Modularity of Biological Networks
by GutsOne thing that has always interested me about computer simulated evolution of networks is that virtually (pun intended) all of them turn out to be non-modular. This has been pointed out in the literature (Thompson et. al 1998).
Modularity itself is something that the front-loading hypothesis predicts:
If life was designed and our analogy to human design is substantial, then we would predict life would be modular…Modularity enhances evolution and thus the perpetuation of design.
The Design Matrix p.167-168
The researchers running these sort of simulations make use of duplication, recombination, mutation, selection until they see the relevant result. However, there is a lot more to the evolution of life-like networks.
The reason why simulated evolution of networks do not evolve modularity is because simply adding a connection would be more advantageous than the less optimal modular solution. This comment puts it this way:
Viewed in this perspective, the modularity of biological networks is puzzling because modular structures can be argued to be less optimal than NN-style, nonmodular structures. After all, modules greatly limit the number of possible connections in the network, and usually a connection can be added that reduces modularity and increases the fitness of the network.
For the answer, he continues, we have to look at Engineering principles:
Modules in engineering convey an advantage in situations where the design specifications change from time to time. New devices or software can be easily constructed from existing, well-tested modules. A nonmodular device, in which every component is optimally linked to every other component, is effectively frozen and cannot evolve to meet new optimization conditions. Similarly, modular biological networks may have an advantage over nonmodular networks in real-life ecologies, which change over time: Modular networks can be readily reconfigured to adapt to new conditions
The optimal solution isn't always the correct one.
The evolution of modular networks have been simulated by introducing modularly varying goals , meant to mimic fluctuating environments. The experiment begins with random circuits that have the versatile and universal digital logic gate "NAND" (NOT AND). The result was the evolution of modular networks that even reused a certain set of network motifs, just like in life.
They later did a similar experiment with a neural network. It was then suggested that gene duplication can do the job of maintaining modularity. Evidence also suggests that network modularity itself is also driven by horziontal gene transfer, and there also seems to be a pattern of less modularity in descendants than in ancestors (Kreimer et. al 2008). I would think that life began with an already existing set of biological functions that can be combined in different ways when the environment changes, or at least, a system that made the evolution of modularity likely in a changing environment. And of course it had the help of other mechanisms, such as HGT and gene duplication.
There is no doubt that there are strong similarities between life and engineering, and one clear explanation for the strong similarities is that both are the result of rational design.
Thompson, A. (1998) Hardware Evolution: Automatic design of electronic circuits in reconfigurable hardware by artificial evolution. Springer.
A. Kreimer, E. Borenstein, U. Gophna, and E. Ruppin (2008) The evolution of modularity in bacterial metabolic networks. PNAS 105, 6976-6981
July 2nd, 2008 at 10:54 pm
Nice post.
Comment by MikeGene — July 2, 2008 @ 10:54 pm
July 2nd, 2008 at 11:05 pm
Progress is linked to better models which in turn can be advanced by better tools (both hardware and software). Better technology enables increased knowledge.
Comment by Bradford — July 2, 2008 @ 11:05 pm
July 3rd, 2008 at 9:55 am
Guts, this is where I get confused. I read your cites, and they seem to say quite the opposite of what you seem to be saying.
Biological Networks: The Tinkerer as an Engineer: This viewpoint comments on recent advances in understanding the design principles of biological networks. It highlights the surprising discovery of “good-engineering” principles in biochemical circuitry that evolved by random tinkering.
Clearly, the word "design" is not being used in the sense of rational conscious planning, but just referring to the functional pattern. And the author clearly claims that it "evolved by random tinkering".
Spontaneous evolution of modularity and network motifs: We use standard evolutionary algorithms to evolve networks. A key feature in this study is evolution under an environment (evolutionary goal) that changes in a modular fashion. That is, we repeatedly switch between several goals, each made of a different combination of subgoals. We find that such ‘‘modularly varying goals’’ lead to the spontaneous evolution of modular network structure and network motifs.
And here they show how standard evolutionary algorithms can result in modular structures if the environment fluctuates.
I'm not sure how these cites support Front-Loading as distinct from orthodox evolution.
—
Front-loading, a set up of initial conditions so as to steer the outcome(s) of subsequent events in a definite direction.
Front-loading, the idea or claim that primoridal life was designed for future contingencies.
Comment by Zachriel — July 3, 2008 @ 9:55 am
July 3rd, 2008 at 10:14 am
Biological Networks: The Tinkerer as an Engineer: Viewed in this perspective, the modularity of biological networks is puzzling because modular structures can be argued to be less optimal than NN-style, nonmodular structures.
The author is here talking about a random neural network, but a scale-free structured neural network has significantly different properties.
Comment by Zachriel — July 3, 2008 @ 10:14 am
July 3rd, 2008 at 11:27 am
Something that has always confused me: What is a "module"? How do biologists identify modules?
(I believe that Jorg Stelling wrote an intersting paper about that.)
Comment by Rock — July 3, 2008 @ 11:27 am
July 3rd, 2008 at 3:04 pm
Zachriel:
Actually, the evolutionary origin of modular networks remains unknown, the quote you refer to is my conclusion, not the author's. The author thinks the reason for the strong similiarity between life and engineering is undiscovered natural laws.
You also completely miss the point. That evolution is a tinkerer is quite clear, the thing is , that it is only tinkering supports the FLE hypothesis:
Zachriel:
No, the environment can fluctuate with standard evolutionary algorithms and modularity would still not evolve in this experiment. They use a very specific type of environmental fluctation, modularly varying goals, along with a very versatile digital logic gate. Also evidence suggests complex mechanisms play a part in driving modularity. "Intelligent use of chance".
Comment by Guts — July 3, 2008 @ 3:04 pm
July 3rd, 2008 at 4:29 pm
Zachriel:
The paper you reference doesn't describe a modular network either. The dynamics of those networks you reference are predominated by hubs, which are very likely to be connected to each other. Those kind of networks are not, in general, systems that can be seperated into a set of independant subsystems.
Comment by Guts — July 3, 2008 @ 4:29 pm
July 3rd, 2008 at 5:52 pm
I apologize for the misattribution. But that makes the comment even less understandable.
The statement says the circuitry evolved by random tinkering. So, I'm still confused on this point.
That's correct. The goals are themselves modular. Though you indicated the evolutionary origin of modular networks remains unknown, Kashtan et al. are proposing this as a plausible mechanism of the evolution of modularity.
Comment by Zachriel — July 3, 2008 @ 5:52 pm
July 3rd, 2008 at 6:02 pm
Zachriel:
By random tinkering of what it is given. I'm not really sure whats so hard to understand.
Zachriel:
Yeah thats what I said in my blog. Not sure what you're on about in this thread.
Comment by Guts — July 3, 2008 @ 6:02 pm
July 3rd, 2008 at 6:22 pm
To me, it still reads as "good engineering" evolved by random tinkering, just as someone might say that dinosaurs evolved by random tinkering. I suppose it must mean something different to you.
My first statement I had admitted to being confused. You just said the evolutionary origin of modular networks remains unknown, while citing a paper that proposes such a model. I'm not sure it's any clearer to me now than before.
Comment by Zachriel — July 3, 2008 @ 6:22 pm
July 3rd, 2008 at 6:26 pm
Zachriel:
You keep leaving out "by what it is given". That is a very important part of the equation.
Zachriel:
Are you really suggesting that because someone proposes a computer model that we now "know" the evolutionary origin? That is extremely bizarre. Not even the author would say that.
Comment by Guts — July 3, 2008 @ 6:26 pm
July 3rd, 2008 at 6:43 pm
I don't see it there. I'll lurk awhile. Maybe it will make sense after some discussion.
Comment by Zachriel — July 3, 2008 @ 6:43 pm
July 11th, 2008 at 9:40 am
Apparently cliques of collaborating scientists also evolve by “random tinkering.”
Comment by Rock — July 11, 2008 @ 9:40 am