4 ms·

Ok, while I understand that this sort of article might be interesting, honestly it's only scratching the surface of the current state of the art (and the idea o

Ok, while I understand that this sort of article might be interesting, honestly it's only scratching the surface of the current state of the art (and the idea of TE's acting as fodder for evolution isn't exactly new). Short reply -- Get Martin Nowak's book Evolutionary Dynamics Long reply -- Even Nowak's work is just the beginning (disclaimer: my current Ph.D. thesis work is building off of Nowak's start). Let's start with this notion that TE's are vital for evolution. Real answer: sort of. You see, there's an awful lot of species that don't have an overabundance of "junk" DNA, yet are still able to adapt and evolve. The reason that TE's at least seem to be more important in higher order plants and animals is because of how such organisms organize their genomes. Ok, before I get carried away on a long rant, here's the heart of the matter for the hacker audience: Proteins fold into domains. These are compact structures with a rough upper limit to their size that typically can carry out one biochemical function. In E. coli, most genes code for proteins with only one domain. So, E. coli can evolve by grabbing new genes, turning genes on or off, or in some circumstances, evolve new functionality from existing domains through random mutation. (In reality, random mutation takes a long time to produce anything useful, and the creation of novel domains appears to no occur. There's a theory growing in prominence that all of the protein domain folds that exist today were present when life began, and may even represent independent life originating events...but I'm getting off track.) In humans, most of our proteins are multi-domain. Not all of these domains, however, are catalytic. That is, in a human protein with 5 domains, maybe only one actually has biochemical activity. The function of the rest is to modulate that activity or localize the protein to one part of the cell or another. Also, the mechanisms controlling when genes get turned on and off in humans is much more complex than in bacteria. Therefore, evolution in higher order plants and animals is much more likely to occur through a "shuffling" of domains and regulatory elements. Because TE's are good at "shuffling" DNA, it's not surprising that having a healthy dose of this sort of "junk" DNA is advantageous. Of course, that's not all...there's also neutral evolution and pseudo-genes and epigenetic inheritance, etc. Biology is really on the cusp of exploding (oh, and I'm writing a book about that too ;-). tl;dr -- The genetics of higher order plants and animals is not unlike a program which relies heavily on many libraries. If you swap out one XML parser for a better XML parser, you'll get better performance (and more customers!). Transposable elements function (sort of) like biology's equivalent of a linker, and can help organisms swap in and out libraries/protein domains.

timr 18y ago
"There's a theory growing in prominence that all of the protein domain folds that exist today were present when life began, and may even represent independent life originating events" Who in the world is advocating for that theory? It sounds silly, on its face...one has only to spend an afternoon browsing the SCOP or PFAM databases to see that there's been a huge amount of recent evolution at the fold level, and that the domains that we know about have appeared over a very long time.
- jballanc 18y ago
  Gah! Ok, apologies. I have to learn to stop over-oversimplifying! What I mean there was this: Mathematical modeling of the evolution of protein folds points toward the impossibility of convergently evolving folds (but not convergently evolving functionality). This implies that two proteins with the same fold can reasonably be assumed to have evolved from a common ancestor protein, even if that conclusion cannot be reached from sequence information. Unfolded proteins (at least, above a certain length) cause problems for living things. Thus, the ability of evolution to freely explore fold-space is constrained. There is some interesting work going on in this space looking at the possibility networks of interrelated folds that don't pass through unfolded intermediates, but I think it's too soon to say, for certain, that these networks are sufficient to generate truly "novel" folds. As for the SCOP classification system, my personal view is that it tends to be on the restrictive side. Of course, that's the point of SCOP: to robustly categorize folds. As for PFAM, it's been a while, but last I looked they still don't consider any 3D structural information in their classifications. I guess what I'm trying to say here is that, whether or not "novel" protein folds are actively appearing depends on your definition of "novel". If I mutate a residue in the middle of a helix that breaks the helix in two, is that a novel fold? If I then insert a few more amino acids and turn that one helix into a helix-turn-helix, is that a novel fold? The theory I alluded to is not my own, but I can admire the logic behind it. The idea is that it is possible to group many folds through sequence and other (i.e. threading) means into derived folds. However, even when you do this, you don't arrive at a rootless tree. Instead, you find that there are somewhere (depending on who you ask) between 800 and 1300 "roots" to the fold family tree. Presumably, these roots represent novel abiogenesis events. At the very least, these root folds must have existed before "modern" biology (i.e. the sort that cannot tolerate unfolded states) began. Whether they all have a common ancestor or not is very much up for debate, but so far I don't know that we have conclusive evidence one way or the other. To be clear, though, I am guilty of oversimplification in the line you've picked out.

timr 18y ago

"There's a theory growing in prominence that all of the protein domain folds that exist today were present when life began, and may even represent independent life originating events" Who in the world is advocating for that theory? It sounds silly, on its face...one has only to spend an afternoon browsing the SCOP or PFAM databases to see that there's been a huge amount of recent evolution at the fold level, and that the domains that we know about have appeared over a very long time.

jballanc 18y ago
Gah! Ok, apologies. I have to learn to stop over-oversimplifying! What I mean there was this: Mathematical modeling of the evolution of protein folds points toward the impossibility of convergently evolving folds (but not convergently evolving functionality). This implies that two proteins with the same fold can reasonably be assumed to have evolved from a common ancestor protein, even if that conclusion cannot be reached from sequence information. Unfolded proteins (at least, above a certain length) cause problems for living things. Thus, the ability of evolution to freely explore fold-space is constrained. There is some interesting work going on in this space looking at the possibility networks of interrelated folds that don't pass through unfolded intermediates, but I think it's too soon to say, for certain, that these networks are sufficient to generate truly "novel" folds. As for the SCOP classification system, my personal view is that it tends to be on the restrictive side. Of course, that's the point of SCOP: to robustly categorize folds. As for PFAM, it's been a while, but last I looked they still don't consider any 3D structural information in their classifications. I guess what I'm trying to say here is that, whether or not "novel" protein folds are actively appearing depends on your definition of "novel". If I mutate a residue in the middle of a helix that breaks the helix in two, is that a novel fold? If I then insert a few more amino acids and turn that one helix into a helix-turn-helix, is that a novel fold? The theory I alluded to is not my own, but I can admire the logic behind it. The idea is that it is possible to group many folds through sequence and other (i.e. threading) means into derived folds. However, even when you do this, you don't arrive at a rootless tree. Instead, you find that there are somewhere (depending on who you ask) between 800 and 1300 "roots" to the fold family tree. Presumably, these roots represent novel abiogenesis events. At the very least, these root folds must have existed before "modern" biology (i.e. the sort that cannot tolerate unfolded states) began. Whether they all have a common ancestor or not is very much up for debate, but so far I don't know that we have conclusive evidence one way or the other. To be clear, though, I am guilty of oversimplification in the line you've picked out.