Nearly there...

Finally, the "Journal of Theoretical Biology" accepted my manuscript for publication as a letter to the editor. The unedited version of the article can be found ahead of print online at

http://dx.doi.org/10.1016/j.jtbi.2008.04.028.

What a relief. I know it's just one little paper and the impact factor of the journal could be higher, but for some reason this paper is incredibly important to me. I don't know if I have made a huge fool of myself or not, but it's too late anyway. I tried to keep the article as short as possible and did not include any acknowledgements, but of course I would not have been able to persevere in this ridiculous struggle had I not had the support of some incredible people along the way. I don't know whether mRNA-tRNA interaction occurs in a 2-1-2-3 way, but I find the sheer oddness of a language that starts with the middle instead of the beginning of an information unit exciting and cannot get the picture of tRNA-precursor molecules forming aggregates with the second codon base acting as an anchor out of my head. Imagine the message
"hteatsiksontosmcuhotseewahtonoenhsayteseenubtottihnwkhtanoonheaysetthuogthaobutthtawihcehvreyobdsyese."
being translated as "thetaskisnotsomuchtoseewhatnoonehasyetseenbuttothinkwhatnoonehasyetthoughtaboutthatwhicheverybodysees." and finally for the information to "fold" into the beautiful quote: "The task is not so much to see what no one has yet seen but to think what no one has yet thought, about that which everybody sees."

Of course if the interaction between mRNA and tRNA occurred in a 1-2-3-way, the importance of the second base might be explained by a longer interval spent reading the base, so the order would roughly be 1-2-2-3. If the binding of codon and anticodon happened in such a way that all three bases bound simultaneously, then the base in the middle might spend the longest time bound to its cognate because the bases 5' and 3' of it would act as a sort of buffer (like velcro, the middle bit usually the hardest to get off first).

With possible closure on the rearrangement of the genetic code in sight, I wonder if somebody else might pick up on the methionine story. Perhaps one group might try to engineer an organism that uses an initiator-tRNA charged with isoleucine, valine, threonine or homocysteine instead of methionine and report on what the resulting phenotype might be...

But all of this has merely been a side project, the biggest reward for me would be if my initial hypothesis about the involvement of S-adenosylmethionine in determining resistance or susceptibility in experimental leishmaniasis, might prove to be useful.