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:
- 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.
- 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.
- There were numerous mutational paths that the λ phage took to arrive at the new function of protein J binding to OmpF.
- 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.
- 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.