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I see that the genome contains large regions of repeating sequences called interspersed or dispersed elements. The long dispersed elements (LINES) such as LINE-1, can reach up to 6-8 kb in length.

I'm wondering, given the amount of repetition that takes place in these regions, wouldn't a system where a pointer (such as in computer programming) existed be more efficient? For example, instead of including a LINE, include a unique 5 base pair sequence acting as a pointer to that LINE. A separate chromosome (containing one copy of each LINE) would then be read at the correct position once the pointer was read.

Do you think that given enough time in evolution, such a system would be more sustainable? Sort of like using a proper functional language instead of Assembler in computer programming, where f(x) can be defined once, and accessed via pointers, instead of being repeated many times?

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    $\begingroup$ Are you sure about what pointer exactly does? As far as my knowledge goes, a pointer stores the address of an object in the RAM. I don't think your analogy is correct. And for function calls: Leave pointers to functions; there are no true equivalents of function calls in biological systems (see this post). It is imperative to understand both the subjects to a basic level before making analogies. $\endgroup$ – WYSIWYG Apr 11 '15 at 6:51
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    $\begingroup$ In the question you'll note I asked why a concept "like" pointers "didn't evolve". In this case of "like" the "object" being pointed would be a LINE. Putting semantics aside, I was curious why heavy extended chains of repeating sequences of carbon atoms would be evolutionarily beneficial when those same repeating chains could be just created once, and then activated as needed. Interestingly in the post you reference, you yourself state it's not the physical implementation, but the underlying concept that is important. It was a question regarding concept, as mentioned in the title. $\endgroup$ – user4779 Apr 11 '15 at 7:32
  • $\begingroup$ There's not much point in conserving space when at least 50% of your genome doesn't do anything at all. To use a computer science analogy: Disk is cheap. (and all processing is parallel so even I/O isn't a deal) $\endgroup$ – Resonating Apr 11 '15 at 17:54
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    $\begingroup$ @Resonating "50% of your genome doesn't do anything at all" is not necessarily true. A large portion of our genome does not have any currently-known function, but that is completely different from saying it has no function whatsoever. $\endgroup$ – MattDMo Apr 12 '15 at 0:17
  • $\begingroup$ The most generous papers have pegged maybe 80% of the human genome as functional. The average estimate is more like 15% even on the generous side. I gave a bit of a margin because much is not known, but there are ~at least~ 800 million bases that do nothing at all. I'm comfortable with my estimate given what is currently known. $\endgroup$ – Resonating Apr 12 '15 at 0:22
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Short answer: Pointers already exist within the genome, in terms of transcription elements (such as repressor/activator systems). These systems can remotely activate a specific gene for transcription based on concentrations of specific chemicals within the cell.

The problem with LINEs are that they are thought to be ancient retroviruses which lost their capacity to infect other cells, instead jumping around within the genome. They are therefore parasitic in nature, and they reproduce by inserting multiple copies of themselves into the genome. It makes more sense to think of LINEs as nearly inactivated retroviruses instead.

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