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

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April 19, 2012 Tags: Design

Today's entry was written by Dennis Venema. You can read more about what we believe here.

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

Note: 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 than one 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.

For 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.


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. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.

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George Bernard Murphy - #69407

April 19th 2012

I don’t think irreducible complexity proves that God tinkered with the parts.

This idea of God with a little monkey wrench swimming along near a paramecium and improving the design of the flagellum. demeans the Almighty in my view.

 In a universe dominated by Heisenberg’s uncertainty principle and virtual particles, tinkering with a flagellum seems unnecessary. Other more sophisticated tools are available.


Chip - #69473

April 23rd 2012

Hello Dennis,

The reference cited** proposes a model for how an ancestral gene sequence might be inferred from several current ones.  But even if it is directly relevant (i.e., if such an amino acid was the “non-essential component” shown above), this is only a small subset of the larger model you propose here.  It says nothing about, for example, how “non-IC systems then may become IC if small changes make the new parts essential” or how “over time the system comes to depend on those parts.”  Which systems?  Which parts?  What small changes?  At what point in its evolutionary development did these particular unnamed parts of this unidentified system become essential?  How did this happen?  How do we know?

Given the thesis of your post, certainly you’re capable of providing an actual example from the literature which is demonstrated to have taken “an indirect evolutionary route that produces an IC system from a non-IC precursor system.” 

Looking forward to your reply, 

**http://biologos.org/blog/evolution-and-the-origin-of-biological-information-part-3-csi-on-steroids


dennis.venema - #69478

April 23rd 2012

Hi Chip, 

The the post you cite is one such worked example (steroid receptors that become specific for certain hormones over time after an ancient gene duplication event). In upcoming posts we’ll look at a few more examples from the paper I cite in this post - some genes in Drosophila that are the result of recent duplication events that now are necessary for survivial. 


Bilbo - #69481

April 23rd 2012

Hi Dennis,


Behe has responded to the example you cite, maintaining that it is not IC.  If you wish to maintain that it is, I think you need to engage his arguments, which can be found here:

http://www.discovery.org/a/3415


dennis.venema - #69484

April 23rd 2012

Hi Bilbo, 

Behe’s comments are not very substantial, wouldn’t you agree? I don’t think he’s really done the Thorton paper justice. That and I don’t see much to his argument beyond “the paper doesn’t show much.” But be that as it may, I’m not overly interested in rehashing that example, since I’ve tackled it in a lot of detail before. 

In the next post, I’ll be exploring some examples from the Chen 2010 paper. I think it will be pretty hard to dispute that these are examples of recently evolved IC systems. They’re the result of recent gene duplications, and now the organism dies if you remove them. 

Dennis


Bilbo - #69483

April 23rd 2012

George wrote: This idea of God with a little monkey wrench swimming along near a paramecium and improving the design of the flagellum. demeans the Almighty in my view.


Cool, George!  I always pictured God in a white lab coat, sitting at a bench, tinkering with a cell under a microscope.  I never thought of the idea of God shrinking Himself down to the microscopic size and swimming around the cell, retro-fitting it with a flagellum.  How fun would that be?!  I bet that’s how He did it. 

 


Bilbo - #69522

April 24th 2012

Hi Dennis,

You wrote:  “Behe’s comments are not very substantial, wouldn’t you agree? I don’t think he’s really done the Thorton paper justice. That and I don’t see much to his argument beyond “the paper doesn’t show much.” But be that as it may, I’m not overly interested in rehashing that example, since I’ve tackled it in a lot of detail before.”

I thought Behe’s comment were substantial, but I am just a layperson, and no doubt  I could be very mistaken.  If you really think this is an example of an IC system,  it would be nice to hear more detail on why Behe is mistaken.  Otherwise we laypeople are left to try to muddle through it on our own.

“In the next post, I’ll be exploring some examples from the Chen 2010 paper. I think it will be pretty hard to dispute that these are examples of recently evolved IC systems. They’re the result of recent gene duplications, and now the organism dies if you remove them.”


I believe that Behe discussed the Chen paper, also.  So I hope you discuss his comments, too.


dennis.venema - #69544

April 25th 2012

Bilbo, do you have any links to Behe’s comments on the Chen paper? I haven’t been able to find any. 


Bilbo - #69551

April 25th 2012

Hi Dennis,

I had difficulty finding it myself.  The problem was that Behe doesn’t refer to is as the Chen paper, but as the Long paper.  He discusses it (about half way down the blog post) here:

http://behe.uncommondescent.com/2011/01/even-more-from-jerry-coyne/

 


dennis.venema - #69553

April 25th 2012

Thank you! I doubt I would have ever found that on my own. 


Chip - #69567

April 26th 2012

Yes, Bilbo, thanks for the link. 

It is remarkable the extent to which (at least some) critics of ID/Behe will go to sling mud at the theory and the man—particularly when those doing the slinging claim that they the ones wrapped in the mantle of alleged scientific objectivity.  I really wonder if these folks really believe they’re being objective (and are thus fooling themselves), or if they know that they’re not, but make the argument anyway in the hopes that their audiences are naïve enough to buy it. 

In any event, below is an excerpt from Behe’s response to Coyne.  Behe may be wrong, but at least his arguments are based on research and data.  Coyne and his ilk, on the other hand, consistently wield derision as their primary rhetorical weapon.  And in my experience, those with an argument to make, make it.  Those who don’t, rely on made-up references to “magic poofs”... 

Try as one might to keep Darwinists focused on the data, some can’t help reverting to their favorite trope: questioning Darwinism simply must be based on religion. Unfortunately Professor Coyne succumbs to this. Introducing his blog post he writes:

What role does the appearance of new genes, versus simple changes in old ones, play in evolution? There are two reasons why this question has recently become important…. The first involves a scientific controversy…. The second controversy is religious. Some advocates of intelligent design (ID)—most notably Michael Behe in a recent paper—have implied not only that evolved new genes or new genetic “elements” (e.g., regulatory sequences) aren’t important in evolution, but that they play almost no role at all, especially compared to mutations that simply inactivate genes or make small changes, like single nucleotide substitutions, in existing genes. This is based on the religiously-motivated “theory” of ID, which maintains that new genetic information cannot arise by natural selection, but must installed [sic] in our genome by a magic poof from Jebus. [sic]

Anyone who reads the paper, however, knows my conclusions were based on the reviewed experiments of many labs over decades. Even Coyne knows this. In the very next sentence he writes, schizophrenically, “I’ve criticized Behe’s conclusions, which are based on laboratory studies of bacteria and viruses that virtually eliminated the possibility of seeing new genes arise, but I don’t want to reiterate my arguments here.” Yet if my conclusions are based on “laboratory studies”, then they ain’t “religious”, even if Coyne disagrees with them.

Professor Coyne is so upset, he imagines things that aren’t in the paper. (They are “implied”, you see.) So although I haven’t actually written it, supposedly I have “implied not only that evolved new genes or new genetic ‘elements’ … aren’t important in evolution, but that they play almost no role at all….” [Coyne’s emphasis]

“Play almost no role at all”? When I first read these “implied” words that Coyne wants to put in my mouth, I thought the argumentative move rang a bell. Sure enough, check out the Dilbert comic strip from November 1, 2001 (http://tinyurl.com/6y6upgc), where Dilbert complains that a co-worker “changed what I said into a bizarre absolute.” If one person says that an event is “very unlikely”, and an interlocutor rephrases that into “so, you say it’s logically impossible and would never happen even in an infinite multiverse”, well then, the second fellow is setting up a straw man.

Contrast Coyne’s imagined “implications” with what I actually wrote in the review…


Eric 'Siggy' Scott - #69609

April 28th 2012

A great deal of mud-slinging and reactionism occurs on both sides.  Uncommon Descent, the Panda’s Thumb, and Coyne’s blog are all great resources for finding examples of failed and self-justifying dialogue.

I don’t find it useful to try and pin the title “The Bigger Mudslinger” on either camp, though.  Both camps think the viciousness of the battle is the other side’s fault—the same as in any war, it’s never my fault!

As a non-believer, I come to BioLogos and other places like Todd Wood’s blog to find a Christian perspective that tends to be moderate, scientific, and unoffensive (though of course not perfect).  It’s my way of seeking out the good in the Other.

The important part is to try to do due dilligence and to be fair and respectful ourselves.  That is the only guaranteed way to improve the tone of conversation.  Pointing fingers at others for not being fair and respectful is as likely to create more drama as anything else. 


James Kohl - #69632

April 30th 2012

In a recent paper published in Socioaffective Neuroscience & Psychology (open access: http://dx.doi.org/10.3402/snp.v2i0.17338), I used the honeybee as the model organism that links the pre-existing genetic diversity of the ‘first cell’s’ complex intracellular signaling to nutrient dependent stochastic gene expression and diversificaton of species from microbes to man. Simply put, what the queen bee eats determines her pheromone production and everything else about the dynamic social interactions of the colony, including the neuroanatomy of the worker bees brains.

The irreducible pre-existing complexity of the first cell is apparent, as are epigenetic effects of sensory stimuli from the environment. All individual organisms must acquire sufficient nutrient chemicals to ensure their survival, and the metabolism of nutrient chemicals to pheromones controls reproduction and species survival. Another recent publication by a 28 member team extends the honeybee (invertebrate) model to vertebrates using the stickleback fish model organism of ecotype-dependent social niche formation and speciation (http://dx.doi.org/10.1038/nature10944).

I conclude that “Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans” and offer citations from recent published works for detailed scientific support. An expert comment on the stickleback paper stated: “...that stickleback evolution is accelerated by the use of pre-existing genetic variation, instead of waiting for new, random mutations to arise.”

To my knowledge, no one has proposed a model, or model organism, in which random mutations cause adaptive evolution. Why has the random mutation theory of evolution been so well accepted by atheists and agnostics, when it has no explanatory power and no scientific support? How does a random mutation, or a series of random mutations, cause adaptive evolution?


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