Greetings all, A few comments over Francis' message.
There are several theories on the usefulness of junk DNA, and probably they all are correct, in the sense that they all explain plausible reasons for its existence. One of them is that junk DNA has a structural purpose. An analogy: you need concrete walls in an office building, even if the walls don't take part in the functioning of the corporation working inside. Another, more relevant perhaps, is that junk DNA gives robustness to mutations. In other words, if there is a certain probability of mutation, if all your DNA is functional, you will be changing function with every mutation. If only 1% of DNA is functional, only one mutation in a hundred will cause this. Also, this gives the possibility to explore neutral landscapes. In other words, a neutral mutation (i.e. to non-functional DNA, which does not cause any change in phenotype) can explore possible new genes without destroying old ones. It seems that the amount of required junk DNA will depend on the amount of functional genes one has, and the adaptability one would require. For example, bacteria need to mutate very quickly, to adapt to changing environments. Since they are so many, it is good to "sacrifice" every now and then some mutants, just in case these will be the only survivors to an antibiotic. In less unstable environments, where reproduction is much slower, you don't want to explore mutations so quickly, because you need first to sustain the species. Also, what Francis mentioned, junk DNA could perform "internal control" over expressing genes. However, I believe that only a small part of junk DNA would be like this, otherwise any mutation would cause changes in phenotype... You need also to explain where would new genes come from. Since not all combinations of adenine, cytosine, guanine, and thymine will produce useful genes (via proteins or other genes), you would expect that there will be several "non useful" chunks of DNA. In the workshop of a sculptor, you don't see ONLY finished works, do you? (especially if the sculptor likes to work on several works in parallel) Just as a side note on random Boolean networks, there have been studies on multiple-valued random networks, e.g.: Sole, R. V., Luque, B., and Kauffman, S. A. (2000). Phase transitions in random networks with multiple states. Technical Report 00-02-011, Santa Fe Institute. http://www.santafe.edu/research/publications/wpabstract/200002011 and they generalize the boolean case, but it seems that it doesn't make a big difference, and people have continued using Boolean models. For the people who still don't like discrete cases, and like differential equations, Leon Glass (http://www.cnd.mcgill.ca/bios/glass/glass.html ) has been extending Kauffman's model to the continuous case, using differential equations per node... If anyone is curious on what the hell are random Boolean networks, you can check the introduction I recently prepared to the topic: http://homepages.vub.ac.be/~cgershen/rbn/tut/index.html http://uk.arxiv.org/abs/nlin.AO/0408006 Best regards, Carlos Gershenson... Centrum Leo Apostel, Vrije Universiteit Brussel Krijgskundestraat 33. B-1160 Brussels, Belgium http://homepages.vub.ac.be/~cgershen/ "We can control much better how we accept things than things themselves"
