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The Evolutionary Origins of Irreducible Complexity, Part 4

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May 31, 2012 Tags: Genetics

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

The Evolutionary Origins of Irreducible Complexity, Part 4

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 examine evidence that proteins in irreducibly complex (IC) systems can form and refine new interactions through gradual mechanisms.

Can IC systems add new components?

In the last post in this series, we discussed the evidence that a new gene (p24-2) in one species of fruit fly had picked up functions distinct from the “parent” gene (Éclair) from which it was copied. For new proteins to pick up new functions, new interactions between proteins need to form – new binding sites that allow proteins to come together to do specific tasks. One line of evidence that p24-2 had acquired a new protein-protein interaction was the observation that a series of amino acids concentrated in one region of p24-2 were markedly different than those in Éclair. This observation suggests the possibility that this region allows p24-2 to participate in a protein-protein binding interaction that Éclair cannot, though this hypothesis has not yet been tested.

The ability of an IC system to develop new protein-protein interactions is a subject that Michael Behe discusses at some length in The Edge of Evolution. Specifically, Behe states:

The conclusion from Chapter 7 – that the development of two new intracellular protein-protein binding sites at the same time is beyond Darwinian reach – leaves open, at least as a formal possibility, that some multiprotein structures (at least ones that aren’t irreducibly complex in the sense defined in Darwin’s Black Box) might be built by adding one protein at a time, each of which is an improvement. But there are strong grounds to consider even that biologically unreasonable. First, the formation of even one helpful intracellular protein-protein binding site may be unobtainable by random mutation. The work with malaria and HIV, which showed the development of no such features, puts a floor under the difficulty of the problem, but doesn’t set a ceiling. Maybe my conservative estimate of the problem of getting even a single useful binding site is much too low. What we know from the best evolutionary data available is compatible with not even a single kind of specific, beneficial, cellular protein-protein interaction evolving in a Darwinian fashion in the history of life. (p. 157)

So for Behe, the formal possibility remains open that non-IC systems might be able to add parts one protein at a time, though he considers even this possibility as unlikely. Note, too, that IC systems are excluded from this possibility altogether.

(Note: I realize that Behe has already been shown to have been mistaken about HIV not forming any new protein-protein interactions, though this is usually blunted by appealing to the very large mutation rate that HIV has. While this is a genuinely serious critique of Behe’s argument, I will not re-hash this example here).

The challenge of time

Studying processes that span millions of years or more has unique challenges. Take continental drift, for example. When continental drift was a new idea, it did make sense of a wide array of observational data: the suggestively complementary shapes of Africa and South America, the rock and fossil formations on their coasts that matched the right locations on the other continent, and so on. Later work discovered the mid-Atlantic ridge, and other lines of evidence that supported the idea that all modern continents were once a supercontinent called Pangaea. Nowadays we can measure the tiny, incremental movement of continents with great precision. These measurements provide experimental data that neatly dovetails with the historical and observational lines of evidence. Together, they paint a consistent picture of how the continents got to be where they are today.

A critic of continental drift, however, might argue that researchers have not connected the observational evidence with the experimental evidence: after all, the amount of continental movement we observe is small, and the observational evidence is circumstantial. Also, the amount of change suggested by the observational data is huge, but we observe only tiny changes in the present. How can we be sure that we have an adequate explanation for the mechanism(s) of continental drift?

While this is something of a hypothetical example (since critics of continental drift are relatively few and far between) the issues are the same for studying how protein-protein interactions arise over evolutionary history. As with continental drift, evolutionary biology is supported by a wide array of data (comparative genomics, for example) that suggests robust change over millions of years. Likewise also, studies we are capable of running in the present have an extremely short duration (perhaps at best decades) compared to the long-term process we are studying. Not surprisingly, we expect the changes we observe in the present to be modest. Despite these issues, however, certain elegant experiments do manage to document changes in great detail. Of particular relevance for assessing Behe’s argument is some recent work that “caught” the development of a new protein-protein binding site in the act, as it were.

Consider the phage

The study of interest was done in the laboratory of Richard Lenski, the same laboratory running the Long Term Evolution Experiment on E. coli that we have discussed before. In this instance, the object of the experiment was a virus that infects E. coli and breaks it open as part of its replication cycle (with lethal consequences for the bacterial host). Since the virus is a “bacteria eater” it goes by the title “bacteriophage”, in this case bacteriophage lambda, or alternatively “λ phage”. λ phage starts the process of infection by using one of its proteins to attach to a protein on the bacterial surface, and the researchers were interested to know how hard it would be for the phage to develop the ability to attach to a new protein and use that new protein to infect its host.

Normal λ phage uses its protein called “J” to bind to a host protein called LamB. The researchers used a genetic trick to almost entirely remove LamB from a population of E. coli hosts, making them impervious to the presence of λ phage. To keep a tiny amount of λ phage alive in the bacterial culture, however, the researchers rigged it so that every so often a susceptible host with LamB would be produced. With things balanced in this way, most E. coli in the culture were unable to be infected, but a tiny minority of hosts kept a small population of λ phage going alongside them. If λ phage could figure out a way to use another host protein to infect these resistant bacteria, it would have access to a large number of hosts it could not previously access.

What the researchers found was that λ phage was able to switch over to use a different host protein, one called OmpF. OmpF and LamB are similar in overall shape, but not that similar at the sequence level. Since the switch happened over a matter of weeks in a controlled environment, the research team was able to document the mutations that led to the switch. The study produced some interesting findings:

  1. The change to using OmpF instead of LamB required at least four mutation events in protein J. These changes clustered together in one protein region.
  2. The probability of these four mutation events happening simultaneously is pretty much zero, yet the λ phage managed to “find” these mutations over and over again without much trouble, with the mutations happening sequentially, not simultaneously.
  3. There were numerous mutational paths that the λ phage took to arrive at the new function of protein J binding to OmpF.
  4. The mutations did not remove the ability of protein J to bind LamB, but improved its binding. This was important, since at no point could the λ phage lose the ability to bind LamB if it was to survive.
  5. The λ phage strains that gained the ability to bind OmpF can still use LamB to infect cells that have it. This means that the new protein-protein interaction between J and OmpF is a gain of a new function without any loss of the prior function.

Taken together, these results suggest that the ability to form new protein-protein interactions may be much easier than Behe has estimated. In the next installment in this series, we’ll continue to examine the implications of this study for Behe’s argument, and evaluate Behe’s response to this important work.

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.
Meyer, J.R., Dobias, D.T., Weitz, J.S., Barrick, J.E., Quick, R.T., and Lenski, R.E. (2012). Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335; 428-432.
http://www.sciencemag.org/content/335/6067/428.abstract


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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Ashe - #70210

May 31st 2012

There's a related paper in the same issue (Tenaillon et al). They evolved 120 lines of E. coli to high temperature for about one year, and then sequenced all 120 lines at the end of the experiment.   So they know every basepair responsible for the adaptation. This let them get at the question of how often does evolution proceed via the same mutations, the same genes, or the same pathways. They identified a couple of thousand mutations. Many are likely LOF. But some seem to be tweaking amino acids.
Roger A. Sawtelle - #70213

May 31st 2012

Thank you Dennis for another illustration of how alletypes adapt to different biological niches.


Bilbo - #70322

June 7th 2012

Hi Dennis,

After your previous post on IC, I emailed Professor Behe, asking him if my comments were on the right track.  He provided the following reply and has given his permission for me to reprint it here: 

“I’ve now read Professor Venema’s posts and all of the comments. Most of the pro-ID points are right on the money. However, there are a couple of points that no one has mentioned that I think are important for the discussion.

First of all, Venema confuses “irreducibly complex” with “essential for the viability of the organism”. The two concepts are not the same. For example, a person can survive with a missing blood clotting factor, where the IC clotting system is broken. Thus the factor is needed for the clotting system to work, but is not necessary for the viability of the organism. On the other hand, a factor can be essential for life but not irreducibly complex. A simple example is hemoglobin. It is not IC, but an organism will die without it. Thus Venema is mixing up concepts. An IC system (like a mousetrap) *cannot work* if a piece is removed. An organism, even a dying one, will survive a while if, for example, it’s lungs are pulled out.

You rightly take him to task for not spelling our what the ID system is, but that point should be pounded home much more. The putative new binding site of p24-2 is likely not a necessary part of the overall IC system. Let me explain. Suppose as Venema does, that Eclair and p24-2 are parts of systems that transport specific other proteins that they bind in the cell. Imagine an analogous mechanical system that has a rotating metal wheel at the top of a pole. To two places on the wheel are attached wires that at the bottom hold a claw that has an oval hole in it. When the wheel rotates, every half turn it encouter a metal bump which pushes up the wire and causes the claw to open. Once it passes the brief bump, the claw closes. During that time the claw can pick up an object that has a part of it shaped like the oval hole in the claw. As the wheel makes another half turn, it encounters a small depression, which causes the wire to dip down, opening the claw, and releasing the object. At the other end of the oval-shaped object is a little array of magnets, that match a second object. That second object gets transported with the claw, attached to the magnetic end of the oval shaped object.

Now what we have here is an already-intact transport system. At best, the amino acid changes in p24-2 would be analogous to re-arranging the magnets at the end of the oval-shaped object, so that it could transport a different object than before. But that is just taking advantage of an already-existing IC system; it is not a new one.

A final point is that there are five specific amino acid differences between Eclair and p24-2. Professor Venema seems not to comprehend that they may not have arisen by ransom mutation. Once one gets beyond one or two random mutations, one can’t assume that multiple further mutations arose by chance. In other words, as far as anyone knows, those five point mutations may have required guidance or design in their appearance.”


melanogaster - #70329

June 8th 2012

Behe:
“A final point is that there are five specific amino acid differences between Eclair and p24-2.”

Bilbo, note that Behe uses correct terminology here. Then, to fool you, he goes completely off the rails:

“Professor Venema seems not to comprehend that they may not have arisen by ransom mutation.”

Funny typo aside, this is utter gibberish. These are differences. Behe, who accepts common descent, pretends not to comprehend that he can’t know which is parental, if either are.

His thesis regarding mutation has been demolished, so to cover that up, he uses “mutation” in a way that working biologists do not.

“Once one gets beyond one or two random mutations,…”

These are DIFFERENCES, not mutations. See the difference? For all Behe knows, both ALLELES for each difference were already present in the population of the common ancestor. He covers this up by pretending that the are mutations.

“… one can’t assume that multiple further mutations arose by chance.”

What Behe is doing to fool you is conflating “mutations arising” with “alleles becoming fixed in a population by selection or drift.”

“In other words, as far as anyone knows, those five point mutations may have required guidance or design in their appearance.”

Behe hasn’t shown that those five differences, or alleles (which he falsely labels as “mutations”) weren’t already present in the ancestral population.

Bilbo, how long does it take to create a new, incredibly high-affinity protein-protein binding site by genetic variation and selection? Would you like me to specify the increase in Kd?


Bilbo - #70339

June 8th 2012

Hi Melano,

You wrote:  “Bilbo, how long does it take to create a new, incredibly high-affinity protein-protein binding site by genetic variation and selection? Would you like me to specify the increase in Kd?

Sure.  And explain what Kd is while you’re at it, please.  And also explain why you only responded to Behe’s last point and to nothing else that he said.


Dennis Venema - #70323

June 7th 2012

Hi Bilbo,

Thanks for passing on Behe’s response - I will likely address portions of it in future posts. Already in this post are some threads that speak to Behe’s rebuttal, though - for example, the point that we can observe proteins changing binding partners, through mutation, one amino acid change at a time (i.e. that the changes need not be simultaneous). I’ll speak to this more in the next post, and I’ll welcome your feedback on it once I’ve fleshed it out. 


Dunemeister - #70553

June 20th 2012

Why don’t we get Dr. Behe to comment directly on this site, and he and Dr. Venema can converse as we see in the “Southern Baptist” dialogue?


melanogaster - #70569

June 20th 2012

Behe tends not to engage in environments he does not control.


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