What’s Wrong About Darwin’s Theory of Evolution ?

Posted on January 25, 2015

What’s Wrong About Darwin’s Theory of Evolution ? by Jeffrey Dach MD

There Were A Few Things. 
The Tree of Life is Really a Network

This article is part one.
For part two, Click Here,

Central to Darwin’s Theory is the “Tree of Life”.  The massive tree trunk represents simpler life forms such as amoebas, protozoas, and one-celled organisms etc.   The more complex organisms such as fish, birds and land mammals are represented by smaller branches at the top of the tree.   

Header Image courtesy of the Chive.
Left magazine cover courtesy of New Scientist. 


According to Graham Lawton in a 2009 article in New Scientist, Why Darwin was wrong about the tree of life , this “iconic concept of evolution, has turned out to be a figment of our imagination.”

Darwin’s tree has been rendered obsolete by the discovery of Horizontal Gene Transfer.    Instead of a Tree, we have a new model represented by a network of inter-related life forms.
Left Image: This “Tree of Life” sketch is seen in Darwin’s  notebook (Image: courtesy of Mario Tama / Getty).


Darwin Wrote His Theory of Evolution in 1859


This isn’t the only flaw in Darwin’s theory. Since 1859 when Darwin wrote his theory evolution, there has been considerable progress in molecular biology.  In 1953, the double helix structure of DNA was elucidated by Watson and Crick, along with its genetic code.  In 2003, the genetic code for the entire human genome was sequenced.  These advances provoked a paradigm shift in thinking about evolution.  Darwin’s simple 19th century Theory of Evolution required drastic revision in order to incorporate all this new knowledge.


The Evolution From Simple to More Complex


Left Image: Charles Darwin 1880 Courtesy wikimedia commons,

The idea of evolution of life from the simple to more complex is an old idea and can be found in ancient writings. Darwin’s theory started with this concept and sought to explain the mechanism. of evolution.   Darwin’s theory of evolution is the idea that over many generations, small incremental changes lead to emergence of entirely new species.  This idea seemed plausible to professional animal breeders with extensive experience “breeding-in” desirable traits in their dogs, horses or livestock.

Darwin’s idea was that “Mother Nature” would act in place of the professional animal breeder.  Nature would select traits which provided survival advantage, and reject traits that impaired survival.  Animals with better survival advantages would win the battle for reproduction.

This is called “Natural Selection“.   In 1859, Charles Darwin then took the next step.  He proposed Natural Selection as the mechanism for evolution.  Left Image Darwin Gets a Haircut Courtesy of Wikimedia Commons.

To summarize Charles Darwin’s theory of Evolution:

1) Random genetic mutations in the herd provide variation.

2) The genetic variants most adapted for survival will survive, while less adapted will not.  This is called Natural Selection.






Questioning Natural Selection as the Mechanism


Newton Replaced by Einstein

Just as Newtonian Physics has been superceded  by new physics of Relativity and Quantum Mechanics, so too have Darwin’s 19th century ideas been antiquated and replaced.  Darwin’s mechanism of evolution has been found insufficient to explain new discoveries in molecular biology.  Current knowledge of the human genome, and cell biology reveals that random mutations in the genome are insufficient to create new species.  Quite the opposite, genomic changes have been found to be non-random, and predictable in a process described as “Genetic Engineering”.






Natural Selection Replaced by Genetic Engineering


Left image courtesy of James A Shapiro PhD
James A Shapiro at the University of Chicago proposes Genetic Engineering as the new mechanism for evolution.  He says that genome change is a regulated biological function, and natural genetic engineering processes are subject to biological feedback at multiple levels.  Here is his slide show about   Natural ENGINEERING OF GENOME STRUCTURE by James A Shapiro.  



Dr Shapiro says: “Cells have a large toolbox of biochemical systems that carry out genome restructuring at all levels of
complexity” 

James A Shapiro is author oi the book,Evolution: A View from the 21st Century (left image cover)



Read a book review by William Dembski on Dr Shapiro’s Book:Borderline Heretic James Shapiro 21st Century Evolution Review Dembski

Article in Boston Review by Dr James A Shapiro: Shapiro.1997.BostonReview1997.ThirdWay
Interview with Dr. James Shapiro : Evolution Paradigm Shift by SUZAN MAZUR May 2012.


Common Questions Raised by Darwin Dissenters: 
How does random change (mutation) in the genome add information to a genome to create progressively more complicated organisms?


It Doesn’t. Evolution is Non-Random.  James A Shapiro says “Genome change arises as a consequence of natural genetic engineering, not from accidents.” (from James A Shapiro_2009_Revisiting_Central_Dogma)

A multi-national team of biologists has concluded that developmental evolution is deterministic and orderly, rather than random, based on a study of different species of roundworms.  Another molecular biologist from Princeton, David Stern, says that evolution is predictable because mutations tend to occur at hot spots in regulatory genes.  Even Richard Dawkins, an atheist and Darwin’s most vocal defender says that evolution is non-random, referring to Natural Selection as a “non-random mechanism” in a Salon interview.

Lack of Gradualism in the Fossil Record. 

Left image courtesy of Stephen Jay Gould.
Another flaw in Charles Darwin’s original theory is the geological record which did not support Darwin’s prediction of gradual transition between life forms.  To explain this lack of  gradualism in the fossil record, Stephen Jay Gould invented a new theory called Punctuated Equilibrium.  Rather than finding gradual transition forms in the fossil record, paleontology has found sudden bursts in appearances of life forms, as well as long periods of stasis or little change in the fossil record.


Cambrian Explosion


One example of this is the Cambrian Explosion about 555 million years ago when 40 body plans appeared over a ten million year period with no preceding transition forms.
These findings had to somehow be incorporated into Darwin’s theory, adding to the complexity of the theory. Thus, the invention of “punctuated equilibrium”.

Left: Cover of Time Magazine 1995 Cambrian Explosion.
Cornelius Hunter author of Science’s Blind Spot: regards Punctuated Equilibrium as a form of “Post-Hoc” reasoning to be analogous with the Epicycles of the  pre-Newtonian Geo-Centrists who claimed the earth was the center of the universe.   Galileo’s telescope disproved Geocentrism.  Left Image Courtesy of Discovery Magazine.

How does the first living cell arise spontaneously to get evolution started? 

The spontaneous origin of life is called abiogenesis, and Neo-Darwinism does not even address this issue.

Science doesn’t have a clue as to how the first living organisms originated.    Stephen Meyers refines this question further as the question of the origin of “biological information” encoded in the DNA of the first cell.  We have no scientific explanation for the appearance of this first information.

The Human Genome Project showed that only 1-2% of Human DNA codes for proteins, or about 25,000 genes.  

Are these enough  to account for the complexity of the organism?  What is the other 98% of the genome’s function?  We don’t have answers to these questions yet.  In the recent past, this non-coding DNA had been called “junk DNA”, a misnomer and a false prediction made by neo-Darwinists resulting in the delay of molecular biology research for the past 25 years.
New research suggests this 98% of the genome, the “junk DNA”, is not junk and in fact is very functional.  It regulates development and gene expression.  Does this non-coding DNA also direct the evolution of the species?  We don’t know yet.  New findings in molecular biology by scientists like Dr. Shapiro  and Dr. Stern are leading the way.

Central Dogma Refuted

The Central Dogma says that genetic information follows in only one direction from the genome to the protein.  The discoveries of reverse transcriptase and retroviruses showed reversed flow of information back to the genome from the environment.  A new concept  called the “fluid genome“  replaced the Central Dogma.  This has profound implications for evolutionary theory.

Directed Evolution

Another promising new theory of evolution is “Directed Evolution” described in Michael J. Denton’s book, “Nature’s Destiny: How the Laws of Biology Reveal Purpose in the Universe”.  Denton suggests a concept called “directed evolution” in which changes in the genetic code leading to speciation (new species), which were previously thought to be caused by random mutations, are instead “directed” by the genomic information contained in the DNA (possibly in the non-coding portion of DNA previously called “junk DNA”).   New findings in molecular biology by Shapiro at U of C and by Stern at Princeton are lending support to this view.


An Analogy from Embryology

An analogy is drawn from embryology, in which the genetic code in the DNA directs the tiny embryo to follow well defined steps to “evolve” into the mature organism.  This idea can be applied to evolutionary theory itself.  The intracellular nuclear DNA could contain “directed information” for the steps leading from primitive life forms to more complex life forms in over billions of years of evolution. Hopefully, we will see more of these fascinating ideas in print over the next few years.






The Snowflake – Self Organizing Properties of Matter

A small particle of water grows into a beautiful snowflake with no two patterns  alike.  The snowflake is a complex orderly object which arises because of the self-organizing properties of molecules of water.  There is no need to invoke randomness as an explanation.   Likewise, the first life forms could have arisen from the self-organizing properties of matter without invoking randomness as an explanation.




Evo-Devo

Another new approach is called evo-devo and Sean Carrol’s Book, Endless Forms Most Beautiful: attempts to reconcile new findings in molecular biology and embryology with the theory of evolution.

Gert Korthof

If you plan to study the topic of evolution, a good place to start is Gert Korthof’s web site which exhaustively reviews dozens of new books on evolution, intelligent design, evo devo, molecular biology, etc.


Mainstream Scientists Who Dissent

As of April 2014, here is a list of scientists who dissent from Darwinsim.  They all signed this statement:

“We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged” .

Click here for pdf of list: Scientists Who Dissent From Darwinism

1) James A Shapiro Ph.D. Professor of Microbiology University of Chicago: “Genome change arises as a consequence of natural genetic engineering, not from accidents.”
 
2) Stanley N. Salthe Ph.D. Zoology, 1963, Columbia University.“So, with current neoDarwinian theory, we can claim that it does not model evolution, only short term survival from one generation to the next.”
“As to its ability (neo-Darwinism) to explain the evolution of organisms (as opposed to the evolution of gene systems), it has not, after some 60 years of development, delivered a very convincing mechanism.” see: Natural Selection neo Darwinian theory of evolution 2006 Salthe.
Left image courtesy of Stanley Salthe.


3) Stuart Kauffman professor at the University of Calgary with a shared appointment between biological sciences and physics and astronomy.  He is the author of The Origins of Order, At Home in the Universe: The Search for the Laws of Self-Organization, and Investigations.
 
4) Lynn Margulis Distinguished University Professor Microbial Evolution and Organelle Heredity Department of Geosciences at the University of Massachusetts.”She does, however, hold a negative view of certain interpretations of Neo-Darwinism, excessively focused on inter-organismic competition, as she believes that history will ultimately judge them as comprising “a minor twentieth-century religious sect within the sprawling religious persuasion of Anglo-Saxon Biology.”  Left Image courtesy of Lynn Margulis and Carl Sagan.

5) David Stern, group leader at the Janelia Research Campus. From 2008 to 2011, he was an HHMI investigator at Princeton University.
“Although mutations are thought to occur randomly in the genome, the distribution of mutations that cause biologic diversity appears to be highly non-random.”   (Science Feb 2009)
“Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. ” (Evolution. 2008 Sep)


Physicians Dissent from neo-Darwinism

According to a 2005 poll, 112,500 or 15% of licensed physicians in the US reject neo-Darwinism.  An even greater number, 315,000 believe that “God initiated and guided an evolutionary process that has led to current human beings.”   There are 750,000 licensed physicians in the US.
When asked to select between two choices,
1) Evolution or
2) Intelligent Design,
a full one third of phyicians polled selected Intelligent Design. That extrapolates to 250,000 physicians accept Intelligent Design rather than neo-Darwinian Evolution.  The press release is here.

The Big Bang and The Universality of Genetic Code
Implies a Common Ancestor 

Science tells us that all Life evolved from matter originating 15-20 billion years ago at an event called the “Big Bang”, or “Singularity”.    This theory suggests that first inanimate mater and then life forms evolved from this singularity event.   This theory also implies that all life forms share a common ancestor going back in time to that first instant of the “Big Bang”.
In addition, the genetic code is universal for all life forms, implying that all life forms are related by a common ancestor, a common design, or both. (Note: the genetic code translates encrypted DNA codons into amino acid sequences).

Conclusion: 
Although our current knowledge indicates all life forms are related and share a common ancestor, the exact mechanism of evolution has not yet been elucidated by science.  Some day, in the future, science may discover the mechanism.
To be honest about our current scientific understanding, we must admit that science does not know the following items listed:
1) How the Universe originated.
2) How Life originated.
3) The Correct Mechanism of Evolution.
4) How Human Intelligence Originated.
Jeffrey Dach MD
link to this article: http://wp.me/p3gFbV-2wq

Articles With Related Interest:
Saying Thank You for a Trillion Cells
In the Beginning You Were a Single Celled Organism

References and Links:
1) For the free full text of the 2009 Graham Lawton New Scientist article click here.   Here  is a pdf of the article: New Scientist Why Darwin was wrong about the tree of life 2009 Graham Lawton
2) http://shapiro.bsd.uchicago.edu/index3.html?content=genome.html
What general principles operate in genome function and genome reorganization?
• All genome functions are interactive (no Cartesian dualism, genome always in communication with rest of cell);
• Every genome component operates as part of a complex information-processing system (no “one gene-one trait” correlation);
• Genome systems are organized and integrated into cell networks by repetitive DNA;
• Genome change is a regulated biological function;
• Natural genetic engineering processes are subject to biological feedback at multiple levels.
3) http://www.truthnet.org/creation/evolution/
Creation/ Evolution
4) http://en.wikipedia.org/wiki/Uncommon_Dissent
Contributor Edward Sisson sees the key question in the debate over biological evolution as whether all life is “the result of chance events occurring in DNA (or perhaps elsewhere) that are then ‘selected’ in some fashion without the need of any guiding intelligence”, thereby undergoing “unintelligent evolution”, or whether at least some of the diversity of life on earth can be explained only through “intelligent evolution”, in which “an intelligent designer (or designers)” causes preexisting species to undergo designed changes in DNA.
His view is that “no data has been found that amounts to real evidence for unintelligent evolution as the explanation for the diversity of life”, that “science is ignorant of how the diversity of life came to be”, and that “an intelligent cause is necessary to explain at least some of the diversity of life as we see it”.[12]
5) http://www.discovery.org/scripts/viewDB/filesDB-download.php?id=496
DARWINIAN EVOLUTIONARY THEORY AND THE LIFE SCIENCES IN THE 21ST CENTURY by Roland F. Hirsch. This essay was originally published in “Uncommon Dissent” (ISI Books, 2004) edited by William Dembski.
These complete genome sequences have revealed several complexities that Darwinian evolutionary theory did not anticipate. Four of these will be discussed here:
1) the major role played by transfer of genes from one species to another as opposed to inheritance from ancestors;
2) the fact that bacterial species do not evolve solely in a random fashion, but show a bias toward deletion of genetic material;
3) the discovery that much of the portions of the genome that do not code for proteins is not “junk DNA” but in fact has a critical function; and the observation that expression of genes is controlled by regulatory circuits that are as complicated and as precisely arranged as the most sophisticated engineering diagrams.
To sum up this section, Darwinian evolutionary theory failed, in this author’s view, to anticipate several key discoveries about genetics, inheritance, and gene expression and development.
In each case, evolutionary theory should have guided researchers to make these discoveries, but in fact the opposite seems true: changes were made in evolutionary theory after the fact to account, for example, for the significance of horizontal gene transfer or to explain the complexities of regulation of gene expression.
Conclusion: I have no doubt that these and other technology-driven advances in the life sciences present a serious challenge to the validity of the main principles of Darwinian evolutionary theory. Much of what was taught forty years ago has had to be unlearned or has become irrelevant; much of what today’s experiments and field research reveal about life cannot be explained by the evolutionary theory of the past.
Life as revealed by new technologies is more complicated than the Darwinian viewpoint anticipated. Thus evolutionary theory, which was considered to be a key foundation of biology in 1959, today has a more peripheral role.
Adam S. Wilkins, the editor of the review journal BioEssays, put it this way in introducing an issue of his journal devoted to evolution in December 2000: The subject of evolution occupies a special, and paradoxical, place within biology as a whole. While the great majority of biologists would probably agree with Theodosius Dobzhansky’s dictum that “nothing in biology makes sense except in light of evolution,” most can conduct their work quite happily without particular reference to evolutionary ideas. “Evolution” would appear to be the indispensable unifying idea and, at the same time, a highly superfluous one.
Perhaps the reader will recognize from the preceding examples that to assume all one needs to know about an organism is contained in its genome is an unsatisfactory way to study biology. The much anticipated completion of sequencing the human genome—and of many other genomes—has only revealed that life is more complex than the previously dominant gene-oriented evolutionary theory led scientists to believe. Biologists are now increasingly turning to a systems approach to study biology, using, for example, the concepts of engineering and design.
There is good reason to believe that this trend will continue as the 21st century progresses. In the view of this author, modern science makes it possible to be a scientifically informed doubter of Darwinian theories of evolution.
6) http://www.faithfacts.org/evolution-or-creation/origins-and-silly-putty/darwinian-mechanism-problems
Problems with the Darwinian Mechanism
7) http://www.faithfacts.org/evolution-or-creation/origins-and-silly-putty/good-science-or-bad-philosophy
Materialistic naturalism—the foundational principle of evolution—is not a science at all, but a philosophy. It is an assumption, designed to eliminate God by definition. Thus evolution is deeply rooted in the philosophical assumption of materialism.
8) http://post-darwinist.blogspot.com/2008/12/top-ten-darwin-and-design-stories-of.html
The top ten Darwin and Design stories of the year
9) http://www.scoop.co.nz/stories/HL0807/S00053.htm
Altenberg 16: An Exposé Of The Evolution Industry
Sunday, 6 July 2008, 12:32 pm  Article: Suzan Mazur
THE ALTENBERG 16 – Will the Real Theory of Evolution Please Stand Up? By SUZAN MAZUR AN EXPOSÉ OF THE EVOLUTION INDUSTRY An E-Book in 8 Parts – Part 1 – Chapters 1, 2 & 3
10) http://www.uncommondescent.com/intelligent-design/jerry-fodor-natural-selection-has-gone-bust/
13 October 2007 Jerry Fodor: Natural Selection Has Gone Bust
Paul Nelson
11) http://www.southerncrossreview.org/40/cruse.htm
WAS DARWIN WRONG?  Yes — His Logic was Fatally Flawed
by Don Cruse
12) http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html?full=true
Why Darwin was wrong about the tree of life .  21 January 2009 by Graham Lawton
13) http://www.rtforum.org/lt/lt124.html
Biochemist Roland Hirsch, in an essay published in 2004, while noting that the Darwinian theory of evolution, in the Darwin Centennial Year of 1959, was confidently proclaimed to be the foundation of the science of biology, maintains that “such confidence is not warranted today,” because “new technologies have revealed that life is more complicated than was imagined in 1959” (Hirsch, p. 1).
By 2004, base sequences for more than a hundred genomes had been determined, and “these complete genome sequences have revealed several complexities that Darwinian evolutionary theory did not anticipate.”
Four of these unanticipated complexities are the following:
a) transfer genes;
b) bacterial species evolving also by deletion of genetic material;
c) the finding that some portions of the genome that do not code for proteins are not, nevertheless, “junk DNA;”
d) the finding that “the expression of genes is controlled by regulatory circuits that are as complicated and as precisely arranged as the most sophisticated engineering diagrams” (Hirsch, pp. 2-3).
But, says Hirsch, “how could a function requiring multiple proteins in a cellular machine ever arise through the required random mutations that developed one protein molecule at a time and in a stepwise manner, and gave no intermediate product with any function that would allow Darwinian natural selection to work?” (Hirsch, p. 11).
To Roland Hirsch it is clear that the accepted idea of organisms evolving from simple to complex does not apply to the protein synthesis machinery that works “with a precision exceeding that of the most complicated devices designed and engineered by humans” (Hirsch, p. 13).  It is Hirsch’s general conclusion that much of what was taught forty years ago in keeping with Darwinian theory “has had to be unlearned or has become irrelevant,” because it cannot explain much of what today’s experiments and field research reveal about biological life (Hirsch, p. 19).
Basic concept of the Darwinian theory of evolution is that the species living today emerged from prior living species by a process of random mutation and natural selection. ‘
14) http://en.wikipedia.org/wiki/The_Language_of_God:_A_Scientist_Presents_Evidence_for_Belief
FRANCIS S. COLLINS AND THE LANGUAGE OF GOD reviewed by John F. McCarthy [Francis S. Collins, The Language of God: A Scientist Presents Evidence for Belief (New York: Free Press – Simon and Schuster, 2006 – viii plus 294 pages – available also from Amazon.com ] Part I.  Random Change Versus Intelligent Design. dr dach.
15) http://www.aaas.org/news/releases/2002/1106id.shtml
AAAS Board Resolution Urges Opposition
to “Intelligent Design” Theory in U.S. Science Classes
The AAAS Board recently passed a resolution urging policymakers to oppose teaching “Intelligent Design Theory” within science classrooms, but rather, to keep it separate, in the same way that creationism and other religious teachings are currently handled. dr dach.
“The United States has promised that no child will be left behind in the classroom,” said Alan I. Leshner, CEO and executive publisher for AAAS. “If intelligent design theory is presented within science courses as factually based, it is likely to confuse American schoolchildren and to undermine the integrity of U.S. science education.”

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