Evolution, Part VI: Even More Challenges for Evolution

Read Part IPart IIPart IIIPart IV, Part V

Irreducible complexity

Another hurdle for evolution is to explain so-called “irreducible complexity.”  The challenge is how evolution, through small, incremental steps can explain complex systems with many intricate, interdependent parts. Basically, since the entire system depends on each individual part to function, it could not have been formed gradually, because there would have been no intermediate function or advantage for natural selection to select.

Famous examples of irreducible complexity include the bacterial flagellum, the blood clotting function, and the immune system.  The “simple” bacterial flagellum includes bushings, stators, universal joints, rotors, drive shafts, etc.1  Blood clotting involves a very complex process with well over a dozen interdependent steps.  Not only is the entire process irreducibly complex, but so is each individual step in the chain.2  The immune system is an incredibly complicated, interdependent system designed to recognize invaders, differentiate them from healthy cells, and effectively destroy harmful ones, even when the organism has never experienced them before.3  In each of these examples, the processes are mind-numbingly intricate and could not have evolved in a step by step process since each individual step depends on the previous one to operate.

Evolutionists have tried unconvincingly to answer irreducible complexity.  The primary argument is that the individual pieces or processes could have originally had different functions that did offer an advantage, but eventually and gradually morphed into a new structure with a different purpose.  For instance, the parts of a flagellum are similar to those used by the bubonic plague bacteria to inject toxins.4  Or the process of blood clotting seems to “involve the modification and elaboration of proteins that were originally used in digestion.”5

Unfortunately, both of these examples miss the entire point.  Irreducible complexity does not refer to the individual parts, but to the entire system.  It is the system that is irreducible.6  Certainly, similar parts could exist or have a purpose in a different system, but that in no way removes the challenge.  For the new system to arise, the necessary parts still need appropriate modification, assignment to a new function, and interdependent coordination with multiple other, new parts to be effective.  The evolutionists proposed solution is akin to saying that since lumber exists, a fully built and functioning house needs no explanation!

Richard Dawkins tries to explain away irreducible complexity by saying that the intermediate steps have provided some advantage even if not the advantage of the fully functioning system.7  For example, “half an eye” could help animals distinguish between light and dark, which is better than no sight at all.  Or “half a wing” could slow a descent and help prevent injury or death from a fall, even if flight were not possible.  Dawkins then suggests that “gliding or parachuting animals” and the eye of a flatworm prove his point.

Unfortunately for Dawkins, they really don’t.  Common or similar function does not prove common descent (though it is consistent with common design).  If Dawkins is going to suggest that wings evolved from earlier structures like the stretchy patch of skin used in flying squirrels (an example of the “gliding” animals he cites), he has to propose a model for how a patch of skin turns into a wing with bones, muscles, and feathers.  And he has to show how flying squirrels evolved into birds.  Strangely, he does not try to do this.  He simply makes his unsupported analogy and moves on.

Or perhaps Dawkins would like to explain where the flatworm fits within the evolutionary pathway of humans to explain the development of our eyes?  Recognizing the ignorance of such a position, evolutionists now admit that “in various families of organisms, eyes have evolved independently,”8 possibly as many as 65 separate times!9  That’s certainly convenient.  Since no evolutionary pathway can be found to explain the eye (because of its complexity), it must have actually evolved independently dozens of separate times in many different creatures!  That sounds like a truly desperate attempt to avoid the design inference, and one that is philosophically rather than evidentially based.

The Bounds of Naturalistic Evolution

As stated numerous times, biological change does occur.  And mutation plus selection is adequate to account for these relatively minor changes, like bacterial antibiotic resistance.  The real question is whether these “micro” changes can account for the “macro” developments required for the vast biological diversity around us.

Evolutionists clearly believe that “micro” changes plus vast amounts of time will lead to “macro” evolution.  They believe this despite the fact that mutation plus selection utterly fails to account for the creation and development of new information or new morphologies.  They accept it based on philosophical desire, not evidential proof.

The facts strongly suggest that the biological changes we observe operate within narrowly defined bounds and are of the fundamentally wrong nature to account for “macro” evolution.  Macro evolution does not occur from simply adding up a lot of “micro” changes.10  As we have seen, small scale changes do not account for the creation of new biological information.  Nor do they create new organs, structures, or irreducibly complex systems since these cannot be built piece by piece.  These require a fundamentally different mechanism that does not build from the “bottom up.”  Likewise, the fossil record does not support a “bottom up” record of development.

Georgia Tech geneticist John McDonald notes the “great Darwinian paradox” which can be paraphrased as “the kind of mutations we need for major evolutionary change we don’t get; the kind we get we don’t need”11.  Dr. Douglas Axe notes that natural selection has “failed as an inventor” and proven itself merely a “fiddler.”12  In other words, naturalistic evolution can work to improve what is there, but it does not create something new.  Evolution is akin to the analogy of someone tinkering in a shop and fortuitously fixing their bicycle so that it works better.  But it simply cannot explain how the bicycle developed in the first place.  And no amount of tinkering will ever turn the bicycle into a Boeing 747.


The existence of consciousness is something naturalism, and therefore evolution, is at a complete loss to explain.  If life is nothing more than various elements from the periodic table, arranged in a particular manner, and combined with an energy source, then things as abstract as consciousness, emotion, and free will are very difficult to explain.  In fact, they are impossible.

Stephen Hawking admits as much on page 178 of The Grand Design.  He posits that free will is not actually free.  Rather, our decisions are predetermined by the immutable laws of physics and chemistry.  In fact, everything and every action since time began is determined by these factors.  We only appear to have free will because there are too many variables involved in a given decision for us to predict the outcome, so we mistakenly believe we have a choice.  While Hawking applies this principle specifically to free will, it also necessarily applies to all forms and acts of consciousness.  It also applies to purpose and morality.  Ultimately, if naturalism is true, then nothing and no one has any actual purpose or value.  This is an inescapable conclusion.

It is interesting to note that evolutionists must believe these facts if their worldview is true, but none of them live as if it is so.  If we have no true free will and are just “dancing to our DNA,” why are activist atheists like Richard Dawkins so committed to getting us to believe evolution?  If he’s right, then we can’t choose to change our minds anyway.  Furthermore, he really doesn’t believe in evolution because of the evidence, but because of the unavoidable decrees of the universe’s physical and chemical laws.  And if there is no value or purpose to life, why does it matter what we believe?  It certainly doesn’t seem as though Richard Dawkins, Daniel Dennett, Sam Harris, David Mills, and other atheist writers actually believe this to be the case.  Why would someone vehemently support a given worldview but then lead their lives as if the exact opposite is true?  Dawkins loves to rightly point out the hypocrisy of certain religious leaders but fails to recognize his own blatant version of it!

The typical atheist assertion is that the the “mind” (consciousness, will, etc.) is nothing more than a “manifestation of matter.”13  Consequently, there is no non-physical consciousness, soul, etc. apart from the physical brain.  They support this idea by pointing out that damage to certain parts of the brain causes the loss of specific functions and conscious abilities.  Therefore, since the mind is inextricably linked to the physical brain, it must be physical.  All indications to the contrary are illusory.

However, this belief totally misunderstands the idea of a non-physical consciousness.  Humans are physical beings and we have physical limitations.  The fact that our consciousness is linked to a physical brain for expression does not mean it only exists within the brain.  As an analogy, a race car and its driver are inextricably linked.  If the engine breaks or a wheel falls off, etc., the driver is powerless to operate the car.  But the fact that the car won’t work does not mean there is no driver.  Likewise, the fact that brain damage may prevent the expression of a non-physical consciousness does not mean that the consciousness does not exist.  The fact remains that despite decades of research, science cannot physically explain consciousness and our own experience indicates that it is both real and non-physical.


Darwinian evolution is a tremendously important topic for Christians to understand.  There is no question that it has become one of the hottest “battlegrounds” in the debate about whether God exists.  This trend is certain to continue as naturalism increases its philosophical influence on American culture and education.

But if the evidence for Darwinism has so many problems, why does it persist?  More importantly, why is its acceptance so broad among educated scientists who study biology for a career?  The answer is surprisingly simple.  They have no other choice.  Theoretically, science is supposed to search for truth and follow the evidence wherever it leads.  However, since Darwin, it has become greatly influenced by the philosophy of naturalism.  Consequently, it is now accepted, even among religious scientists, that scientific explanations must be grounded in physical, naturalistic causes.  No supernatural or divine influences are allowed by definition.  Unfortunately, this means that science has moved from a search for truth to a philosophical commitment to naturalism.

Scientists are not shy about admitting this point.  For example, a 2002 Scientific American article states “science welcomes the possibility of evolution resulting from forces beyond natural selection. Yet those forces must be natural; they cannot be attributed to the actions of mysterious creative intelligences whose existence, in scientific terms, is unproved.”14  More to the point, geneticist Richard Lewontin states “…we have a prior commitment, a commitment to materialism… that materialism is absolute, for we cannot allow a Divine Foot in the door.”15 Kansas State University biologist Scott Todd perhaps said it most clearly when he wrote “Even if all the data point to an intelligent designer, such a hypothesis is excluded from science because it is not naturalistic.”16  That’s about as straightforward as one can get!

If Darwinian evolution is proven false, the entire philosophy of naturalism dies.  Without a purely physical explanation for life and its dizzying complexity and grandeur, atheism totally collapses under the weight of the evidence we see around us every day.  This fact is one reason naturalists fight the idea of supernatural creation and intelligent design so vehemently.  They are literally fighting for the life of their worldview.

Ironically, the Christian is under so such pressure.  If evolution were somehow proven to have occurred, naturalism only becomes possible, not certain.  There are many Christians that believe evolution did occur, though it was directed by God and was the process through which He brought life into existence.  Dr. Francis Collins, leader of the Human Genome Project and Director of the National Institute of Health, is one example of such “theistic evolutionists.”  It is important to recognize that Logic & Light does not believe in or support the idea of theistic evolution.  We only bring up the topic to demonstrate that the possibility of evolution does not threaten the existence of God, though it does require a metaphorical interpretation of parts of Genesis that is not readily apparent from the text.

In conclusion, a few things are clear.  There is evidence consistent with the theory of evolution. But the totality of evidence very clearly points toward the requirement of an intelligent, intentional design behind life.  There is simply no other logical conclusion based on the evidence and our experiences.  Unfortunately, most scientists have barred themselves from accepting such evidence.  So evolution is proclaimed a proven fact, despite its many challenges, while scientists privately search for an answer to why the evidence they see does not fit with the naturalistic philosophy to which they are committed.


As this series is being finished, two new 2018 articles from evolutionists were published by reputable, scientific sources.  Both point to the further unraveling of naturalistic evolution!

The first was published in Nature Communications by Jordi Paps and Peter Holland.  The paper confirms that hundreds or thousands of new and unique genes and groups of genes are needed for the emergence of new, multicellular organisms.17  The lead author comments, “We discovered the first animal had an exceptional number of novel genes, four times more than other ancestors. This means the evolution of animals was driven by a burst of new genes not seen in the evolution of their unicellular ancestors.”18  In other words, massive amounts of new genetic information simply appeared.  That is not how naturalistic evolution is supposed to work!

The second paper was written by Mark Stoeckle and David Thaler and published in the journal Human Evolution.  Darwinian evolution predicts that large, dispersed populations should get more genetically diverse over time.19  However, the authors found that this is not the case, contradicting evolutionary thought.  More surprising, however, is that they also discovered 90% of the world’s current species came into existence at roughly the same time, estimated at 100,000-200,000 years ago.  Based on evolutionary theory, this finding “is very surprising, and I (co-author Thaler) fought against it as hard as I could.”20  Furthermore, the authors also concluded that “species have very clear genetic boundaries, and there’s nothing much in between.”21  Let’s summarize:  1) multiple evolutionary predictions are wrong, 2) the vast majority of existing species came into existence at once instead of separately over eons, and 3) there are vast genetic gulfs between species, indicating that required “transitional” forms are absent both from the fossil record and living animals.  Are you starting to see a trend?…


  1. Behe, Dr. Michael. Darwin’s Black Box.  New York, NY:  Free Press 2006.  71.
  2. Pg. 87.
  3. Pgs. 120-124.
  4. Rennie, John. https://www.scientificamerican.com/article/15-answers-to-creationist/
  5. Ibid
  6. Behe, Dr. Michael, Op. Cit. 261.
  7. Dawkins, Dr. Richard. The God Delusion. New York, NY:  New Mariner Books 2008. Pgs. 149-150
  8. Rennie, John. https://www.scientificamerican.com/article/15-answers-to-creationist/
  9. Wells, Dr. Jonathan. Zombie Science: More Icons of Evolution. Seattle, WA:  Discovery Institute 2017. Pg. 132.
  10. Meyer, Dr. Stephen. Darwin’s Doubt.  New York, NY: HarperCollins Publishers 2013. 269.
  11. Pg. 262
  12. Axe, Dr. Douglas.   New York, NY:  HarperCollins Publishers 2016.  Pg. 103
  13. Dawkins, Dr. Richard. Cit.  Pg. 209
  14. Rennie, John. https://www.scientificamerican.com/article/15-answers-to-creationist/
  15. Meyer, Dr. Stephen. Cit. Pg. 386
  16. Wells, Dr. Jonathan. Cit. Pg. 179.
  17. Discovery Institute. 6/7/2018.  https://evolutionnews.org/2018/06/groundbreaking-paper-shows-thousands-of-new-genes-needed-for-the-origin-of-animals/
  18. Ibid
  19. Quincler, Cristina. 5/28/2018.   https://www.msn.com/en-my/news/techandscience/sweeping-gene-survey-reveals-new-facets-of-evolution/ar-AAxUobQ?srcref=rss
  20. Ibid
  21. Ibid