Wider Reading Frames

So far, Fatcat and its multiple Freds are still reading backbone chains one molecule at a time. That makes them backwardly compatible, so they can still produce a Fred, Roscoe, and the other 'legacy' proteins that were originally built from just two amino acids. The new multiple-Fred system can also transcribe any of the four-amino-acid proteins that evolved since the first alt-Caleb assimilation. So far, nothing has really changed in protein transcription, except perhaps a switch to faster reactions and higher replication accuracy (thanks to the separation of functions, and the use of pre-loaded Freds). It's a workable system for the eight-molecule stage of life in the RNA world, but it also has reached its limit. Because there is only so much variation possible in chain molecules, Fred really can't distinguish between more than about four different chain molecules, which means it can only specify four different amino acids. That's still not a very good selection of 'building blocks' for proteins. Any organism that could manage a larger number of amino acids would gain a huge selective advantage. So it's time to look at some possible changes that could have occurred in the transcription process, to make that happen. Double-Wide Fred How could Fred manage to assemble more amino acids? Let's consider a new version of Fred that can add a fifth amino acid, from a four-molecule genetic chain. This new Fred might have resulted from a fortuitous mutation that affected the positioning of both the elbow and the knee. This mutant Fred's elbow is wider, and instead of linking to a single nucleotide, it arches across and links to two. We'll call it a 'double-wide' Fred because of this property. New Fred's knee is also different, so it happens to bind with a new, fifth amino acid, that is different from the usual four. During protein transcription, this new Fred might intrude when Fatcat had reached a particular combination of two chain elements. It would then insert the fifth amino acid, instead of an original. The result would be a protein with a brand new amino acid substituted in place of one or two amino acids from the original chain (the size of the replacement would depend on where the next Fred inserted itself). Evolutionary Advantages As usual, insertion of a random new amino acid in a protein would rarely be advantageous. There may have been thousands of mutant 'double wide' Freds that appeared on the scene, and then quickly killed off their organism by producing a non-functional version of some important enzyme. However, by sheer random happenstance, eventually a new five-amino-acid protein would appear was an improvement over the previous version of that chain. That cell would then have an advantage, which would translate into reproductive success, and an increase in numbers. In the long haul of thousands or millions of years, organisms capable of using five amino acids would have then been able to evolve a wider variety of useful new proteins, and double-wide Fred would have become more common. Reading Frames and Old Fred Unfortunately, there is a major problem with jumping too quickly to a wider reading frame, and it's time to talk about it now. Cassius contained a moderately large number of enzymes that were transcribed from the older one-molecule reading systems, and they needed to be preserved, if Cassius were to continue transcribing Freds and Roscoes, as it always had. Eventually, the new more-than-two component proteins would have become much better than the originals, since they could be built from a wider variety of amino acids (up to 16 with a two-molecule reading system that used four chain molecules, providing 42 permutations). However, Cassius needed to keep its 'legacy' proteins for a while, at least. That means that Cassius needed two different reading systems, at least during a transition period until the older, essential proteins were all replaced by newer enzymes. In other words, any double-wide Fred that interfered with the existing two-component proteins would be lethal to that Cassius, and not an improvement at all. Pair Restrictions Fortunately for Cassius, there is a tidy way around this problem-- but it only works if double-wide Fred appeared very soon after the merger of a Clem and an alt-Clem. All of Caleb's original genes were built from the two molecules in the first Sofia (for convenience, we'll call them 'A' and 'G'). The genes that came from alt-Caleb used the molecules from alt-Sofia (we'll call them 'C' and 'T'). If a double-wide Fred confined itself to chain sequences that were a mixture of a chain molecule and an alt-molecule, it would never make a bad transcription from any of the original chains. In other words, double-wide Freds that used AA, AG, GA or GG would cause problems with the original enzymes in Cassius. If they used CC, CT, TC or TT, they would cause problems with the original enzymes from alt-Cassius. Any of those double-wides would intrude the wrong amino acid into an existing 'legacy' enzyme, which would probably be lethal. However, double-wide Freds that read mixed pairs (AC, AT, GC, GT, CA, CG, TA and TG) would not conflict with 'old style' transcriptions of any 'old' enzymes. That means that the switch to a two-molecule reading frame could add only eight new amino acids to protein transcription instead of sixteen (Cassius would have to skip eight of the possible permutations, to avoid making lethal substitutions). However, a Cassius capable of building enzymes from twelve different amino acids would still have had much better potential for new, improved enzymes than one that could only use four. Double-Wide Timing Could the double-wide system have happened earlier-- say, back when there were just two chain molecules in early versions of Caleb? Probably not. The problem is that double-wide Fred would have interfered with regular Fred-style transcription (if double-wide Fred matched with an AA, there would be no way to know whether it was supposed to be used as two of the original A amino acid, or the new AA one). The switch to double-wide coding would have required Caleb to abandon the original Sofia and Sorrel genes, and there was no way to replace them quickly enough with double-wide versions. When Caleb assimilated an alt-Caleb, it just happened to create a 'window of opportunity' for a new coding system to arise without breaking the original genes. In fact, that 'window' was open for a relatively brief amount of time. Once an eight-molecule organism evolved its first protein that used all four amino acids, the opportunity to switch to a wider reading frame was lost. Double-wide Fred would have interfered with those newer mixed chain enzymes, even if it skipped the restricted combinations. More Problems with Double Wides So far the double-wide system seems plausible, and we've found a theoretical way to work around the problem of conflicting with the 'old Fred' transcription problem. Unfortunately, there are some additional weaknesses in the double-wide system. First of all, it still won't provide enough new amino acids. With four different chain molecules and a two-molecule reading frame, Fred and Fatcat can theoretically distinguish between sixteen (42) different amino acids. However, they would need to skip eight restricted combinations to avoid breaking older enzymes. As a result, the practical maximum for the double-wide system was a mere eight amino acids. Secondly, the double-wide system probably always had a problem with ambiguous reads. When Fatcat came up to a double-wide combination, it could just as easily accept a regular Fred, instead of the double-wide version. That would insert two 'old' amino acids into the protein, instead of one 'new' amino acid. There might have been a way to give priority to the double-wide Freds, so they could have 'first right of refusal' for the two-molecules sequences. But it's hard to imagine how that could work all the time without fail, and it's even harder to imagine how it could extend to more and more additional amino acids. In general, it seems that mixing one-molecule and two-molecule reading frames in the same genetic chain is a rather awkward system. Because of its problems, the double-wide system may never have actually developed-- and even if it did, it probably never got very far. Switching to a wider 'reading frame' is a great idea, but there is a better way to make it work, and it's time to look at it now. Previous Home Next