Chapter 8  The Case for Intelligently Driven Changes in Life Forms

If you arrived by spaceship on planet earth and saw its marvelous environment, living organisms, including the incredible human beings, would you not rationally conclude that it was somehow developed by intelligence?  If you studied in depth the incredible complexity of the DNA mechanism and the chemical and biochemical processes that make it all function, would that conclusion not be made even more emphatically reasonable?

How then were we led away from this simple, most logical conclusion about life on earth?  What faith or logic were we following?  What non-scientific conclusions were we bowing to; under the assumption that they were scientifically proven conclusions?

Because of our limited knowledge and understanding humans must have faith in things they cannot see or understand to allow their life to function effectively.  It is a human necessity.  The decision of how to live life must be made without full knowledge of past and future.  One cannot wait until the end of life to figure out how to live life.  But such faith must be based on the best possible knowledge and understanding.  Truth must always take precedence.

Scientific methodology is a fantastic tool.  It can show much that is not true.  But it simply cannot answer the important questions about things like the origin or purpose of the human spirit and how to live.

The human spirit is a creative and designing spirit.  Is this the highest and only spirit in the universe?  Why would we conclude that?  Why should there be such opposition to belief in a greater or supernatural spirit?  Where did the human spirit come from?  Was it purposed and designed?  Or is it the result of mere random, chance chemical meanderings?  Such a conclusion seems totally impossible and irrational.  Should we believe the conclusion of our human intelligence?  I think we should and not accept anything less than absolutely scientifically proven answers to contradict that belief.

Why would we believe in a greater spirit?

Consider why we believe dark matter and dark energy exist.  Why should we believe they exist when we cannot detect them?  ...By the effects they have on what can be seen!  We may not be able to detect dark energy and dark matter directly, or to understand what they are and how they can work, but we believe they really exist by the physical effects they seem to cause on the material we can see and evaluate.  In a similar manner I think the universe, the earth, its environment, the living organisms, and the human spirit should evoke the conclusion that this was developed by intelligence, not by mere random happenstance.

Living organisms have increased in number and changed dramatically since their first appearance as fossils three and a half billion years ago.  Thousands upon thousands of humans have applied themselves to the task of finding, extracting, and analyzing these fossil organisms and understanding the geologic context in which they are found.  It has been a major academic endeavor.  The sequential changes in those organisms and the general timing of the changes are clear in the fossil record and can be scientifically proven.  This was emphasized in chapters 6 and 7.  The cause and purpose is what cannot be scientifically proven.  These have to be concluded in the realm of belief and faith.

What is not scientifically proven from the fossil record is the cause of the observed changes… 

The causes of the major changes in living organisms through time is anything but scientifically proven.  Only hypotheses can be suggested and those are primarily influenced by the belief and faith of the evaluator.  If one’s faith is that of materialism then the only option that can be hypothesized is that natural processes have caused all the changes.  For some of the observed changes such natural causes may well be true.  But to suggest that random natural processes produced all the fantastic complexity observed in the chemistry of living and fossil organisms of the world logically staggers the imagination. 

Even Charles Darwin had a hard time shaking his conclusion that there was an intelligent God responsible for human beings.  Note this quote from his autobiography which was written near the end of his life…

“Another source of conviction in the existence of God, connected with the reason and not with the feelings, impresses me as having much more weight.  This follows from the extreme difficulty or rather impossibility of conceiving this immense and wonderful universe, including man with his capacity of looking far backwards and far into futurity, as the result of blind chance or necessity.  When thus reflecting I feel compelled to look to a First Cause having an intelligent mind in some degree analogous to that of man; and I deserve to be called a Theist.

This conclusion was strong in my mind about the time, as far as I can remember, when I wrote the Origin of Species; and it is since that time that it has very gradually with many fluctuations become weaker.” (The Autobiography of Charles Darwin 1809-1882, p. 77)

Thomas Huxley has been called Darwin’s bulldog.  Perhaps he and other prominent materialistic philosophers of the day were also bullying materialists that greatly influenced Darwin’s thinking.  The scientifically errant theology of the day didn’t help support Darwin’s faith either.

A materialistic belief and approach has now dominated virtually every prehistoric science, whether it be geology, paleontology, archaeology, or even early history.  One would not be accepted as a credible professional in any of these sciences without espousing a materialistic faith and philosophy.  Why should this be so?

Science is the study of the material world.  It is materialistic by nature.  To suggest a supernatural cause cannot be processed by scientific methodology so such a suggestion is automatically excluded from any scientific discussion, publication, or work.  Such a suggestion is not unreasonable, irrational, or illogical, but it is not scientific.  So merely by definition any supernatural activity is excluded from even serious consideration.  Things proven by scientific methodology are true.  But scientific methodology is not the only path to objective knowledge.  Much knowledge and understanding humans need are outside “the science box.”

To a materialistic scientist, invoking God to explain any physical result is like considering that God has to intervene to make a mathematical equation work.  It is correctly illogical and irrational to think that God has to specifically intervene to make a mathematical equation work…Or an airplane to fly. But such an analogy is simply a wrong analogy.  Living organisms do not function as mathematical equations.  They are acted upon by various external forces and in ways that cannot be mathematically defined.  Human beings can act upon other living organisms or physical materials in rational or irrational ways.  Human behavior is not determined by mathematical equations but by the human spirit.  Humans create new technologies by that human spirit.  Why would we conclude that an intelligent God did not do the same?  …Especially when we have no scientific proof against it.

 Considering the Evolution of Living Organisms as the Product of Intelligence

Materialists often chide believers for “God of the Gaps Thinking.”  There are numerous examples where this type of thinking has drawn absolutely wrong conclusions.   However, currently many materialists and popularizers of evolution are guilty of an equivalent non-scientific way of attributing change in the fossil realm.  It could be briefly summarized as: “Natural Selection of the Gaps Thinking.”  It likewise is based more on faith and belief than on science.  True scientific proof of how the actual changes were made in fossil animal DNA is almost totally impossible to obtain.   Because of this, explaining the changes in the fossil record has moved from “God of the Gaps” thinking” to “Natural Selection of the Gaps” thinking without demanding actual scientific proof for how it was done in the specific case.  The shift is from one faith to another faith, not from faith to science.

It is stated… An organism needed to change to survive some change in the environment… And, hocus pocus, at just the right time natural selection produced the needed changes to the organism’s DNA.  This is not science.  It is storytelling based on conjecture and belief.

Evaluating the supernatural by scientific methodology is a misapplication of science.  But constructing hypotheses of how something happened that are impossible to test is also a non-scientific endeavor.  It is a statement of belief.  When examining the changes in fossil lineages in geologic strata the changes are correctly attributed to changes in the genetic material of the organism.  However, proving scientifically how or by what means those changes in the genetic material were made is, in most cases, impossible for fossil organisms.  Yet, almost without fail, the materialist trots out the “Natural Selection of the Gaps Thinking” to explain all the changes.

The fact that the cause of the change is not scientifically provable is often over looked, or glossed over, by most scientists dealing with any such question.  We need to take note of two who openly acknowledge that fact.  Two prominent paleontologists clearly state this lack of proof in the introduction to some of their writings.  (The bold emphasis is mine.)

 Philosophers and other non-scientists have often suggested that evolution may have been due to some Supernatural agency or some mysterious “drive” within the animal itself.  No one can prove, of course, that this is not the case.  But as scientists we attempt to explain the phenomena of nature in terms of natural laws before resorting to supernatural interpretations.  (Alfred S. Romer, The Vertebrate Story, p. 5, Univ. of Chicago Press, 1959).

Nevertheless, much of what appears to be a basic human need, that of understanding the place of man in the universe, lies outside the area of descriptive and interpretive science.  These other parts have traditionally been dealt with by theologians and philosophers.  Consequently, this book will deal with what happened in the history of the close relatives of man and of man himself.  Why this happened remains a matter of individual belief.  (Elwyn L. Simons, Primate Evolution: An Introduction to Man’s Place in Nature, p. v, The Macmillan Co., 1972).

Both of these men had excellent knowledge of what was in the paleontological record.  They acknowledged that why it is there is still an open question.  This is not to imply that they believed that their conclusions on mutation and natural selection were wrong.  They believed they were right.  The importance of the quotes is that they are acknowledging that their conclusions are based on their philosophy and belief, on faith, not science.  What is in the fossil record and when it is there is in the realm of science.  How the changes were made is another matter.

Charles Darwin and Alfred Wallace are celebrated because they discovered a natural method that changed animal’s DNA over time.  The process has been given the name natural selection.  The religious dogma of the day was that animals were fixed in their makeup and did not change.  The observations of Darwin and Wallace were that animals do change substantially with time through natural processes.  This immediately set them at odds with the religious community.   Neither Darwin nor Wallace was aware of the complex genetic system that was responsible for the changes that they discovered.  They had no idea how it worked.  But they did observe that a natural system was changing animals.  What they didn’t know or explore is how much change natural processes were capable of making.  Charles Darwin and later scientists have pushed its capabilities beyond reasonable, and provable, limits.  This pushing natural processes beyond provable limits continues today.

Should we conclude that natural selection was the only, or even the major, mechanism that has made the changes found in animals in the fossil record?  This is a major extrapolation from the observed data.  It is based on the faith that a supernatural intelligence does not exist.  So natural mechanisms are the only ones left to do the creating.

Could such changes have been made by supernatural forces if such forces really exist?  Certainly, but we can’t evaluate supernatural forces with scientific methodology.  Does this then give anyone license to automatically conclude that natural selection did it all? …Without scientific evidence?  What kind of logic is that?  It is logical to posit supernatural forces?  Yes, it is just not scientific, because the supernatural is not subject to direct evaluation by physical means.  Science is a study of the physical and thus is limited to what is physical.  But does that mean that the supernatural must be excluded as a possibility?  Leaving the possibility of a supernatural presence out of the picture may be “scientific,” but it is not logical.  Logic and scientific methodology are two different things.

The human spirit

Human intelligence exists.  What is the human spirit?  It is far above anything else found in the animal world.  Is it natural or super natural?  Is the quality of entanglement of subatomic quanta natural or supernatural?  Or… Are these things “natural” but way beyond our understanding of what “natural” is?

The human spirit designs and creates.  While driven by physical chemical mechanisms it is not totally controlled by them.  It has a mind of its own.  Why would one conclude it is the only free intelligence in the universe?  Is it unreasonable to believe a greater, super-natural intelligence exists?  The presence of the human spirit with its ability to make “unnatural” changes in the physical world should be a factor to consider in evaluating how the changes in the living organisms were made.

It would seem that to be scientifically accurate and truthful we should only attribute natural selection to situations where natural selection can be scientifically proven to be the mechanism that produced the change in the genetic material of the living or fossil organisms.  Otherwise we should be honest and admit, that we  cannot really prove what caused the change.  Our basis for making a definite statement in such a case is based more on our belief and faith than on the actual science.

Genetic material can be changed by internal and/or external forces.  Changes in the genetic material are clearly the mechanism by which evolution proceeds.  The real questions are about what, or who, made the changes in the genetic material.  The cause of the change may be natural selection, artificial selection by intelligence, or direct, intelligent chemical change of the genetic material by human or supernatural intelligence.

In the evolution of modern dogs the original genetic material, with little doubt, came from the wolf.  However, the changes that made 400 or so varieties of dogs (some say a 1,000) were produced by the manipulation of that genetic material by the artificial selection of humans.  The major changes made in the dog’s DNA were not a product of natural selection.  The changes were artificially controlled by human intelligence.  Thus, in the case of dogs, their evolution was driven by human manipulation of their genetic material.  How much more change could have been produced in dogs if the humans at the time had the capability of chemically altering the genetic material rather than just artificially selecting it?  Natural selection, on the other hand, is still producing the wolf.

How was the evolution of fossil animal lines driven?  The real question is not whether or not they evolved, they did, and the fossil evidence proves that.  The question is rather what caused the evolution and change? What the fossil record doesn’t prove is that natural selection was the sole, or even the primary, mechanism for the major evolutionary changes.  That conclusion is driven by a materialistic faith.

 Evolution of Human Technologies 

Evolution is a major aspect of our modern human lives.  Cultures and cultural features evolve.  Languages evolve.  Technologies are in continual evolution and change.  The reason for these changes is human intelligence.  It proceeds as a creative development process.  We build something; use it for a time, then come up with creative ideas on how to modify it to make it even more useful.  The next time we build it we improve it so it works even better.  This creative development process is a major aspect of the human spirit and experience.

An important thing to keep in mind is that human technology is built by constructing and assembling physical things.  The fabrication is directly controlled by the minds of humans.  Physical substances like metal, glass, ceramics, cloth, plastic, rubber, wood, etc. are put together by physical processes.  Human technologies require each item, to be manufactured or put together by intelligent manipulation of the individual physical components.

Living organisms are different.  They reproduce themselves.  They are engineered and changed by changing their DNA.  They build themselves by chemical processes that are under the direction and control of the DNA.  To change the organism, one must manipulate and change the DNA, the blueprint of how the organism puts itself together.

Our human technologies evolve.  Automobiles evolve.  Computers evolve.  Airplanes evolve.  Radio and TV evolve.  Even toilets and paper clips evolve.  It seems nearly impossible to think of any human technology that doesn’t evolve.  Why does human technology evolve?  …Because of the creative power of human intelligence and spirit working with any particular technology.  Technology does not evolve apart from human intelligence.  Intelligence is the driving force for this evolution and change.  Maybe rarely do fortuitous accidents produce a change of value, but the key force driving the change is human intelligence.

Such change is usually not in a direct, upward movement toward a previously visualized “perfect” product.  It is a creatively developing process that unfolds with time and experience.  It is a creative, wandering path, often with many branches, many of which become dead ends.  These are the Edsels or Corvairs of the automobile world.  The end is not seen from the beginning.   I believe this is also the nature of many of the biological progressions and animal lines observed in the fossil record.

The paleontological record shows a similar evolution of design through time for plants, animals and even human beings.  Why should one be reluctant to conclude that these changes are also the product of a creative development process of a higher intelligence? 

Or why would one unreasonably discount any belief in the existence of such intelligence as a mechanism for change?  Why choose to believe in a weaker force, natural selection, as the major mechanism of evolutionary change?  Especially when there is really so little verifiable and repeatable scientific proof that natural selection produces little more than variation within animal groups?  Natural selection seems to primarily be a mechanism for causing variability within a group of organisms, rather than a mechanism for creating new organisms.  

An intelligence would certainly reuse workable DNA sequences in later organisms rather than redesigning everything from scratch.  Just as a computer programmer reuses blocks of code to do similar functions in other applications.

The fact remains that in the paleontological record there is inadequate scientific proof that natural selection has made the major changes found in the lines of fossil organisms.  With scientific methodology we can determine when fossil animals lived and their physical characteristics as far as their preservation will allow.  We can determine what changes occurred in animal lines over time.  We can often date the timing of those changes.  We can test and repeat such observations again and again.  This is science.  What we cannot determine with scientific methodology is what caused the changes in the genetic material to cause the animal to make itself differently.  This is where “Natural Selection of the Gaps Thinking” has to be employed by the materialist.

Fantastic stories are put together about how complex structures, such as the eye, the amniote egg, or legs and digits could have evolved by natural selection.  But this is not science; it is storytelling and un-testable hypothesis making based on a few facts and lots of belief and faith.  Can these stories be scientifically tested and proven?  Can the results be reproduced?  The nature of the paleontological record is such that these hypotheses can never be tested scientifically.  One cannot recreate the animal or its complex environment and have the time to see if the environment can produce the observed changes.  A great extrapolation of the logic and observed facts is necessary to arrive at the conclusion.

What changes, variations and fine tuning, were the result of genetic mixing, drift, and random mutation followed by natural selection and what major changes were the result of intelligent manipulation can most likely never be determined scientifically.  This is why the conclusions are most reasonably based on philosophy and belief while taking into consideration what can be accurately known as fact from geology and paleontology.  The creationist, however, does not have license to dismiss the facts of geology and paleontology in order to maintain his faith in how things were done.

Certainly many observed changes are most logically attributed to natural processes.  This shouldn’t exclude even the origin of some species.  The loss of eyesight or pigment by fish or insects living in lightless caves for long periods of time would seem most logically the result of natural processes; as would be the reduction in size of mammoths that have become isolated on small oceanic islands.   In some species their DNA seems to allow rather dramatic changes to occur regularly.  One example of such a group would be the cichlid fish (Barlow 2000).  The genetic material in some groups would seem to accommodate more variable possibilities than in others.  The wolf line and resulting dogs indicates a wealth of change possibilities in the genetic material of these canines.  Of course, somehow, at some time, all those possibilities had to be assembled into wolf DNA by some mechanism or intelligence.

Misplaced emphasis on transitional forms

A missing logical link in a sequence of fossils might be the result different things.  Poor preservation may not have preserved the links that actually lived.  On the other hand, if the design process had been an intelligent one, the link may only have existed in the mind of the designer and never have been an actual living entity.  In technology one can find examples of both transitional links and of missing links.  

 ​Because either may be true, arguing over missing links and transitional forms in the fossil record can be misleading and unproductive.

Whether the missing transitional forms ever existed or not remains a factor to consider for both science and belief.   Many major gaps have been filled by transitional fossil forms.  A recent example of this is the whale line. (Gingerich,2015).  Other thousands of gaps will probably never be filled.  A perfectly seamless transition is almost never found.  We must not eliminate the thousands of legitimate gaps from the evaluation process.  Why do they exist?  Is it really just poor preservation?  That seems unlikely.  There are just too many.  They are an important part of what is in the physical record that must be considered.  However, in specific cases their presence or absence is not definitive.

In human technologies transitional forms may or may not be present.  Consider sequences of automobiles or computers.  Usually transition models exist but many times a substantial leap is made without transitions.  It’s an intelligence thing.  The same type of variation seems to be true in the sequences of fossil organisms.

Would the fossil record, no matter how continuous and complete, prove it happened by random chance?  Do transitional forms prove it was not done by intelligence?  Modern technology is replete with transitional forms.  That is how creative design process of intelligence works! 

Comparing human technology with the evolution of living organisms is certainly not scientific proof that it happened this way.  It is evidence by analogy.  But the analogies are remarkably similar to one another.  The analogy can be instructive and provide remarkable insight for a subject that is not subject to absolute scientific validation and proof.

The Tree of Life

I have on the wall of my study a marvelous graphic of the tree of life.  It is a generalizing sum of all fossil and living forms of life.  It groups them into like groups of organisms and portrays them in generally geologic order.  The living forms of the groups are at the tips of the branches.  The older fossils are closer to the trunk and/or base of the tree.  It is a wonderful visual summary of the living and fossil world.  Someone has done a nice piece of work putting it together.  I waste a lot of time looking at it and thinking about it.  The chart portrays many realities.  But there are still major unanswered questions which such a chart glosses over.

The question of the missing “phantom progenitors”

A funny thing about the chart is that nowhere on the whole chart is there a single organism on the main trunk or on any of the main side branches.  All precise organisms are located only at the tips of the branches or slightly off the main trunk and branches.  Why should this be?  Even a 400+ million year old brachiopod or a 300+ million year old dragonfly or cockroach is at the tip of branches.  Where are all the mainline phantom progenitors?  If they existed, why were they not put in the appropriate places on the chart?  If we really don’t find any of them as fossils, why do we pretend that we do?  Are they purely hypothetical?  These are important questions.  There are some individuals or groups near the main trunk and branches that have some of the characteristics in common with the phantom progenitor but no specific organisms.  All fossil organisms are at least a bit off the postulated main line of descent of the group; which would seem to indicate that we really don’t have scientific evidence and ​proof for the phantom progenitor’s existence.  Is there any animal line for which we do have the actual phantom progenitors all the way down the line?  Is there any actual fossil animal that we can say is the actual ancestor that produced all the offspring of the remaining trunk or branches following it?  If not, why not?

I find this intriguing.  Is it just me and my lack of knowledge?  Or is this a real problem?  In all my studies I do not remember of a single incidence of a single fossil organism that was considered the one and only originator of a line that continued on for millions of years.  They all seem to have some diverse qualities that disqualifies them from being the actual progenitor of the subsequent group.

The Black Box of Phylogenetics

Phylogenetics is a computer based system for analyzing living and fossil organisms to show their relationships to one another.  It has revolutionized the grouping (taxonomy) of living and fossil organisms in the last 20 to 30 years or so.  Complex computer programs are used to analyze and compare the morphology and/or genetics of different organisms to show which are the most closely related based on the characteristics that have been chosen to evaluate.  Computers have proven to be much more capable of making such comparisons than humans have been in the past.  This only mechanizes the process of comparing what organisms are most like other organisms so they can be grouped together.  It does not change the basic assumptions.

Phylogenetics is used by some in an attempt to build a tree of life that encompasses all living and fossil organisms on the planet. (Cracraft and Donoghue, 2004).  It is based on the materialistic belief that all living things have developed by natural forces from an original origin of life event.  That such a tree of life actually exists is the basic and key premise of the phylogenetics system and structures the results.  This is clearly laid out in a current text on phylogenetics.

PHYLOGENETIC PROPOSITIONS

This book is an introduction to phylogenetics philosophy and techniques.  It is founded on five propositions:

1. There is a tree of life that links all living organisms in a genealogical nexus, and it is possible to reconstruct relationships among the species that populate the tree.

2. Relationships among organisms do not have to be invented and treated as some form of scenario; they only have to be discovered.  Our hypotheses reflect our best efforts to discover these relationships.

(Wiley and Lieberman, 2011:3)

The first two propositions are the most relevant for our purpose.  The most important is the statement of belief (or faith) that all forms of life on earth have developed through continuous genealogical lines by purely natural processes from an original life form.  This is, of course, a conclusion of materialistic faith and in direct philosophical contradiction to a theist conclusion.

 The difficulty of constructing a literal tree of life for just one line of animals, the placental mammals, is expressed in Springer, et. al.

Beyond the living eutherian orders, the challenge of integrating molecular and morphological data (fossils included) into a comprehensive and accurate phylogeny for all eutherian orders is formidable. (Springer, et. al., 2005:45).

The challenge for just eutherian mammals is “formidable,” not to mention the rest of the plants and animals. The scientific community is nowhere close to putting together a complete and accurate true tree of life structure for all living and fossil organisms.  This is true no matter how beautiful, artistic, and impressive the current tree of life graphics appear to be.  A skeleton of the fossil record is truthfully presented in such “trees of life” to be sure.  Such trees probably speak a certain truth of the life lines that were developed.  However, similar trees of life could be developed for nearly any human technology.

It can give an indication of sequence and relationship.  What it doesn’t and can’t tell is what made the changes in the DNA or the morphology of the organisms.  Did these changes come by natural means or by intelligent manipulation?  It simply doesn’t address these questions.  Phylogenetics is a very useful tool that indicates sequence and similarity.  It does not prove what caused the sequence and similarity.  The science of phylogenetics can do a good job of showing relationships between living and/or fossil The difficulty of constructing a literal tree of life for just one line of animals, the placental mammals, is expressed in Springer, et. al.

Beyond the living eutherian orders, the challenge of integrating molecular and morphological data (fossils included) into a comprehensive and accurate phylogeny for all eutherian orders is formidable. (Springer, et. al., 2005:45).

The challenge for just eutherian mammals is “formidable,” not to mention the rest of the plants and animals. The scientific community is nowhere close to putting together a complete and accurate true tree of life structure for all living and fossil organisms.  This is true no matter how beautiful, artistic, and impressive the current tree of life graphics appear to be.  A skeleton of the fossil record is truthfully presented in such “trees of life” to be sure.  Such trees probably speak a certain truth of the life lines that were developed.  However, similar trees of life could be developed for nearly any human technology.

It can give an indication of sequence and relationship.  What it doesn’t and can’t tell is what made the changes in the DNA or the morphology of the organisms.  Did these changes come by natural means or by intelligent manipulation?  It simply doesn’t address these questions.  Phylogenetics is a very useful tool that indicates sequence and similarity.  It does not prove what caused the sequence and similarity.  The science of phylogenetics can do a good job of showing relationships between living and/or fossilThe difficulty of constructing a literal tree of life for just one line of animals, the placental mammals, is expressed in Springer, et. al.

Beyond the living eutherian orders, the challenge of integrating molecular and morphological data (fossils included) into a comprehensive and accurate phylogeny for all eutherian orders is formidable. (Springer, et. al., 2005:45).

The challenge for just eutherian mammals is “formidable,” not to mention the rest of the plants and animals. The scientific community is nowhere close to putting together a complete and accurate true tree of life structure for all living and fossil organisms.  This is true no matter how beautiful, artistic, and impressive the current tree of life graphics appear to be.  A skeleton of the fossil record is truthfully presented in such “trees of life” to be sure.  Such trees probably speak a certain truth of the life lines that were developed.  However, similar trees of life could be developed for nearly any human technology.

It can give an indication of sequence and relationship.  What it doesn’t and can’t tell is what made the changes in the DNA or the morphology of the organisms.  Did these changes come by natural means or by intelligent manipulation?  It simply doesn’t address these questions.  Phylogenetics is a very useful tool that indicates sequence and similarity.  It does not prove what caused the sequence and similarity.  The science of phylogenetics can do a good job of showing relationships between living and/or fossilThe difficulty of constructing a literal tree of life for just one line of animals, the placental mammals, is expressed in Springer, et. al.

Beyond the living eutherian orders, the challenge of integrating molecular and morphological data (fossils included) into a comprehensive and accurate phylogeny for all eutherian orders is formidable. (Springer, et. al., 2005:45).

The challenge for just eutherian mammals is “formidable,” not to mention the rest of the plants and animals. The scientific community is nowhere close to putting together a complete and accurate true tree of life structure for all living and fossil organisms.  This is true no matter how beautiful, artistic, and impressive the current tree of life graphics appear to be.  A skeleton of the fossil record is truthfully presented in such “trees of life” to be sure.  Such trees probably speak a certain truth of the life lines that were developed.  However, similar trees of life could be developed for nearly any human technology.

It can give an indication of sequence and relationship.  What it doesn’t and can’t tell is what made the changes in the DNA or the morphology of the organisms.  Did these changes come by natural means or by intelligent manipulation?  It simply doesn’t address these questions.  Phylogenetics is a very useful tool that indicates sequence and similarity.  It does not prove what caused the sequence and similarity.  The science of phylogenetics can do a good job of showing relationships between living and/or fossilThe difficulty of constructing a literal tree of life for just one line of animals, the placental mammals, is expressed in Springer, et. al.

Beyond the living eutherian orders, the challenge of integrating molecular and morphological data (fossils included) into a comprehensive and accurate phylogeny for all eutherian orders is formidable. (Springer, et. al., 2005:45).

The challenge for just eutherian mammals is “formidable,” not to mention the rest of the plants and animals. The scientific community is nowhere close to putting together a complete and accurate true tree of life structure for all living and fossil organisms.  This is true no matter how beautiful, artistic, and impressive the current tree of life graphics appear to be.  A skeleton of the fossil record is truthfully presented in such “trees of life” to be sure.  Such trees probably speak a certain truth of the life lines that were developed.  However, similar trees of life could be developed for nearly any human technology.

It can give an indication of sequence and relationship.  What it doesn’t and can’t tell is what made the changes in the DNA or the morphology of the organisms.  Did these changes come by natural means or by intelligent manipulation?  It simply doesn’t address these questions.  Phylogenetics is a very useful tool that indicates sequence and similarity.  It does not prove what caused the sequence and similarity.  The science of phylogenetics can do a good job of showing relationships between living and/or fossilThe difficulty of constructing a literal tree of life for just one line of animals, the placental mammals, is expressed in Springer, et. al.

Beyond the living eutherian orders, the challenge of integrating molecular and morphological data (fossils included) into a comprehensive and accurate phylogeny for all eutherian orders is formidable. (Springer, et. al., 2005:45).

The challenge for just eutherian mammals is “formidable,” not to mention the rest of the plants and animals. The scientific community is nowhere close to putting together a complete and accurate true tree of life structure for all living and fossil organisms.  This is true no matter how beautiful, artistic, and impressive the current tree of life graphics appear to be.  A skeleton of the fossil record is truthfully presented in such “trees of life” to be sure.  Such trees probably speak a certain truth of the life lines that were developed.  However, similar trees of life could be developed for nearly any human technology.

It can give an indication of sequence and relationship.  What it doesn’t and can’t tell is what made the changes in the DNA or the morphology of the organisms.  Did these changes come by natural means or by intelligent manipulation?  It simply doesn’t address these questions.  Phylogenetics is a very useful tool that indicates sequence and similarity.  It does not prove what caused the sequence and similarity.  The science of phylogenetics can do a good job of showing relationships between living and/or fossilThe difficulty of constructing a literal tree of life for just one line of animals, the placental mammals, is expressed in Springer, et. al.

Beyond the living eutherian orders, the challenge of integrating molecular and morphological data (fossils included) into a comprehensive and accurate phylogeny for all eutherian orders is formidable. (Springer, et. al., 2005:45).

The challenge for just eutherian mammals is “formidable,” not to mention the rest of the plants and animals. The scientific community is nowhere close to putting together a complete and accurate true tree of life structure for all living and fossil organisms.  This is true no matter how beautiful, artistic, and impressive the current tree of life graphics appear to be.  A skeleton of the fossil record is truthfully presented in such “trees of life” to be sure.  Such trees probably speak a certain truth of the life lines that were developed.  However, similar trees of life could be developed for nearly any human technology.

It can give an indication of sequence and relationship.  What it doesn’t and can’t tell is what made the changes in the DNA or the morphology of the organisms.  Did these changes come by natural means or by intelligent manipulation?  It simply doesn’t address these questions.  Phylogenetics is a very useful tool that indicates sequence and similarity.  It does not prove what caused the sequence and similarity.  The science of phylogenetics can do a good job of showing relationships between living and/or fossilThe difficulty of constructing a literal tree of life for just one line of animals, the placental mammals, is expressed in Springer, et. al.

Beyond the living eutherian orders, the challenge of integrating molecular and morphological data (fossils included) into a comprehensive and accurate phylogeny for all eutherian orders is formidable. (Springer, et. al., 2005:45).

The challenge for just eutherian mammals is “formidable,” not to mention the rest of the plants and animals. The scientific community is nowhere close to putting together a complete and accurate true tree of life structure for all living and fossil organisms.  This is true no matter how beautiful, artistic, and impressive the current tree of life graphics appear to be.  A skeleton of the fossil record is truthfully presented in such “trees of life” to be sure.  Such trees probably speak a certain truth of the life lines that were developed.  However, similar trees of life could be developed for nearly any human technology.

It can give an indication of sequence and relationship.  What it doesn’t and can’t tell is what made the changes in the DNA or the morphology of the organisms.  Did these changes come by natural means or by intelligent manipulation?  It simply doesn’t address these questions.  Phylogenetics is a very useful tool that indicates sequence and similarity.  It does not prove what caused the sequence and similarity.  The science of phylogenetics can do a good job of showing relationships between living and/or fossilThe difficulty of constructing a literal tree of life for just one line of animals, the placental mammals, is expressed in Springer, et. al.

Beyond the living eutherian orders, the challenge of integrating molecular and morphological data (fossils included) into a comprehensive and accurate phylogeny for all eutherian orders is formidable. (Springer, et. al., 2005:45).

The challenge for just eutherian mammals is “formidable,” not to mention the rest of the plants and animals. The scientific community is nowhere close to putting together a complete and accurate true tree of life structure for all living and fossil organisms.  This is true no matter how beautiful, artistic, and impressive the current tree of life graphics appear to be.  A skeleton of the fossil record is truthfully presented in such “trees of life” to be sure.  Such trees probably speak a certain truth of the life lines that were developed.  However, similar trees of life could be developed for nearly any human technology.

It can give an indication of sequence and relationship.  What it doesn’t and can’t tell is what made the changes in the DNA or the morphology of the organisms.  Did these changes come by natural means or by intelligent manipulation?  It simply doesn’t address these questions.  Phylogenetics is a very useful tool that indicates sequence and similarity.  It does not prove what caused the sequence and similarity.  The science of phylogenetics can do a good job of showing relationships between living and/or fossil ​​organisms.  But it shows relationships, not the cause of the changes that make relationships. In phylogenetics the cause of change is assumed to be evolution by purely natural processes in reproducing lines.  The results are all interpreted based on this assumption.  The dice are loaded.

Chapter Summary

We live in a world in which faith is increasingly dominated by arrogant and bullying materialists.  Their faith is that no God, no metaphysical or spiritual intelligence exists.  The physical world that can be sensed and somehow measured physically is all that exists.  They are often forceful and bullying in expressing this faith.  But it is indeed faith.  Its basis is not provable science.  It is outside of science methodology to prove or disprove.  This does not, however, give us license to toss out the true knowledge that materialism can teach us. The theological world itself has its own arrogant and bullying fundamentalists.  Bullying and arrogance is a human thing.

In summary, let’s consider of three main ways the changes in an organism’s genetic material may be made:

1. Natural selection based on natural processes selecting beneficial changes brought about by gene mutation,  unique combination of genetic material, genetic drift, recombination, isolation, etc., etc.

2. Artificial selection by intelligence (human or supernatural).

3. Physical chemical changes of the genetic material directly made by intelligence (human or supernatural).

Physically identifying which is true in any particular fossil organism is subjective and probably not scientifically provable.  For changes in the fossil record, materialists consider only the first possibility a viable consideration.  While this is definitely scientific, it is not necessarily logical.  A theist has all three possibilities to consider.  It is reasonable to believe we are looking at a creation designed to run without need of constant intervention to fix and patch things; and to allow it to develop within reasonable parameters in natural ways.  This in no way eliminates the need or possibility of a supernatural intelligence.

While I don’t consider myself  part of the Intelligent Design movement, I do think there is good reason to consider overall design by intelligence in the biological realm.  There is a need to look outside the science box to find what seems most logically true. This, of course, does not give permission to theists to allow sloppy reasoning, emotional bias, or to ride roughshod over valid and true scientific facts.  Truth from whatever source is true.  When it comes to belief, truth is still trump!

Human beings may be animals.  Even the Bible states as much (Ecclesiastes 3:18-21).  But what an amazing animal the human being is!  Humans have a unique spirit above all other animals.  They are different!  Who is building the zoo and who is inside the zoo?  How many books in the world were written by apes or chimps?  What technology was ever created by apes?   What ape, or group of apes, has the power to destroy life on earth?  Would you want your daughter to marry one?  Look and think about what a human is and can be!  What a dramatic difference between the two.  An ape and a man are worlds apart even if they share 98% of their genes!  Apes are truly remarkable but they didn’t go to the UK to study Jane Goodall and her relatives.

 

 

 

References for Chapter 8

Barlow, George W.
2000  The Cichlid Fishes: Nature’s Grand Experiment in Evolution.  Perseus Publishing, Cambridge, MA.

Cracraft, Joel and Michael J. Donoghue, editors
2004  Assembling the Tree of Life.  Oxford University Press.

Darwin, Charles
1958  The Autobiography of Charles Darwin 1809-1882.  W. W. Norton & Company, Inc.

Gingerich, Philip D.
2015  Evolution of Whales from Land to Sea.  In Great Transformations in Vertebrate Evolution, edited by Kenneth P. Dial, Neil Shubin, and Elizabeth L. Brainerd, pp. 239-256.  University of Chicago Press.

Romer, Alfred S.
1959  The Vertebrate Story.  University of Chicago Press.

Simons, Elwyn L.
1972  Primate Evolution: An Introduction to Man’s Place in Nature.  The Macmillan Co.

Springer, Mark S. William J. Murphy, Eduardo Eizirik, and Stephen J. O’Brien
2005  Molecular Evidence for Major Placental Clades.  In The Rise of Placental Mammals, edited by Kenneth          D. Rose and J. David Archibald, pp. 37-49.  The Johns Hopkins University Press.

Wiley, E. O. and Bruce S. Lieberman
2011  Phylogenetics, 2nd ed.  Wiley-Blackwell, John Wiley and Sons, Inc.



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