Was Darwin Wrong? Section One

The Tree of Life is Really a Network

Central to Darwin's Theory is the Tree of Life. This Tree idea is that simple life forms like one-celled organisms are represented by the tree trunk, and more complex organisms such as land mammals are represented by smaller branches at the top of the tree.  According to a recent article in New Scientist, 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 HGT, Horizontal Gene Transfer.

Darwin's Tree of Life has been transformed into a network or bush.  (see diagrams below)

       
Left Image: This "Tree of Life" sketch is seen in Darwin's  notebook (Image: courtesy of Mario Tama / Getty). Right Image: New Idea is the Network or Web of Life courtesy of Doolittle.

Darwin Wrote His Theory in 1859

Since Darwin wrote his  theory in 1859, there has been considerable  progress in science and molecular biology.  The double helix structure of DNA was discovered by Watson and Crick in 1953, and the  human genome was sequenced in 2003.  These new discoveries have made paradigm shifts in thinking about evolution, and Darwin's 19th century theories have been antiquated by advances in molecular biology over the last 15 years. 

Evolution From Simple to More Complex

Darwin's theory is that biological diversity results from natural selection acting on heritable variations in the population.  There are two components of the theory: 1) Random mutations provide variation and 2) Natural Selection provides that the variants most adapted for survival will survive, while less adapted will not.  Over many generations, small incremental changes  in the population will leads to emergence of entirely new species.  This is the mechanism explaining the evolution from simple one-celled organisms to more complex multi-celled organisms.

Newton Replaced by Einstein

Just as Newtonian physics remains valid for special cicumstances, so does Darwin's theory.  And just as Newtonian Physics has been superceded by Einstein and Quantum Mechanics, so too have Darwin's 19th century ideas been superceded by new discoveries in molecular biology over the past 15 years.

Questioning Natural Selection as the Mechanism

Darwin's idea of Natural selection is a useful concept for animal breeders of the 19th century, who successfully bred animals with desired traits.  Darwin's idea was that Nature could act in place of the animal breeder, select certain traits providing survival advantage and reject traits that impaired survival.  In 1859, Darwin then took the leap and proposed Natural Selection as the mechanism driving evolution from simpler to more complex organisms.  This was a good theory for the 19th century, but modern discoveries have made this antiquated.  

New Science Replaces Natural Selection with Genetic Engineering - James A Shapiro PhD

 

One such high powered scientist is James Shapiro at the University of Chicago (above image courtesy of James Shapiro) .

Recent work by James A Shapiro shows Genetic Engineering as the 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 are a few of the Natural Genetic Engineering Modalities discovered by Dr. Shapiro.

• Homology-dependent exchange & gene conversion:
- DS break repair
- Rearrangements by crossover at dispersed homologies
- Cassette exchange, protein diversification
• Non-homologous end joining (NHEJ)
- DS break repair
- Targeted and untargeted rearrangements
• Mutator polymerases
• Terminal transferase - insertion of novel sequences
• Site-specific recombinases
- Integration of horizontally transferred DNA
- Regulation of protein synthesis, protein diversification
• DNA transposons (replicative, cut-&-paste, rolling circle helitrons)
- Amplification and insertion of repeat elements
- Large-scale rearrangements (in particular, duplications)
• Reverse transcription-dependent retrotransposons (retroviral-like, LINEs, SINEs)
- Amplification and insertion of repeat elements
- Integration of processed RNA cDNA copies
- Small-scale movement of genomic segments (e.g. exon shuffling)
• Homing and retrohoming introns
Quoted from link

Above Images: Charles Darwin 1880 Courtesy wikimedia commons, James A Shapiro courtesy of University of Chicago Web Site

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."  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 ocurr 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. 

Gould invented a new theory called Punctuated Equilibrium to explain lack of gradualism in the fossil record.  Rather than finding gradual change in the fossil record, paleontology has found sudden appearances of life forms, as well as long periods of stasis or little change in the fossil record.   One example of this is the Cambrian explosion about 555 million years ago when 40 body plan appeared over a ten million year period with no preceding transition forms.   These findings had to be incorporated into Darwin's theory, adding to the complexity of the theory.   Cornelius Hunter regards this type of post-hoc reasoning to be analogous to the epicycles of the  pre-Newtonian Geo-Centrists who claimed the earth was the center of the universe.

How does the first living cell arise spontaneously to get evolution started?  Science doesn't have a clue as to how the first living organisms originated.  This is called abiogenesis, and neo Darwinism does not even address this issue.  Stephen Meyers refines this question further as the question of the origin of "biological 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 Shapiro at U of C and Stern at Princteon 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 

This dissent is by scientists on scientific grounds,  which in no way advocates Creationism, Intelligent Design or "God Did It".

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."

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."

5) David Stern Molecular Biology at Princeton.

" The predominant model in evolutionary biology, traceable back to Darwin, suggests that continuous variation within populations is gradually selected upon to generate species differences. ...However, there is little empirical evidence to support or reject this view."

 "we currently have almost no idea how genetic variation is transformed into phenotypic variation."   "Although mutations are thought to ocurr randomly in the genome, the distribution of mutations that cause biologic diversity appears to be highly non-random."   "Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. "

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:  1) How the Universe originated. 2) How Life originated. 3) The Correct Mechanism of Evolution. 4) How Human Intelligence Originated.

Preface to Section Two: Is Intelligent Design Science?

Although advocates of  Intelligent Design (ID at the Discovery Institute) have written extensively that Intelligent Design is Science. I have always had the opinion (for many years now) that Intelligent Design is Not science and is in fact philosophy.

Objective Knowledge is Science and
Subjective Knowledge not Science  

My opinion is based on the difference between two forms of knowledge, objectively verifiable knowledge and subjectively verifiable knowledge. 

Objective Knowledge can be verified by repeatable experiments or observations and is the basis for scientific investigation.  Subjective knowledge is different.  This type of knowledge cannot be verified by others, or with experiments.  An example of subjective knowledge is knowledge of a dream last night. We can remember the dream and write it down and tell it to others.  Yet this knowledge cannot be verified by others. They will have to take our word for it.  Another example is love.  How do we know when we love some one.  We just "know" it.  Any type of direct sensory input is subjective knowledge.  We cannot directly feel another's pain, yet we know they have pain.  We can know of their pain but we cannot experience it directly.  Knowledge of the present moment, and  our memories of past events are examples of subjective knowledge. There are many other examples of subjective knowledge.

Intelligent Design is Subjective Knowledge and Not Science

Intelligent Design relies on the knowledge that an object in nature appears to have been "designed" based on "complexity" or "coded language" such as DNA codes.  Again, this is subjective knowledge which can not be objectively verified. That is why Intelligent Design is not science. 

Is There An Intelligent Design to Life and the Universe?

Science is the study of  nature, and presupposes that the universe is orderly.  This means that Science presupposes the concept of order, another word for "Intelligent Design".  The problem is that although Science first presupposes an Intelligent Design of the Universe, it then ignores this presupposition, claiming that there is no scientific evidence for Intelligent Design.  This is actually a semantic argument, or a verbal sleight of hand.

Does the Intelligent Designer Exist?

This brings us to the "Intelligent Design" argument and the question of "is there a creator of the universe?"  This is an obvious question raised from biology, which reveals DNA, the genetic code, and complex life forms in the world.  All life forms share the same underlying genetic code which translates base pairs into proteins.  The existence of a code, or "alphabet" is a language which implies an underlying intelligence for its creation.  Encrypted or coded messages do not happen by random chance, and implies an intelligent author.  Again,  whether this appears true or false depends on subjective knowledge, and not objective knowledge.  Currently, we have no objective way of concluding if an encrypted message in nature (such as the genetic code) is the result of an intelligence, or the result of nature.  If we did have such objective criteria, then there would be no debate over Intelligent Design.

 My Own Opinion

My own opinion, based on subjective knowledge,  is that encrypted messages in nature (such as the genetic code) indicates intelligence.  This underlying intelligence  permeates all life and the entire universe.   Not everyone agrees. 

A staunch atheists such as Richard Dawkins would disagree.  However it is interesting to note that even Richard Dawkins admits to  1) being thankful for Life 2) Having quasi-religious feelings when contmplating nature-But Einstein had that feeling, I have that feeling, you'll find it in the writings of many scientists. It's a kind of quasi-religious feeling.

The Watch Maker Argument

Here it the original discussion of 
The Watch and the Watch-Maker Argument:

Originally credited to William Paley (1743-1805).

If you were walking on the beach and came across a functioning clock or watch on the sand, would you assume that the watch was created by a watchmaker, or would you assume the watch parts randomly self assembled on the beach? 

The Watchmaker Argument

Science views the universe as a giant watch and tries to figure out how the parts work, and where the parts came from.  Science assumes that there is a pattern in the watch mechanism that can be understood.  Science accepts that the watch is there in the sand and is not concerned with who made it.   "Intelligent Design" picks up on this question and asks, " Who made the watch.  Was there a Watchmaker"

Intelligent Design or Designed Intelligently?

In my opinion, "Intelligent Design" is not a scientific theory and does not compete with other scientific theories about the universe and life in it.  Rather, "Intelligent Design" is a way of thinking about the questions which Science leaves unanswered.  As stated above, Intelligent Design can be regarded as a presupposition to the activity of Scientific Investigation.  The subject of scientific discovery and investigation is the order or "design" of the universe.

 Who Designed This?

Left Image:  9 week human embryo courtesy of wikimedia commons.

The Human Embryo

Take a look a the human embryo (above).  This embryo starts from a single cell and grows in a self-directed manner into an adult human, who has self-awareness and is capable of asking the question,"Where did I come from ?".

The above human embryo is vastly more complex and sophisticated than anything ever designed by human intelligence.   Molecular biology is less than 50 years old and still in its infancy. Science has yet to discover and  work out the mechanism that controls the growth of a single cell into an adult organism.  Science has yet to discover and work out the mechanism of evolution.  It certainly is not Darwin's natural selection from the 19th century.  It may take centuries of new science in the future  to "crack the case" of the mechanism of evolution.  This is the exciting thing about science that can draw our young people into careers in science.  The great discoveries are yet to be made.

Education in our Public Schools - ID vs. Science

There is a controversy about education in our public schools with the ID people and the Evolution People at odds with each other.  The Evolution People don't want ID talked about in science class, claiming that ID is a religion like creationism.  The I.D. people object to this, claiming that Darwin's theory of evolution imposes an atheist worldview on the students.  They claim that academic biologists are mainly atheists and they don't want their kids indoctrinated into atheism. Atheists claim they do not woshipo anything.  However, the reality is that that Atheists typically replace Deism with another "ism", such as hedonism, naturalism, communism, nationalism, narcissism, etc.

Although religious fanatics on school boards seem to be the only proponents of Intelligent Design in the classroom, I.D. is not a religion.  Discussing I.D. in the classroom is not the act of practicing a religion, nor is it science.  It is a form of philosophy and rightly included in a classroom course covering philosophy, linguistics, semantics, history of civilization or comparative religions.

Many concerned parents see the theory of evolution as an attempt to introduce an atheist worldview into the classroom,  supportive eugenics, and authoriarian government.  The opposing worldview points to design and order in nature, as suggesting an "intelligence" or plan to the universe, this is a subjective worldview that leads to the idea of a creator of the universe. 

Solution:

Don't Teach Intelligent Design as an alternate scientific explanation.  It is a non-scientific alternative explanation.  College courses cover comparative religions and the history of western civilization.   Religious writings, practices, and institutions have been strong factors in the sweep of history. High School should include an introduction to the history of religion and civilization.

Although the AAAS passed a resolution opposed the teaching of "Intelligent Design Theory" within science classrooms, they still allowed it to be taught separately outside the science classroom.  This seems reasonable.

Panties All in a Twist Over Darwinism

The above article must have touched a frayed nerve in a University of Minnesota biologist, Paul Z Myers, who got his panties all in a twist over my article.  I was flattered that he devoted the time and energy for a rebuttal, even though  a dismal failure.   See my reply to this guy.  

Myers is an atheist who publicly displays  death threats that he receives from disgruntled readers.  No wonder, since he typically uses Nazi Style smear tactics, and childish name calling.  Many of his comments are clearly libel, so any attorneys out there interested in quick money, take a look at his blog.

250,000 Physicians Dissent

About 30%  (250,000) of licensed physicians in the U.S. agree with Intelligent Design in a 2005  poll.   A full 15% (113,500) doctors do not agree with Darwin's Theory of Evolution. If agreement with Darwin is a prerequisite for  a doctor to practice medicine, then 30% of all US doctors would be eliminated.  

Evolutionary Biology Should NOT be used for the Practice of Medicine

Evolutionary biology is the product of one man, Randolph M. Nesse MD at the University of Michigan who admits,"evolutionary knowledge does not often change what a physician does in his or her day-to-day practice; instead, it guides research.  Treatment decisions are, and should be, based on controlled studies on humans, not on theory or on experiments performed on model organisms alone. Darwinian medicine does not often give direct practice guidelines."

Academic Biologists Are Atheists

Polls show that although atheists are only 15% of the general population, 95% of academic biologists are atheists.  Biologists are indoctrinated by their superiors early in their training to an  atheist world view.  This brings us to the real debate going on here, which is a debate between two world views, Atheism and Deism. 

Abraham, the First Monotheist 

The first man to fight the battle against idolatry was Abraham, the first monotheist,  and this battle has been going on for centuries.  Currently the battle is waged under the guise of  evolution against intelligent design.  Atheism, a primitive non-theistic form of religion (worship of self, money, nature, etc..) has been clandestinely slipped into our public school system under cover of the "good science" argument.  It is not "good science" to insist on an atheist world view proposed by Richard Dawkins.  This is indoctrinating our children into idolatry.  Do we really want that?

Richard Dawkins Refuted

A vocal atheist and defender of neo Darwinism is Richard Dawkins, whose book, the God Delusion was refuted by another book The Dawkins Delusion ? by Alister McGrath.  Dawkin's God Delusion book is also refuted by Depak Chopra MD in a 6 part article here.

Update 6-25-09

Is ID Science?

Stephen Meyer would claim that , YES ID is science. Stephen Meyer's new book, Signature in a Cell, Evidence for Intelligent Design , argues that the best explanation of the origin of biological information (an example is the DNA code) is an intelligent cause.  Discovery of the coded instruction set in the DNA of the cell is best explained as designed by an intelligence.   He also claims that this specific inference is a scientific argument which  was used by Darwin himself, called best inference from the evidence.   Video of Meyer's book presentation here.

Meyer stops short  with his argument, staunchly refusing to then infer the nature of the designer, as this would be outside the realm of scientific exploration.  Nonetheless he goes on to says that in his opinion, two possible candidates for the designer are extra-terrestrial beings as suggested by Crick with his life seeding earth hypothesis.   Another candidate is God the Creator.  He goes on to say that Big Bang cosmology suggests a cause before the creation of matter, space-time which would be compatible with the idea of a supernatural creator.

Is There Intelligence in Nature?

The claim that there is intelligence (other than human intelligence) in nature is not a new one.   As a matter of fact this claim has been present in human thought since the earliest recorded written documents for thousands of years.   The inference that this intelligence is God the Creator has also been present for millenia in human recorded thought.

What is new about Meyer's presentation is the packaging of the claim in the cloak of a scientific methodology which was used by Darwin himself.  Using this methodology does indeed make the claim of intelligence in nature a valid scientific claim.  To be scientific, the claim must be falsifiable, and his book goes through this line of reasoning as well.

Space Odyssey 2001 by Stanley Kubrick

As usual, popular media predated Stephen Meyer's book by 41 years.

Stanley Kubrick's Space Odyssey 2001 (1968) is the movie that does this.

See the 2001 Principle which explains the movie and the socio political implications of discovering a non-human intelligence in the universe.  In the movie, an Obelisk (or Monolith) is discovered on the far side of the moon, obviously the result of an intelligence. 

In Stephen Meyer's book, this obelisk or Monolith (see diagram below) has been replaced by the coded instruction set in nuclear DNA.

In the movie, the Monolith was present at the dawn of human life (see above image), and was also present on the far side of the moon, discovered by moon exploration.

The message from the above image is that Stephen Meyer's discovery of intelligence in nature, his example being the coded instruction set of DNA, is knowledge understood by early man at the dawn of written history all the way up to the presetn day.

Information in Both Animate and Inanimate World

I would suppose that Meyers waould say that there is information in nature throughout both the living (animate) world and the inanimate world.  Again, science has been useful in bringing this information to light.  Take, for example, the laws of electromagnetism in Maxwell's equations.  This could be taken as an instruction set for the inanimate world.  An instruction set implies an intelligence.   There are myriads of examples.

 The Great Accomplishement of Stephen Meyer

Stephen's Meyer's great accomplishement is the reframing of this knowledge of intelligence in nature in a form which is acceptable to the vast population of reasonable people, a format which uses the usual tools of science and abides by the usual rules of science.

Related Content:

Panties in a Twist Over Darwinism

Scientists Say No Dice to Darwinism

Atheist Talks to God

Why Are Atheists Ignorant?

Recommended Reading :

This web site covers this topic quite thoroughly with references:  http://www.2001principle.net/

Genesis and the Big Bang Theory :
The Discovery Of Harmony Between Modern Science
And The Bible, by Gerald Schroeder 1990 Bantam

The Science of God , by Gerald Schroeder 1997

The Hidden Face of God : Science Reveals the Ultimate ruth, by Gerald L. Schroeder 2001

Nature's Destiny: How the Laws of Biology Reveal Purpose in the Universe by Michael J. Denton .

Why Darwin was wrong about the tree of life .  21 January 2009 by Graham Lawton  

References and Links:

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.

http://www.truthnet.org/creation/evolution/
Creation/ Evolution

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]

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. dr dach.

http://www.faithfacts.org/evolution-or-creation/origins-and-silly-putty/darwinian-mechanism-problems 
Problems with the Darwinian Mechanism

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. dr dach.

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

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 dr.dach. 

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

http://www.southerncrossreview.org/40/cruse.htm
WAS DARWIN WRONG?  Yes — His Logic was Fatally Flawed
 by Don Cruse 

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

http://www.rtforum.org/lt/lt124.html
Biochemist Roland Hirsch, in an essay published in 2004,4 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). dr. dach.

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).  dr. dach.

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. ' dr.dach.

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.

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."