisms could be synthesized from inorganic elements, it began to be believed that science could experiment with combining various chemical elements and ultimately produce self replicating life. 

       The science community began to believe that matter proceeded mind and everything that exists has come about as a result of chemical elements fortuitously coming together.  Intelligence came to be seen as the interaction of chemical elements as well. This view is often called scientific materialism as it is believed to be supported by scientific evidence. This view postulates it is matter, and not a supernatural intelligence, that has always existed and is eternal. Under this view, all existence, including the existence of intelligence, is the result of the fortuitous activity of chemical elements. 


       Nucleotides appear in a particular sequence in the DNA and when that sequence is in some manner rearranged, it is said a mutation has occurred. Mutations are analogous to word processing errors that may occur when copying a text.  In copying a text, words are sometimes misspelled, left out, substituted with other words, etc.  Depending on the extent of such copying errors, the text could end up saying something different from what was originally intended.  Mutations are substitutions, deletions, insertions, duplications and inversions of the nucleotides as they are being copied to create new cells.

       As discussed in addendum #3, when cells divide, they make a duplicate set of their chromosomes which are passed on to the newly created daughter cells. When the chromosomes duplicate, they don’t always do a perfect job copying the encoded information (nucleotides) on the DNA. Therefore, errors are produced. These are called point mutations as they involve rearrangement of specific nucleotides in the DNA. It is believed by Neo-Darwinists that it is these copying errors (point mutations) that are responsible for evolutionary development of organisms. Is this the case?  Is this even possible?

       There are over three billion nucleotides in the human genome. It has been experimentally shown that each nucleotide contributes in a tiny way to the overall construction of the genome. Every letter plays some role in genetic construction. At the beginning of genetic research, it was believed that much DNA was neutral because no identifiable function could be found and therefore no contribution to the viability of the cell could be identified. It was even given the name, “junk DNA.”  As genetic research has continued, more and more DNA has been identified as having specific function and therefore not neutral.  Geneticists are coming to believe there is no such thing as an entirely neutral DNA where nucleotides have no specific function.  Every nucleotide interacts with some other nucleotide in the formation of code.  This would be akin to every letter in this addendum having function in the overall construction of this paper. 

       Evolutionists have often criticized creationists by pointing to “junk DNA” as an example of a very imperfect genome which is filled with useless information, mistakes and fragmentation's and therefore reflects millions of years of random genetic activity rather than the product of intelligent design. It is asked why an intelligent designer would produce such an imperfect product.  In June of 2007, a group of geneticists concluded the human genome is more complex than previously thought and most nucleotides not only have specific function but are poly-functional in that they play multiple functional roles. For example, non-protein coding DNA that was previously thought to be “junk DNA” has since been found to direct the production of RNA that regulates the activity of protein coding DNA, controls RNA processing editing and splicing, regulates DNA replication, repairs DNA and provides a host of other functions. There doesn’t appear to be any such thing as “junk DNA.”  I highly recommend reading the 2009 published book entitled Signature in the Cell, by Stephen C Mayer for much greater elucidation of this issue. 

       Getting back to mutations, it is apparent all mutations have some impact on an organism regardless of how close to neutral such mutations may be. Since most mutations are deleterious to an organism, even the relatively neutral detrimental mutations will have some negative impact, though most will be very slight.  The further a detrimental mutation is from close to neutral, the greater its negative impact on the organism.  To repeat, the vast majority of mutations are deleterious.  They harm the organism. They do not contribute to survival of the organism and do not lead to a higher level of development. 

       The Neo-Darwinian concept of random mutation and natural selection predicts that deleterious mutations will be eliminated as they do not benefit organisms or contribute to their fitness.  Since the overwhelming majority of mutations are detrimental, natural selection eliminates them or their impact on the organism is so minor that natural selection has no bearing on them.  Only selected beneficial mutations contribute to evolution. But, beneficial mutations are extremely rare. Furthermore, it has been demonstrated that the majority of these rare beneficial mutations are close to neutral and have little impact on the organism and therefore would not be selected and simple drift out of the population.  Therefore, it is extremely problematical that natural selection of the relatively few occurring significant beneficial mutations is responsible for the evolution of life. 

       Some researches have estimated the ratio of deleterious to beneficial mutations to be one million to one and one researcher concluded the rate of beneficial mutations to be so low as to prevent any meaningful measurement. A glaring witness to the improbability of mutations generating evolution of life forms is found in the area of breeding plants.  For decades, plant breeders purposely created mutations in plants in hopes of producing beneficial mutations that would lead to improved varieties and better crops.  Large numbers of mutant plants were produced which were largely sterile, deformed and dwarfed.  Most telling is that there was virtually no significant crop improvement.  Very few beneficial mutations were observed that led to plant improvement.  Even where plant development was accomplished to produce a specific end result, it came at the expense of the plant losing or having a previous viable function reduced.

       Let’s look at low phytate corn as an example.  Corn, as is true of many grains and legumes, contains a compound called phytate.  Phytate is a salt or ester of phytic acid and is capable of forming insoluble complexes with certain minerals such as calcium, zinc and iron and thus can interfere with their absorption by the body.  Plant breeders, by mutanizing corn, were able to select for strains where the genetic code directing the production of phytic aid is damaged with the result that less phytic acid is produced. This has resulted in animal’s better absorbing minerals from animal feeds.

       What we have here is certain nucleotides in the genome being rearranged to produce loss of information leading to an altered phenotype within corn.  While this altered phenotype may be beneficial to animal digestion, at the same time it removes a benefit of phytic acid which has ability, in conjunction with other nutrients, to protect against disease by increasing the activity of killer lymphocytes in the body. There are phytic acid based supplements sold in health food stores as cancer fighters because of the enhancing effect of phytic acid on the immune system. 

       This is not the kind of mutation driven genetic change that leads to evolutionary development of simple to complex organisms.  As previously discussed, mutations do not increase information. Some may argue that a change in genetic information is the same as increasing information since you are seeing a different arrangement of nucleotides leading to a change in phenotype. It must be remembered, however, that the great majority of such rearrangement is deleterious to the organism and therefore could not be the engine by which evolution occurs.  While there certainly are beneficial mutations in nature, their rarity makes it extremely problematical they are the mechanism responsible for the great variety of life forms both extinct and extant.

       Even where mutation is seen as beneficial such as with low phytic corn, one must be aware of where the benefit occurs.  In the case of the corn, the benefit is not to the corn but to the animals eating the corn. The corn has actually taken a step backwards in losing the capacity to produce phytic acid.  Since phytic acid has demonstrated benefit to an organism, its removal is deleterious to the corn as it removes a beneficial component. This mutation is not beneficial to the corn and while lack of phytic acid may improve mineral absorption in animals eating the corn; it may also lead to less immune protection for the animals.


       Neo-Darwinism postulates there are enough beneficial mutations occurring over time to facilitate evolution.  Since beneficial mutations are rare, Darwinians must conclude it has taken multiple millions of years for beneficial mutations to manifest themselves through a process called natural selection. Mutations occur at the molecular DNA level of an organism and result in a change in the genotype of such organism. This change in genotype manifests itself as a change in the phenotypes of such organism.  Phenotypes are all the characteristics that are manifested in an organism. Natural selection is seen as the environment determining whether change in a particular phenotype survives and is passed along to succeeding generations.  It is believed the environment accommodates phenotypic change that enhances survival of the organism relative to its environment and does not accommodated phenotypic change that does not. 

       As already discussed, the vast majority of mutations are deleterious and lead to non-beneficial genomic change and loss of genetic information.  Phenotypic change derived from such genomic change is detrimental to the organism and does not contribute to its survival.  We see this in various genetically caused diseases.  Natural selection is seen as weeding out such non-beneficial phenotypes over time and eliminating them from the population. Since most genomic change is non-beneficial, most genomic change leads to non-beneficial phenotypic change if it leads to any change at all.

       Natural selection is seen as eliminating non-beneficial mutations by eliminating the phenotypic changes such mutations create.  Such elimination takes place as the phenotype interacts with the environment surrounding the whole organism.  Since most phenotypic change is due to non-beneficial mutations, most phenotypic change is eliminated.  Evolution requires an increase in and survival of phenotypic change.  Since beneficial phenotypic change is rare due to beneficial genotypic change being rare, natural selection, as the mechanism for phenotypic advancement into more and more complex organisms is very problematical.

       By postulating that natural selection determines what phenotypes survive and which ones don’t, the evolutionist is saying natural selection is determining the survival or demise of mutations that occur within the genome. The external environment of organisms ultimately determines which arrangements of nucleotides survive and which do not.  Some evolutionists believe this process takes place at the environmental level of the genome itself where non-beneficial mutations are largely eliminated before they lead to non-beneficial phenotypes.  It is believed this leaves mostly beneficial mutations to be selected at the molecular level and it is these mutations that then lead to survivable phenotypes. 

       However you choose to define the role of random mutation and natural selection; it doesn’t remove the fact that most mutations are harmful to the organism and will not lead to evolution of survivable phenotypes. Since beneficial mutations are rare, it is only by postulating multiple millions of years of gradual, minute, incremental phenotypic development, can the Neo-Darwinian promote the evolutionary conclusions so largely accepted by the scientific community. 

       Unfortunately for the Neo-Darwinist, postulating multiple millions of years of gradual, minute, incremental phenotypic development doesn’t square with the facts.  The Cambrian strata at the bottom of the geologic column shows completely formed organisms with no evidence of incremental transitional stages.  This is also true of all the strata above the Cambrian. We have seen that sedimentary rock can be formed rather quickly and fossils are mainly formed by rapid disposition of sediment. Then there is the evidence that genomes respond to environmental triggers resulting in phenotypic change and such change can and does occur in relatively short periods of time. In addition, we have the entire history of human experience where life is only seen to come from pre-existing life and cognitive activity is behind all activity.  Therefore to postulate self replicating life appeared spontaneously from inorganic elements devoid of intelligent direction is rather preposterous and not supported by the evidence.  

       What the evidence does show and support is the sudden appearance of millions of developed organisms which were in some manner suddenly entrapped in rapidly formed vertical strata of horizontal layers of sedimentary rock.  Since we know from experience and experiment that such sedimentary rock strata generally forms from the action of water, the evidence is strong for a massive flood being responsible for not only the Cambrian strata but the geological column in general. 

       Science needs to seriously reconsider its position in face of the evidence against Neo-Darwinian evolution.  It is apparent developmental phenotypic plasticity plays a major role in the development of organisms and the changes seen in phenotypes should be looked at within the context of such development.  Therefore, it may be appropriate for the scientific community to see evolution of life forms within the framework of genetic response to the environment than in it being environmental response to genetic mutation. While mutational activity plays some role in phenotypic change, it should be evident such role is small in view of most mutations being deleterious to an organism.

       When all the dynamics of the creation/evolution issue are objectively evaluated and the evidence is honestly examined, we must conclude that life results from the design and creation facilitated by a powerful intelligence.  It is apparent this powerful intelligence designed and created basic body types and set in motion the genetic machinery that allows them to adapt to changing environment which can and does produce change in phenotypes. This appears to be the process whereby much of the diversity we see in life forms, both extinct and extant, has developed.   


       Intelligent design has become an acronym for the teaching that there is conscious, cognitive intelligence behind the existence of the material universe and life.  This teaching does not attempt to define the nature of this intelligence but simply postulates there is sufficient evidence that such intelligence exists and therefore this approach should be equally considered along with other postulations as to origins.  The scientific community, by and large, dismisses intelligent design as not provable and therefore unscientific.  It is believed that postulation of intelligent design runs contrary to the scientific method. Since it is assumed the scientific method is the only way to arrive at the truth of a matter and since it is assumed the concept of intelligent design cannot be supported by the scientific method, it is concluded intelligent design is an unprovable concept and should be discarded as an explanation of origins.  Is this a valid conclusion?  Let’s examine the scientific method and see if the concept of intelligent design is as disconnected from this method as claimed and let us see if evolutionary theory is supported by the scientific method as claimed.

       The scientific method involves a basic approach to determining the truth of something.  It begins by making an observation of some phenomenon and, based on the dynamics associated with such phenomenon, proceeds to draw tentative conclusions about the cause of that phenomenon which is usually called a hypothesis.  This hypothesis is then used to make certain predictions as to how the phenomenon functions or comes to be.  These predictions are then tested through experiment or observation and the hypothesis is modified or left as is based on the results of the experiments or observation.  Experiments and observation are often repeated many times to insure the results are the same.  When such experimentation and/or observation consistently produce the same result, the hypothesis becomes a theory and provides a coherent set of propositions which explain particular phenomena. If repeated testing and observation continues to support the theory, it is accepted as being valid beyond reasonable doubt and is used as a framework whereby other observations are explained and predictions are made.

       The scientific community often accuses intelligent design advocates of being unscientific because it is believed intelligent design does not meet the standards of the scientific method. Therefore, it is believed intelligent design should not be taught as science in our public schools. Furthermore, it is believed the concept of intelligent design is intrinsically associated with the supernatural and therefore is a faith based concept that cannot be scientifically demonstrated to be true.  

       The scientific method is used to establish a level of probability that something is true.  Using the scientific method as outlined above, let’s consider intelligent design at the human level.  We observe material objects and events coming into existence on a constant basis. By observing the dynamics of their existence, we see material things are designed and manufactured (created) as a result of intelligent activity performed by living, cognitive human agents. Therefore, we can develop the hypothesis that intelligent design is responsible for the existence of material objects and events. This hypothesis can then be tested by observing humans exercising intelligent design leading to the creation of objects and events.  Based on the observed relationship between intelligent design and the production of various objects and events, we can purpose the theory that human intelligent design is responsible for the coming into existence of material objects and events.  If repeated testing and observation continues to support the theory, it is accepted as being valid beyond reasonable doubt and can be used as a framework whereby other observations are explained and predictions are made.    

       Our theory of human intelligent design becomes an obvious truth based on the mammoth amount of evidence available. Since the evidence is overwhelming as to the connection between human intelligent design and the existence of material objects and events, a prediction can be made that the agents of such intelligence, and the materials they use in design and creation, were themselves produced by intelligent design and creation. This is in keeping with the scientific method which allows for a theory accepted as being valid beyond reasonable doubt used as a framework wherein observations are explained and predictions are made. In view of the evidence seen at the human level, it is reasonable to infer that intelligent design is the mechanism at work throughout the universe.  It is a universally observed phenomenon that information arises from conscious activity.

       Therefore, it should be considered scientific to postulate that living intelligent cognitive agents were themselves designed and created by a living, intelligent cognitive source.  Humans, expressing cognitive intelligence have designed and created countless objects using materials found on and in the earth.  Why should it be considered unscientific to postulate human intelligence which produces design and creation of what is designed were not themselves designed and created by a conscious, cognitive intelligence? 

       It has been readily admitted by evolutionary biologists from Darwin to Dawkins that biological organisms have the appearance of design.  Yet these same biologists insist the appearance of design in biological organisms is illusory because they believe natural selection acting on random mutation of chemical elements can fully account for the appearance of design without direction from an intelligent source. The massive evidence of intelligence design associated with the creation of physical things is totality ignored as predictive of intelligent design being a dynamic in the appearance and development of life forms or the existence of the physical universe.  In view of the problems that have been identified with mutations modified by natural selection being the basis for the appearance and development of biological organisms, it seems indeed odd that the scientific community is so inflexible in there refusal to consider other propositions as to origins.

        The scientific community claims proponents of intelligent design have not published peer reviewed articles supporting their theory and therefore their theory is unscientific. When articles are published in scientific journals in support of intelligent design, the editors of such journals are taken to task for publishing such material because it is claimed intelligent design is unscientific. The circular reasoning here should be apparent. Furthermore, it should be understood that establishing the truth of something should not be based on artificially determined parameters of investigation such as the scientific method or whether there are peer reviewed articles published that are based on such method.  Determination of truth should be based on dispassionate and objective examination of all dynamics associated with an issue and allowance of the evidence to determine level of belief.  Truth should always be considered as provisional in so much that one should always be open to an objective reexamination of an established paradigm when challenged to do so.

       It is sometimes argued that science must be based on the assumption there exists no powers that cannot be defined in naturalist terms.  It is believed science must be based on natural law and natural law must be defined as what can be observed and tested.  It is believed anything outside of this approach is only speculation and should not be considered scientific. This position is problematic in so much as it fails to recognize that, although natural law can be observed and tested, its origin cannot be identified through such observation and testing. One can observe and test the law of gravity. Such observation does not identify where the law of gravity came from or how it is sustained. While the testing of a proposition is vital to establishing its validity, test results can be used to infer the validity of additional propositions which may not be able to be tested in like manner.  If science truly seeks to understand reality, it must not set arbitrary limits on investigation.  

       Science establishes validity on the basis of demonstrating that a phenomenon can be repeated over and over again, producing the same result.  The phenomenon of human intelligence producing design is constantly being repeated and constantly producing the same result which is creation of material objects and events. The repeated occurrence of the appearance of objects and events due to the exercise of human intelligent design provides overwhelming evidence to this being a mechanism whereby things come to be. All of human experience demonstrates information is generated by conscious cognitive human agents exercising intelligence.  Why then, is it considered unscientific to postulate that the production of information necessary to produce such agents comes from a conscious, cognitive, intelligent, information producing source? 

       The establishment of evidence for something should be based on a preponderance of evidence and evidence beyond reasonable doubt. The preponderance of evidence is that conscious, intelligent agents are responsible for the design and creation of objects and events.  This is the overwhelming and undeniable evidence of human history. Therefore, it is extremely likely that conscious, intelligence is the source for the design and creation of physical elements and physical life. In reality, intelligent design, as an explanation of life, is based on a much more sound scientific footing than is Neo-Darwinian evolution.  Neo-Darwinism postulates life arose from non-living sources and gradually developed over many millions of years through random mutation and natural selection.  Because of the great amount of time required, this process cannot be repeated in a laboratory setting nor can it be observed.  It can only be hypothesized on the basis of problematical mutational/natural selection theory, questionable interpretation of how fossil containing sedimentary strata came to be and on disputed dating methods of fossils and the rock they are found in. When all the challenges to evolutionary theory discussed in this series are taken into consideration, a scientific basis for evolution becomes highly problematical.

       On the other hand, intelligent design of life and the material universe is a highly probable truth based on the observation that intelligent design is a readily observed phenomenon and is at work on a continuous basis throughout the entirety of human history. While this does not provide absolute prove this process was responsible for the origin of life and the physical universe, it provides a very high level of probability that this is the case.  In this respect, intelligent design is more scientific than evolution as an explanation of the origin of life and the material universe. In view of the discussions presented in this series, it is reasonable to conclude intelligent design is responsible for the creation of a number of body types having informational systems enabling them to replicate and expand into a variety of organisms within established parameters of reproduction.  It is likewise reasonable to conclude the constituents of the physical world that are used by human intelligence to design and create where themselves designed and created by a powerful intelligence.  

       There is no question this conclusion involves philosophical/religious considerations as it should. By postulating intelligence is responsible for life and the material universe, we raise the obvious questions as to the nature of such intelligence. For Christians and Jews this intelligence is the God identified in the Biblical Scriptures.  For Islam, it is the God identified in the Koran. Other religious systems have other understandings as to this intelligence. Diversity of perspective as to the nature of this intelligence should not, however, prevent its consideration as an explanation of origins. 

       If the scientific method is to be the criterion for what is permissible for discussion in a school system, intelligent design actually meets such criterion better than evolution and should be part of any discussion of origins. Why not allow students to hear all sides of this issue and make up their own minds?  Such allowance does not have to involve discussion as to the nature of a possible intelligent designer. Intelligent design theory does not purport to identify the nature of the intelligence.  This theory is simply based on our experience that human intelligence produces complex and functionally specific information systems and many other arrangements of matter. Therefore, human intelligence can be seen as the causal agent in the production of such arrangements of matter.  Humans and all other biological organisms are themselves complex informational systems.  Based on our knowledge that complex information systems result from application of intelligence in the physical world, it is reasonable to conclude intelligent is the same dynamic involved in the creation of biological organisms. Furthermore, such a conclusion constitutes the best available explanation for the design and creation of biological organisms as no other explanation has produced sufficient evidence for how life came to be. 

       Discussion of the nature of such intelligent is another matter and one that should be taken up in the study of religion and philosophy.  I personally believe students, beginning at the High School level, should have access to comparative religion and philosophy courses where the various philosophical and religious systems of the world can be taught in a comprehensive matter of fact manner allowing students to examine the evidence and make up their own mind as to what is valid beyond reasonable doubt. 

       I personally believe our educational system is sadly lacking in teaching students critical thinking. Students are taught to parrot back what others believe to be true and are not taught to question and critically examine and evaluate what others believe.  This often leads to blind acceptance of social, political, scientific and religious doctrine.  This is very unfortunate.   

       In our next installment in this series, we will examine some specific ways Neo-Darwinism is taught and determine if such teaching is supported by the evidence.