Behe, Lenski and the “Edge” of Evolution, Part 4: IC and Exaptation

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November 16, 2012 Tags: Genetics

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

Behe, Lenski and the “Edge” of Evolution, Part 4: IC and Exaptation

Note: In this series, we reexamine the claim made by Intelligent Design proponent Michael Behe to have found a limit to “Darwinian” evolution in light of recent results from the laboratory of Richard Lenski.

In previous posts in this series, we evaluated Behe’s claimed “edge” for what evolution can (and allegedly cannot) accomplish by examining the step-by-step path that bacteria in the Long Term Evolution Experiment (LTEE) took to arrive at a mechanism for utilizing citrate under aerobic conditions. In this post, we look at the implications of these results for another of Behe’s related ideas: that of irreducible complexity.

Behe and IC

Since we have previously explored Behe’s idea of irreducible complexity in an entire series, we will not revisit it here in great detail. It is important, however, to reemphasize how Behe defines irreducible complexity (IC). As we noted in the first part of that series, Behe frames his ideas on IC as a counter to Darwin’s ideas of gradualism.

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.

Behe and exaptation

The standard response to Behe’s argument from IC is to discuss the evolutionary concept of exaptation: that new systems and functions are cobbled together from components that have functional roles in other systems already present in the cell. Behe discusses, and ultimately dismisses this idea in Darwin’s Black Box as follows:

In Chapter 2 I noted that one couldn’t take specialized parts of other complex systems (such as the spring from a grandfather clock) and use them directly as specialized parts of a second irreducible system (like a mousetrap) unless the parts were first extensively modified. Analogous parts playing roles in other systems cannot relieve the irreducible complexity of a new system; the focus simply shifts from “making” the components to “modifying” them. In either case, there is no new function unless an intelligent agent guides the setup.

So for Behe, two points are clear: parts selected for function in one system cannot be exapted for use in other systems since they would require too many modifications; and the emergence of a new function is the indication that an intelligent agent is guiding the process.

Behe has responded to my previous posts to claim that the tandem duplication event that brought about the Cit+ actualization event should not be considered a gain-of-FCT mutation under his criteria:

The gene duplication which brought an oxygen-tolerant promoter near to the citT gene did not make any new functional element. Rather, it simply duplicated existing features. The two FCTs comprising the oxygen tolerant citrate transporter locus -- the promoter and the gene -- were functional before the duplication and functional after. I had written in my review that one type of mutation that could be categorized as a gain-of-FCT was gene duplication with subsequent sequence modification, to allow the gene to specialize in some task. Venema thinks the mutation observed by Lenski is such an event. He has overlooked the fact that there was no subsequent sequence modification; a segment of DNA simply tandemly duplicated, bringing together two pre-existing FCTs.

As an aside, quibbling over whether this mutation constitutes a “genuine gain-of-FCT” mutation is not my purpose here, since the definition is Behe’s to define, and I am not aware of anyone else in the scientific literature who uses Behe’s definitions. That said, I consider it passing strange to claim that a series of events that produced a gene that has a new sequence and functional properties distinct from either of its component parts does not constitute the production of a new “functional coded element.” If nothing else, it is a functional coded element that has not previously existed, cobbled together from parts of other functional coded elements, displaying new, adaptive properties. If according to Behe’s definition that’s not “new” or a “gain” then I guess it’s not, but that seems to me to torture the words “new” and “gain” beyond recognition. But I digress.

The important point for our purposes, however, lies elsewhere. Note carefully how Behe describes the Cit+ actualization event. By dividing the new aerobic citrate transporter gene into two previously existing FCTs, Behe is describing an exaptation event. The one FCT (the aerobic promoter) starts off as a necessary component of a gene transcribed when oxygen is present. As such it is under selection for that function, which has nothing to do with expressing a citrate transporter. The second FCT (the citrate transporter amino acid coding sequence) is under selection to be a citrate transporter, which has nothing to do with the function of the gene the promoter comes from. The Cit+ actualization event, then, exapts these two FCTs by placing them together to create a new function (which Behe does not mention).

And here’s the kicker: the new system (expression of the citrate transporter when oxygen is present) requires both FCTs in order to work. It has become a system of “well matched, interacting parts that contribute to the basic function” (i.e. transporting citrate in the presence of oxygen) “wherein the removal of any one of the parts causes the system to effectively cease functioning.”

In other words, it is a new IC system – a small and relatively simple system, yes, but nonetheless IC. Now, I’m fairly sure that Behe would not define this system as IC, since the documentation of an IC system evolving would seriously undermine his thesis. I am interested, however, in how he will handle this development, on two fronts. First, he would need to explain specifically why two exapted FCTs that are required together for a basic function does not constitute an IC system (if indeed he wishes to preserve his definition). Secondly, given that he allows for exaptation in this case, he needs to explain how exaptation is not a threat to IC in general. In Darwin’s Black Box he disallows exaptation altogether, but that option is no longer on the table.

In the next post in this series, we’ll continue to explore the evidence for exaptation as a means to build new FCTs, and go on to examine the implications of this evidence for Douglas Axe’s proposed limit to evolutionary mechanisms.

For further reading:

Blount, Z.D., Barrick, J.E., Davidson, C.J. and Lenski, R.E. (2012). Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489; 513- 518.

Michael J. Behe, Darwin’s Black Box: The Search for the Limits of Darwinism (New York: Free Press, 2006).

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

Michael J. Behe (2010). Experimental evolution, loss-of-function mutations, and “The first rule of adaptive evolution”. The Quarterly Review of Biology 85(4); 419-445.


Dennis Venema is Fellow of Biology for The BioLogos Foundation and associate professor of biology at Trinity Western University in Langley, British Columbia. His research is focused on the genetics of pattern formation and signalling.

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Eddie - #74453

November 16th 2012

Interesting series, Dennis.

You may not know that Behe has replied to some earlier parts:

http://www.evolutionnews.org/2012/11/rose-colored_gl066361.html

I mention this in case you want to publish a rejoinder.

I also hope that you will continue the conversation with Kirk Durston:

http://biologos.org/blog/behe-lenski-and-the-edge-of-evolution-part-2

His last reply, 74313, has been up for about five days now.  It’s a good, polite, substantive conversation between the two of you, and I’d like to see it continue, if you have the time.  It’s not often we get such a detailed technical exchange between a TE and ID scientist, so it’s a treat for the reader.

 


Dennis Venema - #74613

November 21st 2012

Hi Eddie,

I’ve replied to Kirk. Sorry for the delay. 

Dennis


Ashe - #74456

November 16th 2012

I think he knows about Behe’s reply since he responded to a portion of it in this post.


Bilbo - #74462

November 17th 2012

Hi Dennis,

I’m glad you are feeling better.  I hope your family is feeling better as well.  If my memory hasn’t failed me, Behe didn’t disallow exaptation, which I think he referred to as an indirect route for achieving an IC system.  Instead, he said that the more parts to the system, the more unlikely that exaptation could occur.  In the case that you are discussing, there are two “parts” to it.  So even if we call it an IC system, I don’t think it would be a big threat to Behe’s IC argument.


Dennis Venema - #74615

November 21st 2012

Hi Bilbo,

Consider this system before these events happened. It was “parts ordered for a purpose” - i.e. to transport citrate into the cell under anoxyic conditions. This is an IC system - all the parts are needed for this function, and there are many such parts. If any parts are removed, the system stops working. 

After the events (tandem duplication that fuses two FCTs together in a new combination to produce a citrate transporter that is expressed in the presence of oxygen) we have a system that retains the original functions, but has added a new one - now the transporter is expressed in both oxic and anoxic conditions. 

So, new functions can be recruited to IC systems through step-by-step mutational events. These mutations do not have to be simultaneous, as Behe’s model requires. 

Ergo, when looking at an IC system as Behe defines it, Behe cannot be confident that it was not also assembled by adding components and functions over time through a step-by-step process. Yet Behe’s entire method of infering design is to point to IC systems.

It will always be possible for Behe to claim that any given observed change in a lab setting “isn’t good enough” or “isn’t significant”, etc. That’s not really the point.

The point is that the changes we observe have been documented to happen by mechanisms that Behe claims do not happen. 


Bilbo - #74667

November 24th 2012

As I mentioned before, I find this format of commenting rather confusing.  So I’ll put my reply at the very bottom of the comments.


HornSpiel - #74551

November 20th 2012

In response to the previous article in this series that Venema mentions above, Behe writes:

Venema argues that perhaps all of complex functional biology could be reached by gradual, beneficial mutations. Well, bless his optimistic heart, but the data give us no reason to think that… all routes to complex systems involving multiple distinct elements will be. Quite the opposite, as I have often argued.

It’s funny how all the fine technical arguments boil down to faith. Could it be that there is no scientific proof for whether or not naturalistic evolutionary mechanisms are adequate for explaining evolution? In many ways it seems to hinge on definitions. What is science? What is irreducible complexity? What is a FCT?

However the definitions are not equivalent. Science has been defined now for hundreds of years as naturalistic explanations for natural phenomena—no teleological explanations. Behe on the other hand has created his own idiosyncratic terminology that really only he and his followers find useful. As Venema points out:

If according to Behe’s definition that’s not “new” or a “gain” then I guess it’s not, but that seems to me to torture the words “new” and “gain” beyond recognition.

When Behe both defines the term then judges its applicability, it appears to be a ploy to confer an air of legitimacy on his personal opinion. One does not need to understand the science to see that as suspect, if not illegitimate. 


Martin Neukamm - #74560

November 20th 2012

Brilliant reply Dennis,

but you wrote:

“In other words, it is a new IC system – a small and relatively simple system, yes, but nonetheless IC.”—-

I don’t think that the IC system is that simple! Remember that a series of relatively complicated events and conditions occured:

(1) There was an (unknown) mutation that “allowed” the cit+ phenotype to evolve

(2) Among some 1000 genes two genes (citG, rnk) fusioned in a suitable way

(3) The expression of the genes citG and citT got under control of the regulator gene rnk

(4) The gene complex was duplicated

Selection could not work until these FOUR events occured. I think this series of events is at least as complex as the double mutation that Behe calls “complex chloroquine cluster” (CCC). To my opinion, the observations of Lenski et al. falsify Behes notion that systems which are more complex (or need more complex changes) than “CCC” could not evolve.

Best wishes!

Martin


Dennis Venema - #74614

November 21st 2012

Hi Martin,

There are actually two mutations for your step 1 (potentiation), and 2 and 3 are the same event. That said, you’ll notice in Behe’s reply that apparently the two needed potentiation mutations don’t count according to Behe. I find that pretty curious. I know Behe is at pains to reduce the number of non-selected mutations to keep this under his “edge”, but those two mutations are (a) required, and (b) epistatic to the later ones. As such, contra Behe, they are “directly involved” and thus part of the assembly of the new system. 

Dennis


Eddie - #74572

November 20th 2012

HornSpiel, you wrote:

“Science has been defined now for hundreds of years as naturalistic explanations for natural phenomena—no teleological explanations.”

Do you realize that the first part of your sentence contains a tautological element?  “Naturalistic explanations for natural phenomena”—well, of course!   Do you imagine that any ID proponent would disagree with that?

The question is whether natural explanations are appropriate for *all* phenomena, not just those we know to be natural.  Suppose a phenomenon is supernatural—will you demand a natural explanation for it?  For example, the Resurrection.  Should scientists start trying find out the natural causes of the Resurrection?  And what about phenomena about which we do not yet know whether they are natural or supernatural?  Should we automatically assume that, if we don’t know, they are natural, and look for only natural causes?  Or should we do a more cautious investigation, keeping open both natural and supernatural possibilities?  Take, for example, the origin of life, or the creation of man.  Do we know, in advance of investigation, that these things occurred through natural means? If so, how do we know that?  And if we don’t know, what justifies the assumption that the means were natural?

Note also that in the second half of your sentence you treated “teleological explanations” as if they were the opposite of, or at least the negation of, “naturalistic explanations.”   But the opposite of “naturalistic” would be “supernaturalistic”—not “teleological.”  The opposite of “teleological” would be “by chance, by accident” or perhaps “by necessity.”  We have thinkers who have postulated teleology in nature without postulating anything supernatural, e.g., Aristotle.  So there is no easy equation between “teleological” and “supernatural.”  Or even “non-natural”; for Aristotle teleology was part of nature.


Bilbo - #74668

November 24th 2012

Hi Dennis,

You seem to ignore much that Behe has said, both in his books and in his reply to you.  First, Behe admits in his book that new IC systems can be formed by recruitment of parts from other systems or by combining other systems.  His point is that the more parts that need to be recruited, the less probable for that new IC system to arise.  Fusing two FCTs together to make a third system would not be a falsification of Behe’s position.  Nor does he deny that it could happen the way it did.  In fact, he pointed out to you the creation of new FCTs in his review article.  Why are you ignoring Behe’s point? 

I agree with you that Behe can’t ignore the potentiation mutations as being necessary.  But this doesn’t mean that the process exceeded his edge.  But even if it did exceed his edge, you’ve already admitted that there is an edge (was it five unselected mutations?).  So unless you’ve decided to retract your admission, you are still stuck with a relatively low number of unselected mutations for the edge of evolution.  Given that, your burden of proof—that the edge never had to be exceeded in the whole history of evolution—is rather heavy.  I can understand your accepting neo-Darwinism as a reasonable, working hypothesis.  But to try to pass it off on the rest of the Christian community as a well-proven theory that we must accept or be considered unscientific,  is a little unreasonable.


dennis.venema - #74697

November 25th 2012

First, Behe admits in his book that new IC systems can be formed by recruitment of parts from other systems or by combining other systems.  His point is that the more parts that need to be recruited, the less probable for that new IC system to arise. 

Hi Bilbo,

I’ll be the first to admit that I might have missed/forgotten a part of Behe’s book that says this. Could you indicate a page number for me? I’m working off the sections I’ve quoted in the post itself - and there it seems (to me anyway) that Behe is saying IC systems cannot be built up over time, and that parts for IC systems cannot be exapted from other systems. Yes, Behe talks about new FCTs arising in his article and in his blog response, but he says nothing about them becoming part of IC systems. So, I don’t see me ignoring Behe here - if anything I’m trying to read him closely. 

As for “admitting an edge” to evolution, it’s pretty obvious that evolution cannot rely on multiple, simultaneous mutations. This is not controversial. One would not expect dogs to give birth to kittens either - but that’s hardly a challenge to evolution as a theory!

As I’ve mentioned before to others - get thee to a genome browser, and compare any two species that are reasonably closely related - humans and chimps, various species of Drosophila, or whatever. What you’ll see when you line those genomes up is that there’s nothing separating those species that looks like it needs multiple, simultaneous mutations. Now, can we go back in time and replay the entire thing to be absolutely sure? No, we can’t. Responses will vary at this point - and that’s fine by me. 

 


Bilbo - #74728

November 26th 2012

Reply is below.


darwin-21st - #74702

November 26th 2012

Hi Dennis,

I am not sure that the new results are ready to explain an IC system. None of the criteria ist met:

  • “several” (!) well-matched
  • interacting “parts” (!) of the “system”

Bilbo - #74729

November 26th 2012

Hi Dennis

In Darwin’s Black Box, on page 40, Behe wrote: 
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.

The fusing of two FCTs (which required three mutations before obtaining function) would neither violate Behe’s edge nor his admission that it could evolve indirectly. 

Two questions:  First, I’m a little confused about the use of the term “simultaneous.”  If I understand it, the first two potentiation mutations were not simultaneous.  They were consecutive.  But neither one had any selective advantage.  Is this correct?  If so, then is there an edge or limit to the number of non-selective, consecutive mutations that can be invoked in order to explain the evolution of something?  That is what I understood you to be saying in Part 3:  that if all five mutations had to occur before there was a new function, then it never would have happened. 

And a third question:  Are you saying that there are no new genes between two similar species (e.g., chimps and humans) that need more than whatever limited number of consecutive non-selective mutations that are allowed?


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