Behe suggests that the parts of irreducibly complex biological structures would be useless unless they appear all together, and evolution has no mechanism to build complex structures like this. Natural selection, after all, works just one step at a time. Furthermore, natural selection has no foresight. Put simply, if a change is going to be preserved, that change will generally need to confer some extra benefit—no matter how small—to the next generation. Behe has oversimplified things a little. Evolutionary theory predicts that in small populations, neutral changes—and even changes that are slightly deleterious—will survive sometimes. Still, in general, he is correct. So let’s examine what evolutionary biologists believe about how complex structures are built.

A Seemingly “Irreducibly Complex” System

As Scott Gilbert shows in his textbook Developmental Biology, Eighth Edition, the evolution of the interconnecting bones of the middle ear illustrates how supposedly irreducibly complex structures can in fact be generated by the stepwise process of gradual change and natural selection. Fish, for example, have a special system called the lateral line system that extends along the length of their bodies and enables them to detect vibrations in the water. They also have an inner ear, which is useful for balance and supplements the lateral line system in detecting vibrations. With the movement of certain water-dwelling species to land, the lateral line system became obsolete because what was needed was a way of amplifying the vibrations in air, not water. A bone that had previously been used as a support for the skull became the stapes. Along with supporting the skull, the stapes also transmitted sound vibrations—which come in part through the skull and jaw—to the inner ear. How do we know it’s the same bone? By examining its embryological origin in fish and reptiles. In reptiles, there is just one bone that transmits air vibrations to the inner ear: the stapes.

We can also trace the origin of the two other middle ear bones, the incus and malleus, by looking at fossils from the time of the origin of mammals about 230 million years ago. Until that point, two bones—the articular and quadrate bones—served as the hinge of the jaw. Investigators, however, believe they carried out a second function. Because they were located adjacent to the stapes, it is likely they also aided in transmitting sound vibrations to the stapes.

Here is where the story gets especially interesting. Right at the time of the origin of mammals it turns out there were several species—perhaps many, paleontologists are sure they don’t have all of the transitional species preserved in the fossil record—that had a double hinge at the jaw. Not only did the articular/quadrate bones serve as a hinge, but another pair of bones, the dental/squamosal bones, served that purpose as well. So the articular/quadrate bones, which transmitted sound, no longer had to also serve as a jaw-hinge. This second function became redundant because there was another set of bones doing the same thing.

With that redundancy, the articular/quadrate bones of the jaw were free to become the incus/malleus of the middle ear. We have a record of the transition, and we have a record of the building of a so-called irreducibly complex structure. Parts that were initially used for one function became, for a period of time, useful for two functions. Then, one function was refined while the other function became redundant or unnecessary. In other words, parts that were initially used for one purpose become co-opted for another purpose; and looking back through the fossil record, we can see the intermediates.

The Bacterial Flagellum

In Darwin’s Black Box, Behe focuses on three things he considers to be irreducibly complex: the bacterial flagellum, the blood clotting cascade and the immune system. The elements of these systems are molecular in nature and therefore the evolutionary intermediates are somewhat harder to document. Interacting molecules are not preserved for historical analysis like fossil bones of the skull and middle ear. In his book, Behe suggests that biochemistry gives no clue as to how complex interacting parts like these might have come about, and he confidently states that investigations have run up against a blank wall.

It has now been 13 years since Darwin’s Black Box was written. The structures and processes Behe chose to focus on have been studied quite extensively. Although it is impossible to go back and analyze step by step what actually did happen, much evidence for straightforward evolutionary explanations has accumulated over the years. The diversity in a given structure that we see when we compare different species tells us a great deal about how that structure might have come about.

Consider the bacterial flagellum, the example most commonly used to illustrate the principle of irreducible complexity. First, it is important to point out that the bacterial flagellum comes in many different varieties, sometimes with profound differences between one species and another. This alone illustrates that the flagellum is probably not irreducibly complex. It can be altered, and when it is altered, it does not necessarily lose its function.

There are many species of bacteria, for example, that use the basal parts of the flagellum to deliver toxins into their host. A different set of bacterial species uses a portion of the flagellar machinery for another purpose. Species of the genus Buchnera live inside the sheltered environment of aphid cells in a symbiotic relationship. These bacteria no longer need flagella. However, each tiny Buchnera cell is studded with hundreds of copies of the flagellar base. As a recent paper in the journal Trends in Microbiology shows, the purpose now is to serve as a passageway for the export of proteins and other material into the surrounding environment—the aphid cell in which the bacterium resides. So while we cannot follow the sequence of events step by step to illustrate how the various types of flagella have arisen, we can see how they have changed and, in some cases, even taken on whole new functions. The term for adapting a structure for a different purpose than that for which it originally arose is “exaptation.” This is one important way in which complexity arises.

That is not the whole story, however, because individual parts have to be added into the structure as it becomes more complex or takes on new function. Where do those parts come from? Recently, investigators have shown that the key protein in the molecular motor that causes the flagellum to rotate has a very similar structure to another protein that is used to transport magnesium into and out of cells. Both protein molecules have sections that fold in almost exactly the same manner, and when we analyze the order of their building blocks (amino acids), we see profound similarities. This illustrates a second principle in building complexity: It is done by co-option. Parts that are used for one purpose are co-opted to take on a second function as well. Sometimes, the instructions to build a part are encoded by identical duplicate genes. When that happens, co-option is especially straightforward. One set of instructions for making the original part is preserved while the duplicate set of instructions can gradually be modified through mutation and natural selection, allowing the part to become better and better at carrying out its new function. This illustrates a third principle of assembling complexity: adaptation through natural selection.

Even more revealingly, the supposedly irreducibly complex bacterial flagellum turns out not to be irreducible after all. For example, there is a protein at the base of the flagellum, an ATPase, that drives the key structural subunit (flagellin) of the long hollow tube through its inner core, causing the flagellum to grow in length. Yet, it has been shown that flagellin can be transported to the end of a flagellum without this ATPase. The protein that was thought to be one of the flagellum’s most important parts can be done away with. This illustrates a fourth principle of building a complex structure: redundancy. Inside of cells, there is often more than one way to accomplish a particular purpose; as evolution “tinkers” with a complex structure, there is likely to be redundancy with certain parts at certain stages. One of these redundant mechanisms may become more specialized, and even perfected, as time goes by.

The Eye

Another system that is often held up as an example of irreducible complexity is the eye. People often ask: What good is a partly assembled eye? Is there any logical series of steps that could result in the creation—through the process of natural selection—of a structure so elegant as the eye of an eagle? What would be the starting point, anyway?

Watch "The Evolution of the Eye" from PBS' Evolution: "Darwin's Dangerous Idea".

All light-sensing devices in the animal world make use of a single light-sensitive molecule, retinal, which is derived from Vitamin A. Retinal can change its shape when it absorbs a photon of light. This molecule is always complexed with a protein known as an opsin. The two work together to sense light.

By analyzing the arrangement of the building blocks, or amino acids, in opsin, it is possible to show that all opsins are derived from a single ancestral gene. What purpose could the retinal/opsin combination have had in the earliest days of animal history? It likely functioned to detect light in order to set the internal body clock that regulates the 24-hour cycle of biological processes, known as the Circadian rhythm. In recent years, it has become apparent that living processes inside of cells are tuned to function in a manner that is synchronized with the cycle of sunlight.

Circadian rhythms function throughout the living world, including single-cell organisms. It seems likely, then, that the simplest light-detecting device arose through exaptation of a molecular device that was used to detect light—not so that an organism might move toward or away from the light, but so it could reset its molecular clock. Even the origin of opsin illustrates a basic principle of building complexity, co-option. Opsin is one of many G-protein receptors, which have come to take on many different functions through the history of life. When coupled with the light-sensitive molecule retinal, a G-protein receptor allows the cell to be sensitized to the presence and absence of light. Although we have no fossilized transitions that allow us to trace the various eye intermediates that have occurred in animal history, as we do with the middle ear, we do have a myriad of light-sensing devices in the animal kingdom that allow us to piece together how sophisticated eyes could have been created through a gradual process driven by natural selection. (You can read more about the prospective intermediates that exist in the animal world in a wonderful paper by Ryan Gregory.)

If you choose to explore eye development in detail, be watching for examples of exaptation, co-option, step-by-step adaptation and redundancy. For example, you will note that the evolution of the lens illustrates co-option and redundancy. There are two ways to focus the image on the light-receiving cells at the back of an eye. One way is through an independent lens. The other way is through the transparent cornea in front of the lens. The lens is simply transparent crystallized protein molecules that are assembled in such a manner that they bring the image into sharp focus. There are a variety of proteins that can be crystallized to serve as an effective lens. It turns out that, depending on the evolutionary lineage, various proteins—including enzymes such as alcohol dehydrogenase (an enzyme for breaking down ethanol), glutathione S transferase and protein chaperones—are used for this purpose. This is a simple example of co-option and redundancy functioning together as part of the tinkering mechanism used for building a complex structure like the eye.

Two-thirds of animal phyla have some sort of light-sensing device. Although all of these light-sensing devices make use of retinal and opsins, there are differences in structure that we can trace to differences in evolutionary origin. In his 2003 book, Life’s Solution, Simon Conway-Morris documents at least seven independent origins of the eye resulting in very similar outcomes. For example, the eye of a squid and the eye of a mammal work in a remarkably similar manner. However, the ways the two eyes are constructed during development are quite different. Differences in structure are constrained by how particular bodies are constructed as the embryo develops. Eyes also bear telltale signs of the fact that there has been a certain amount of jury-rigging in their construction. They are not perfect. They have blind spots, are subject to retinal detachment, glaucoma and macular degeneration, all of which are a function of the history of how the eye has been assembled through time.

Read how a recent study has shot down the idea that protein transport is irreducibly complex.

Although we don’t have the eye intermediates preserved in stone the way we can see the simpler assembly of the parts of the mammalian middle ear, we do have a vast array of eye structures in the animal kingdom, any one of which might appear to be irreducibly complex but which, in fact, has been put together through a set of processes that has included exaptation, co-option, step-by-step adaptation and some redundancy at various stages along the way. Indeed, these eye structures themselves are likely intermediates. Everything changes as it passes through the eons of time. This is the legacy of creation through the process of natural selection.

A common argument against evolution is that the theory contradicts the Second Law of Thermodynamics that claims disorder, or entropy, always increases or stays the same over time.  This law has plenty of everyday examples. Buildings break down over time, and food spoils if not eaten soon enough.  In both cases, the amount of disorder increases with time, but the opposite is never true. Buildings don’t strengthen themselves, and no amount of waiting will cause rotten food become edible again.  But because evolution results in an increase in the order and complexity of species — which is a decrease in entropy — some critics claim evolution violates the Second Law of Thermodynamics.

Defining the System

However, this objection is grounded in a misunderstanding of the second law, which states any isolated system will increase its total entropy over time.  An isolated system is defined as one without any outside energy input. Because the universe is an isolated system, the total disorder of the universe is always increasing.

With biological evolution however, the system being considered is not the universe, but the Earth. And the Earth is not an isolated system.  This means that an increase in order can occur on Earth as long as there is an energy input — most notably the light of the sun. Therefore, energy input from the sun could give rise to the increase in order on Earth including complex molecules and organisms.  At the same time, the sun becomes increasingly disordered as it emits energy to the Earth. Even though order may be increasing on Earth, the total order of the solar system and universe is still decreasing, and the second law is not violated.


Misapplication of The Second Law

To claim that evolution violates the Second Law of Thermodynamics is also grounded in a misunderstanding of where the law applies.  Nobody has ever figured out how to apply the second law to living creatures. There is no meaning to the entropy of a frog. The kinds of systems that can be analyzed with the second law are much simpler.

A living organism is not so much a unified whole as it is a collection of subsystems. In the development of life, for example, a major leap occurred when cells mutated in such a way that they clumped together so that multicellular life was possible.  A simple mutation allowing one cell to stick to other cells enabled a larger and more complex life form.  However, such a transformation does not violate the Second Law of Thermodynamics any more than superglue violates the law when it sticks your fingers to the kitchen counter.

There are many examples of order arising from disorder in nature. Research conducted by Ilya Prigogine¹ and others on systems far from equilibrium has shown that order can spontaneously arise in systems that are driven in the right way. It turns out that living systems are characterized as being far from equilibrium.

The Second Law of Thermodynamics also has interesting implications for cosmology, as it requires that universe began in a highly ordered state.

The word evolution can be used in many ways, but in biology, it means descent with modification. In other words, small modifications occur at the genetic level (i.e. in DNA) when a new generation descends from an ancestral population of individuals within a given species. Over time the modifications fundamentally alter the characteristics of the whole population. When the population accumulates a substantial number of changes and conditions are right, a new species may appear.

Universal Common Descent

A cardinal principle of evolutionary theory is that all living things—including humans—are related to one another through common descent from the earliest form of life, which first appeared on earth about 3.85 billion years ago. How the first simple organisms arose is still a scientific mystery, but we know that they carried hereditary information and were capable of self-replication. Over eons, successive generations led to the marvelous diversity of living things that exist today. Common descent is supported by multiple independent lines of evidence, most notably the fossil record and the comparison of many species’ genomes.

Mechanisms of Evolution

When Charles Darwin published The Origin of Species in 1859, descent with modification was not a particularly new or controversial idea. Darwin’s intellectual leap was to propose the mechanism by which evolution occurred. That mechanism, called natural selection, is a description of what happens when variations occur in a population where resources are limited. When more individuals are born than the environment can support, those with advantageous variations are more likely to survive than those without them. This differential reproduction leads to overall changes in the traits of a population over time.

Natural selection is called “natural” not because it occurs apart from God’s activity (after all, many believe natural laws and processes are a reflection of God’s activity), but because it is the usual pattern one observes in nature, in contrast to the “artificial” selection practiced for centuries by farmers and animal breeders.

Other mechanisms of evolution besides natural selection include sexual selection and genetic drift. Sexual selection occurs when individuals of one sex are attracted to mates which manifest certain traits (the peacock’s tail arose this way, for example). Genetic drift is the random (i.e. unpredictable) fluctuations that naturally occur in a population’s gene pool when the population is small. The best adapted individuals do not always survive to reproduce, while poorly adapted individuals don’t always die before passing on their genes. Over time, in small populations, genetic drift can lead to noticeable change.

More recently, it has been proposed that a group of organisms could sometimes benefit from its members behaving in ways that would otherwise be detrimental to an individual organism. This so-called group selection takes into account the survival needs of an entire community of a given species.

Genetic Mutations as the Source of Variation

Darwin recognized from his years of study that when any organism reproduces, new variants sometimes arise. Although he didn’t know it at the time, these differences were a consequence of mutations. Mutations are changes in DNA that occur due to errors in DNA replication or exposures to radiation or certain chemicals. The vast majority of mutations are neutral or harmful and are not preserved, but occasionally beneficial mutations occur that are preferentially passed down through the generations.

Misconceptions

A number of common misconceptions have led to confusion or suspicion about evolution over the years. One common argument is that despite hundreds of years of observation, there has been no experimental proof of one species evolving from another, such as a cat turning into a dog. The truth is, such a drastic transition is not predicted by the theory of evolution. In some cases, scientists have observed speciation, but it is true that we have not observed major changes in form. The reason, is that we simply haven’t been watching long enough.¹ Evolution of new forms—what some people call “macroevolution”—takes a very, very long time.

Next, the claim that humans share common ancestry with other species should not be misunderstood to mean that humans have evolved from any other presently existing species. Humans do share close common ancestry with other living primates, but rather than being direct descendants, we are more like cousins. Other primates have been changing as well over the past 5-6 million years since humans and chimpanzees diverged from a common ancestor.

A third misconception is that evolution is a random, purposeless process. It is true that individual mutations are random, in the sense that they are unpredictable, but natural selection is decidedly non-random. Whether there is any purpose behind the evolutionary process is not a scientific question, and the answer depends greatly on one’s worldview. For believers in the God of the Bible who created and sustains the whole universe, evolution is simply the means by which he accomplishes his praiseworthy purposes of bringing forth life.