Understanding Evolution: The Evolutionary Origins of Irreducible Complexity, Part 1

| By on Letters to the Duchess

One of the challenges for discussing evolution within evangelical Christian circles is that there is widespread confusion about how evolution actually works. In this (intermittent) series, I discuss aspects of evolution that are commonly misunderstood in the Christian community. In this post, we turn our attention to the argument that evolution cannot build “irreducibly complex” structures through gradual mechanisms.

The Intelligent Design argument from Irreducible Complexity (IC)

Since this post, and those that will follow it, depend on an accurate representation of the argument for irreducible complexity (IC), I will take some time to clarify exactly how Michael Behe, the biochemist and Intelligent Design (ID) proponent who has most extensively developed the IC argument, uses the term. For Behe, the argument for IC is a critique of gradual evolutionary processes, of the kind that Darwin saw as necessary for his theory to hold. When Behe introduces and defines IC in his book Darwin’s Black Box, he has a key quote from Darwin on gradualism explicitly in view:

Darwin knew that his theory of gradual evolution by natural selection carried a heavy burden: "If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down."

It is safe to say the most of the scientific skepticism about Darwinism in the past century has centered on this requirement… critics of Darwin have suspected that his criterion of failure had been met. But how can we be confident? What type of biological system could not be formed by “numerous, successive, slight modifications”?

Well, for starters, a system that is irreducibly complex. By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. (Darwin’s Black Box, p. 39)

The definition of an IC system is thus straightforward: it is a matched group of components, where all the components are necessary for the function of the system. The necessity of each component can be demonstrated by attempting to remove it – if the system no longer works if even one component is removed, it is by definition IC. Since an IC system requires all the components to be present for its function, it is not possible for the system, in its current state, to have been produced directly from a non-functional precursor. If one grants this premise, it leaves two options: that the IC system was derived indirectly, from a system that is not IC, or that the system was assembled by fiat and thus represents the actions of a designer. Behe’s criterion for distinguishing between these choices is based on evaluating the probabilities of these competing options:

Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitively rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin's criterion of failure has been met skyrockets toward the maximum that science allows. (Darwin’s Black Box, p. 40)

As we will examine in an upcoming post, Behe attempts to determine the precise limit of what evolutionary processes can (and cannot) achieve in a second book, The Edge of Evolution. For our present purposes, however, it is enough to note that the strength of the argument from IC depends on the perceived implausibility of the opposing explanation – that of an indirect evolutionary route that produces an IC system from a non-IC precursor system.

Building IC, one step at a time?

The presence of IC systems in biology as Behe has defined them is not contentious: there are many biological systems that cease to function when parts are removed. Indeed, the success of classical genetics in “dissecting” which genes are needed for certain functions largely rests on the ability to see some effect on function when a gene is removed from a system by mutation. What scientists dispute, however, is Behe’s claim that identifying IC systems is a hallmark of design. The evolutionary model for building IC is quite simple, and Behe has set it out as an option: an indirect route where non-essential parts are added to a system, and then over time the system comes to depend on those parts. We can diagram this model as follows:

The key to the model is that new parts can be added to a system, and that these parts are not essential when they are added. The resulting system is thus not IC, since it has parts that are not essential to its function, even if the new parts are advantageous in some way. If the new component is taken away at this stage, the system merely reverts to the precursor system. The second part of the model is that these intermediate, non-IC systems then may become IC if small changes make the new parts essential.

The addition of new, non-essential parts can be accomplished in several ways, such as a change in an existing protein that allows it to bind to a “precursor system”. More extreme would be the generation of a new protein that then adds to a precursor system as a non-essential component. Brand new genes, by definition, cannot be essential when they arise, since they arise in an organism that, up to that point, had no need of them. Looking to see if new genes then later become essential would be very good experimental support for the evolutionary model for how IC systems arise.

In practice, it takes a lot of scientific effort to tease out changes to an existing protein that allow it to become part of an intermediate system and then progress to an IC system, though we have examined one such example in a previous post. Looking for brand new genes, however, is much easier – and some recent work in several fruit fly species (Drosophila) has done just that.

The Young and the Restless

So, how to go about finding genes that are new? We have already discussed, in the context of duplicating an entire genome, how duplication of genes may lead to the two copies picking up new functions over time. While duplication may happen rarely at a whole-genome scale, small-scale duplication of small numbers of genes happens quite frequently as an error during cell division. At the time of the duplication, the two copies are the same, and therefore functionally equivalent. Over time, however, the two copies may become different and acquire distinct functions.

One way to look for genes that have arisen due to a recent duplication event is to compare the genomes of closely related species and look for genes that are present in one species but not another, or in a subset of related species. Duplicated genes will show up in a nested hierarchy, much like how pseudogenes appear in the same nested pattern, as we have discussed previously here.

The complete genome sequences for a number of fruit fly species are available, so researchers used this method of comparison to look for new genes that mostly arose “recently” (over the last 35 million years) within flies. Since the speciation times for the various fly species are known to a good approximation, the time of the various duplication events can be estimated as well.

Putting the argument for IC to the test

Using this method, researchers identified 195 recent, “young” genes that arose through duplication events. (Note: this finding, in and of itself, is problematic for the ID argument that significant amounts of new information cannot arise through evolutionary mechanisms). More problematic for the argument from IC, however, is that just less thanone third of these new genes are now essential for development in the species that carry them. This fraction is approximately the same for “old” genes – about one third are essential for development.

The implications are easily grasped: many new genes have arisen through duplication, and a sizeable fraction are now part of IC systems. When they arose, they could not have been essential, but now they are emphatically so. As such, they must have been added to previous systems, and become IC over time. Moreover, this effect is not a rare, one-off event, but rather has been repeated time and again in recent evolutionary history.

In the next post in this series, we’ll delve into some of the details about how these new genes arose, and what sort of functions they have.




Venema, Dennis. "Understanding Evolution: The Evolutionary Origins of Irreducible Complexity, Part 1"
https://biologos.org/. N.p., 19 Apr. 2012. Web. 17 January 2019.


Venema, D. (2012, April 19). Understanding Evolution: The Evolutionary Origins of Irreducible Complexity, Part 1
Retrieved January 17, 2019, from /blogs/dennis-venema-letters-to-the-duchess/understanding-evolution-the-origins-of-irreducible-complexity-part-1

References & Credits

Further reading

Behe, M.J. Darwin’s Black Box: the Biochemical Challenge to Evolution. Free Press, New York, 1996.

Behe, M.J. The Edge of Evolution: the Search for the Limits of Darwinism. Free Press, New York, 2007.

Chen, S., Zhang, Y, and Long, M (2010). New genes in Drosophila quickly become essential. Science 330; 1682-1685.

About the Author

Dennis Venema

Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. 

More posts by Dennis Venema