Nothing new under the sun
As we noted in the last post, Behe has replied to my arguments to claim that “no new functional elements” arose during the actualization step that produced the first Cit+ bacteria in Lenski’s experiment. Rather, he claims that previously existing Functional Coded elemenTs (FCTs) were merely duplicated:
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.
I have already discussed how this seems to seriously strain the definition of “new.” Whatever one chooses to call such an event, there is an emergent function present that did not exist before (in this case, the production of a citrate transporter when oxygen is present). My point here is not to revisit that discussion, but to extend it and consider its implications for Behe’s overall case for irreducible complexity (IC) in light of what we know about protein structure and function. Since Behe accepts that an emergent function can arise through an exaptation event that cobbles FCTs from different genes together, then there is a large body of evidence about protein structure that Behe needs to address. To understand the importance of this evidence, however, we’ll need to take a brief excursion into some details of protein structure and function.
“Domain architecture” of proteins
As the molecular biology revolution picked up steam in the 1980s and 1990s, researchers began to notice that proteins that were otherwise quite different could have short stretches that were highly similar to each other. As more and more proteins were sequenced, these small “motifs” or “domains” became easier to recognize. At the beginning, not much was known about the function of these types of domains, but the fact that they were conserved between different proteins strongly suggested that they had to be functional. Eventually, the functions of many of these domains were identified. Often, they serve as specific docking sites to allow other proteins to bind and perform a function.
One of the classic examples of this sort of thing is what came to be known as an “SH2” domain. It was first identified in a protein called “Src” and “SH2” stands for “Src Homology 2.” (No, we biologists are not very creative with names at times.) SH2 domains are made up of about 100 amino acids that fold up into a defined shape – a shape that recognizes and binds on to another specific shape on other proteins. Individual SH2 domains can vary a bit, of course, so they don’t all bind to exactly the same partners.
Because the SH2 domain has a specific function (binding to a specific protein) that can be separated from other functions, this qualifies as what Behe would call a FCT, as we have discussed previously. What we see then, when we look at proteins, is that many of them are combinations of several domains (FCTs), each with a distinct function. The overall function of the protein, then, is determined by the combination of domains (FCTs) that it has: some FCTs have enzymatic functions, others direct specific protein-protein binding events, and so on.
Implications for Behe
As we noted before, Behe takes a dim view of the notion that parts for one complex system can be exapted for use in another system:
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.
In other words, Behe paints a picture of molecular machines with highly specialized parts that cannot be used in other systems without “extensive” modification – and claims that without a designer, no new functions are possible (for either “making” or “modifying” the parts). Yet what we see in nature looks rather different. Yes, the parts are specialized when examined at the level of entire proteins – but a closer look reveals that these specialized proteins are in fact made up of different combinations of many smaller protein domains with known functions– what Behe would call FCTs. Sequence evidence supports the hypothesis that these FCTs are derived from a common ancestral sequence, and that they have been duplicated, rearranged and exapted into many different proteins. As we have seen, many of these FCTs are modular domains that allow for protein-protein interaction – exactly the sort of effect needed to add new components to molecular systems over time.
Since these domains are found in functional proteins, selection acts to maintain their function. This keeps them around and “available” for duplications and rearrangements that produce new genes with new functions - just as we observed previously for the citrate transporter coding sequence and the promoter from a gene expressed in conditions in which oxygen is present. As such, these domains / FCTs are sort of a “spare parts drawer” in the genome that shuffle every so often – a screw here, a spring there – and contrary to Behe’s assertion, the evidence suggests that they can indeed be exapted for new roles and functions. SH2 domains, for example, are very widespread – in humans there are over 100 genes with SH2 domains, and no two of them are exactly alike. Would it be fair to say that each of these genes have the same function? Of course not, unless one was to claim that new combinations of functions (FCTs) were somehow “not new.” Furthermore, given that Behe already is on record for accepting the mechanism in view (duplication and rearrangement of previously existing FCTs into new combinations with emergent properties) it would seem strange to point to combinations of such proteins as an insurmountable problem for evolution to produce over time.
Implications for Axe
While we have not focused on the work of Douglas Axe (a structural biologist and Intelligent Design proponent) in this series, the observation that proteins are made up of smaller domains that can be swapped between different proteins as self-contained FCTs has implications for his lines of argument as well. As we have mentioned briefly in a previous series, Axe is interested in the origins of stable protein structures (protein folds), and claims that new genes and/or protein folds are inaccessible to evolution:
Basically every gene, every new protein fold… there is nothing of significance that we can show [that] can be had in that gradualistic way. It’s all a mirage. None of it happens that way.
The evidence from Lenski’s ongoing experiment demonstrates that new genes can indeed arise as FCTs recombine, and the genomics evidence that suggests that this mechanism is widespread. If indeed new genes can be produced by recombining FCTs to create new proteins with new properties, it now falls to Axe to explain why this is not a threat to his claim that new genes / protein folds cannot be produced through evolution. Lenski’s work is not just a problem for Behe, but for Axe as well.
Lenski’s Long Term Evolution Experiment (LTEE) continues to provide an interesting glimpse into the inner workings of evolution – and the more we learn through it, the more the theoretical underpinnings of the ID movement are eroded. As the experiment continues, I expect it to continue this trend – and I will be watching it carefully to see if it does. I suspect that those in the ID movement will do the same.
For further reading:
Basu, M.K., Poliakov, E., and Rogozin, I.B. (2008). Domain mobility in proteins: functional and evolutionary implications. Briefings in Bioinformatics (3); 205-216.
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.
Jing, J and Pawson, T (2012). Modular evolution of phosphorylation-based signalling systems. Phil. Trans. R. Soc. B 367; 2540–2555.
Michael J. Behe, Darwin’s Black Box: The Search for the Limits of Darwinism (New York: Free Press, 2007).
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.