The trickiest part in the Design Matrix is to detect the echoes of foresight. In the Design Matrix: A Consilience of Clues, we sketched out two possible ways of recognizing foresight. One way is to look for molecular machines that exhibited Original Mature Design (OMD). What we would have is machine that appears abruptly in the biotic landscape and then is not significantly improved or changed after extensive subsequent evolution. In other words, the designer got it right from the start. OMD can be viewed as an echo of foresight because there is no reason to think the blind watchmaker would have a decent chance of getting things right from the beginning. When the blind watchmaker cobbles something together through cooption, it doesn’t know what it’s producing and is only “solving” the immediate problem at hand. And there is no reason to think a solution to an immediate problem would just happen to work, much as is, billions of years later. A rational mind, on the other hand, can see beyond the immediate state and contemplate how something might need to be constructed in light of possible future contingencies.
The 3-component system that I have described earlier (SRP, RNA, and receptor) appears to qualify as OMD. It is a system as ancient as the ribosome itself and represents a unique and universal design that solves the problem of coupling the universal ribosome to a universal membrane channel. The highly conserved bacterial nature of this core also speaks to foresight, as whatever designed the core got it right from the start: the same basic strategy that works in the simplest of bacterial cells is at work in complex human cells. Even individual parts can be swapped. Of course, says the Duck, it is possible to view all of this as some Frozen Accident. But then, says the Rabbit, we are left pondering how such an accident turned out to be so darn rational.
Remember, these are all just clues, not proofs or powerful evidence. But it gets much more interesting if we view the OMD as a seed to nudge evolution. In Chapter 7 of The Design Matrix we discussed how intelligence can use chance by carefully selecting bait to help the blind watchmaker fish for certain functions at a later time. In this case, given its universal nature, and the fact that a designer could rely on it to be present in the future, might the SRP system have functioned as such bait? If we return the our original discussion of the SRP system as illustrated in this essay, the eukaryotic system was much more complex than the bacterial system. To keep things simple for our analysis, we cut away this added complexity by shifting our focus to the simpler bacterial system. However, it is may be the case that billions of years of bacterial evolution have simplified what was once a much more complex state .
Recall that the eukaryotic SRP has an RNA component known as the Alu domain that is crucial for elongation arrest (the PAUSE function).
The Alu domain is also bound by two small proteins, SRP9 and SRP14. These proteins first stick to each other and then bind to the Alu domain and are likewise important for elongation arrest . Because of its large size and cellular architecture, the eukaryotic cell design may require the PAUSE function as the ribosome is shuttled to a membrane.
The smaller cell size of bacteria, coupled with its different architecture, may not require such a function and, in fact, it is not known if they can even carry out elongation arrest. Bacteria such as E. coli, have no SRP9 and SRP 14 proteins, and also lack the Alu domain in their RNA component. So which state is more like the ancestral state – the eukaryotic system with its larger RNA molecule, Alu domain, and SRP9/14 proteins or the bacterial system with its smaller RNA molecule lacking an Alu domain SRP9/14 proteins?