Transcription and Translation

As a cell biologist, I view genes as tools that contribute to the building and maintenance of different cell types. Vertebrates all have the same types of cells and thus it is no surprise that most of our genes have counterparts in all other vertebrates and all vertebrates have similar gene counts. Invertebrates such as worms and flies have almost the same number of cell types that vertebrates have and thus it is no surprise that invertebrates have almost (if not the same) number of genes that we have.

If one were to argue that we humans are "more complex" then other animals, one would have to concede that this complexity is mostly neuronal. This "increased complexity" is due in part due to an increase in neuronal number (although many animals such as elephants have many more neurons than humans) and an increase in how these neurons are connected.

So the question is: how to increase the "complexity" of our neuronal connections?

Well we may have more neuronal guidance cues through an increase in those types of genes or through processes such as alternative splicing. But probably the biggest difference has to with how, when and where any particular gene is turned on. It's in our genetic program. .

Sticking with this computer program analogy, our genome may not have more code or more functions but the code is such that the final product works more smoothly. So my guess is that our "increased complexity" is due to how our genes are turned on by DNA (and RNA) regulatory elements. These regulatory sequences may be "more complicated" or just "better tweaked" in humans in comparison to other organisms.

But in the end most of our coding genes have roles in cellular functions and in specifying different cell types, not in neuronal guidance or in specifying neuronal connectivity.

*** A FURTHER NOTE on Complexity vs Plasticity a comment by PZ:

I'd argue the other way. Our neuronal complexity is not a product of fancier genetic control at all -- it's an aspect of plasticity. Human neurons are less precisely specified than fly neurons. What they have is a general program for what a neuron should do, refined by specification to broad regions like cortical layer or zone, and they play out that role in the context of their environment. Start with relatively simple rules, expand the playground, and you see more complexity emerge.

I'm not saying that our neurons are more precisely controlled but that the genetic algorithms are better. Whether this results in a higher degree of plasticity, better organization, or a combination I remain agnostic. Mental traits can be selected for in dogs and other animals so in the end brain function will be a result of different genetic algorithms. This is not a nature vs nurture argument. Our brains adapt and respond to the environment based on the genetic algorithms within our genome. But in the end our ability to respond at the developmental level and on a day to day basis is the result of the genetic framework.