Comments on: The Big Bang of the Protein Universe

By: Lucas

Lucas — Sat, 19 Jun 2010 16:54:28 +0000

Thanks for your comment and careful scrutiny of the first figure! The two diagrams represent the two hypothetical different outcomes the authors expected: either the sequences are still diverging (top), or the sequences have reached maximal divergence and are (necessarily, as you rightly noticed) moving towards each other again. This is indeed represented by the blue arrows ‘bouncing off’ the wall. The major difference between the Big Bang and protein evolution, is that the boundaries are considered to be fixed in the latter situation.

However, I wouldn’t be surprised if the hypothetical boundaries of protein space can be considered endless for all practical reasons. Given an extra billion year, it is likely that we don’t recognize the orthology in the most ancient proteins. The boundary might be there, but it might be so far away that we’ll never detect it or proteins will never reach it.

It’s a bit like songs and poetry: the number of songs that can be written is theoretically limited. But still songwriters string notes, chords and words together into new songs year after year, even if common patterns are repeated. Likewise, I think we’ll never have exhausted the pool of all possible songs. There’s always a route or alley that hasn’t been taken before.

On your last point, I consider epistatis to be one of the most fascinating observations in evolutionary research! I wrote more in this topic in the context of the evolution of fluorescence in corals here.

By: Gert Korthof

Gert Korthof — Sat, 19 Jun 2010 12:06:16 +0000

A question about your conclusion “meaning that even the most ancient proteins are still diverging from each other!”
When comparing the two circles (big bang of life) of your first illustration, I see in the top-right diagram 5 species happily moving away from E coli with no boundaries in sight, while the bottom-right diagram all 5 species hit the boundary of sequence space. If you look carefully you see the blue arrows changed direction, I suppose because of hitting the boundary. So, is it correct to conclude that “even the most ancient proteins are still diverging from each other”? Especially, Salmonella and Cyanosarcina are moving back to E. coli. A boundary is a boundary, isn’t? If the length of line from E. coli to the blue dot is a measure of distance, then certainly Cyanosarcina has reaced its maxiumum length and is moving back towards E. coli.
Furthermore, in the diagram the inner circle of the top and bottom diagram are exactly the same (unlike the big bang horizon which is expanding ) so Cyanosarcina simply has to go back. And it does, as the blue arrow shows.

A second remark: I found it highly interesting to read that the fitness effect of a substition is not fixed but depends on the sequence as a whole and so changes during evolution.

By: ResearchBlogging.org News » Blog Archive » Editor’s Selections: Diversity of Ingredients, Rump-Shaking Frogs, and our Lonely Genomes

Thu, 03 Jun 2010 22:27:40 +0000

[...] like the universe, the genomes of life on earth continue to drift apart, forever masking deep relationships and suggesting a wildly divergent deep [...]

By: Daniel Bassett

Daniel Bassett — Mon, 31 May 2010 20:35:24 +0000

Great post. Very interesting. Great analogy!!!!

By: Lucas

Lucas — Sun, 30 May 2010 17:57:23 +0000

Thanks for pointing it out, that honestly slipped my mind! How stupid.. The analogy becomes all the better though, as fitness landscape appear to change on similar timescales as the mountains that rise and drop!

Good to have you back in the blogosphere!

By: Lucas

Lucas — Sun, 30 May 2010 17:36:21 +0000

That’s pretty cool, thanks! What I can quickly glance from the paper, they propose that all proteins may have evolved from a few/a single ancestor protein(s).. Combined with the observation that proteins are still diverging, the Big Bang analogy seems to be really appropriate!

By: Lab Rat

Lab Rat — Sun, 30 May 2010 17:35:42 +0000

Wow, really interesting. I’d never heard divergence from LUCA compared to the big band before, it’s a great analogy.

And I’m pretty sure mountain ranges are still moving either away or towards each other, depending on the continental drift. Just very, very slowly. And probably in slightly more predictable directions as well!

(I am really looking forward to getting back into blogging…)

By: Iddo

Iddo — Sun, 30 May 2010 17:17:53 +0000

Interestingly enough, not the first time the Big Bang metaphor was used to describe protein evolution:

http://www.pnas.org/content/99/22/14132.abstract