The following is the last take-home essay for my developmental class. This essay is about the concept of modularity and how it is being used in biology today. It’s fairly basic stuff and if you are reading this blog, you probably know most of it already! I do hope you find the comparison to Google Chrome convincing though.
(This time we were urged to write in a more popular form so the writing is at a bit lower level and we didn’t have to source anything. I guess you can take what I say here with a grain of salt then. :P)
We are fond of comparing life to computers; the genetic code and the brain being the most frequent contenders. These analogies are often a stretch, however; the brain is notoriously plastic and not as hardwired as a computer and neither is the genetic code – it is not a rigid blueprint as people so often say. While these analogies are indeed a stretch, there is a powerful comparison that can be made between biology and computers and that is modularity.
What is modularity? The dictionary defines it as “the use of individually distinct functional units, as in assembling an electronic or mechanical system” and this is a good description. It means that you have a discrete function unit, or module, that can be used in multiple ways by changing the inputs and the outputs of the system. Furthermore, if something were to break in the module, the upstream components of the system and other modules will not also break down – only the single module crashes. This gives a modular system its strength. Let me give an example.
If you have ever used Google Chrome, you may know that when a tab crashes within the application, the rest of the application does not go down with it (unlike Internet Explorer or Firefox). Instead, the rest of your tabs stay open and function properly. This is an example of modularity: a single tab is a single module, an “individually distinct functional unit.” With Chrome, you never have to worry over losing all of your tabs. This example can be expanded to your computer generally – if an application, say Microsoft Word, crashes, your computer most likely still runs properly. Word is also a module!
But how does modularity apply to biology? I’ll give you three examples, one on a more relatable organismal level and two that show the power of modularity at the level of DNA.Take a quick glance at any arthropod like a lobster and you will notice that it has an entire suite of appendages. Jointed branches are projecting from the lobster all the way down its body; it’s a veritable Swiss army knife!
Each appendage can be viewed as a module, whether it’s a claw, antennule, swimmeret or a walking leg. To stretch our ongoing metaphor a bit, each appendage can be deemed a “tab” and is independent of other “tabs” in the lobster “application.” This is where biology starts to differ from a computer, however: if an appendage were lost on the lobster, there is a good chance the entire lobster would die. A claw is just too essential to lose – the lobster probably wouldn’t even grow into an adult. Evolution can use modularity in a different way though.
All arthropod (insects, spiders, crustaceans, and others) appendages are homologous. This means that a lobster claw and a lobster leg share a common appendage ancestor. Such homology is not too weird – the human arm, bat wing, and whale fin share common ancestors too and are thus homologous – same origins, but different functions. What arthropods have done, however, is duplicate the number of appendages existent in a single organism. We have two pairs of limbs – arms and legs – but lobsters have over 15 pairs of appendages! Hence the Swiss army knife analogy.
What appendage homology tells us is that despite the diversity in appendages, they all come from a single primitive appendage. In crustaceans this could be the biramous limb, but there is ongoing debate as to what exactly the primitive appendage would have looked like. We just know there was one.
How does this tie into modularity? Well, if you take that ancestral limb and multiply it a few times, you now have several identical copies of that limb module. Because they are independent of one another, evolution can mold these copies into unique appendages, such as walking legs or sensory attenules. The duplication of tabs allows each tab to undergo differentiation and have a history separated from the others. (If you duplicate a Facebook page in Chrome, the duplicate can go to Twitter while the original tab remains at Facebook.) This same modularity is what allowed scientists to create flies with legs on their heads instead of antennae; modules were just moved around.
The modularity of limbs reflects modularity at the level of DNA and proteins – perhaps most famously, the Hox genes. The placement of limbs along the body in almost all animals is determined by families of genes called the Hox genes. We have them, flies have them, and lobsters have them. Little is known about how they regulate other genes or even how they themselves are regulated. What we do know is that their expression is correlated with limb placement.Just like lobster appendages, Hox genes have been duplicated and subsequently diverged from each other, encoding unique coordinates along the head-tail axis. For example, one Hox gene can encode the location of the head while another can determine the location for legs or wings. This is akin to duplicating a tab in Google Chrome. Once you duplicate the tab, you can do whatever you want to the duplicate without disturbing the original. Gene duplication allows for more variety to take place – just like the lobster body plan.
One important aspect of modularity is not as easily analogized to Chrome and that is genetic switches. Instead of duplicating a gene hoping the two copies differentiate, a gene can evolve multiple switches that change how that gene is expressed. Now one single module copy is used in multiple ways. This method is particularly useful when a gene is expressed in different parts of the body or in different pathways.Sticklebacks provide an easy and quick example of modularity through switches. Sticklebacks are a family of fish (Gasterosteidae) that exist in marine and freshwater environments. The freshwater species, however, have drastically reduced or eliminated the family’s famed pelvic spines. Reasons for the reduction possibly include lack of predatory fish and/or calcium in the freshwater lakes and most of the variation in spine reduction has been linked to the gene Pitx1. However, because Pitx1 is expressed in multiple tissues such as the thymus and neuromast and not just the pelvis, eliminating the gene kills the animal. Furthermore, there is only one copy of Pitx1. How can this work?
Genetic switches! Each tissue has its own regulatory sequence outside of the coding DNA. This is shown in Figure 3 – each grey dot is a regulatory sequence and the black squares are the actual gene. As marked by the blue X, the freshwater stickleback does not have the hind-limb regulatory sequence and thus Pitx1 is not expressed in the pelvis thus there is a reduction in the pelvic spines. These switches illustrate modularity. By having multiple inputs, deleting one does not disrupt the Pitx1 module. Pitx1 one remains while its inputs and outputs are allowed to change and evolve.
Modularity is powerful. It allows for maximum diversity with minimal work. It is what makes computers so robust and is potentially what allows for evolution to occur. It explains the unity and diversity of life – the eternal paradox of biology – by using the same genes to create different morphologies. The kind of modularity – gene duplication or genetic switches – is at the heart of evolutionary developmental biology and both have their advocates. The answer, as it always is in these falsely dichotomous debates, is that both are important. Both are powerful and explanatory.
Will modularity revolutionize how we think of evolution? Probably not, but it does fill in a lot of gaps. Modularity may not change our understanding of the mechanisms of evolution, but it helps us understand how that evolution was able to take place in the first place. It is one thing to know that selection or genetic drift have driven the reduction of pelvic spines in freshwater sticklebacks, but it is even more fulfilling when we know the molecular mechanisms that took place to enable that change in the first place! Modularity may not even be that new of an idea, but it is not something we have fully grasped. We won’t revolutionize biology with modularity, but we might be able to understand how morphology has changed over time. Modularity is a useful paradigm to work with, whether its lobsters, sticklebacks, or Google Chrome, and we shouldn’t underestimate it.