Bench Press

Happy belated 200th, Charles Darwin.

Charles Darwin brought to the field of biology a revolutionary insight into how species came about. But beyond merely synthesizing a  coherent theory of evolution, Darwin was also responsible for popularizing a way of conceptualizing evolution which continues to be used today: the evolutionary tree.

Darwin’s first (and quite possibly the first ever) evolutionary tree is depicted to the left (dated 1837, from Darwin’s First Notebook on Transmutation of Species on view at the Museum of Natural History in Manhattan) and is, almost ceremonially, directly underneath the words “I think”.

The tree depicts the relationships between a number of species in terms of how they are all related. And, while the concept itself is relatively simple, the actual tree itself is highly complex for three reasons.

First, as the number of species increases, it becomes much harder to generate complete and accurate evolutionary trees to cover all the possible evolutionary relationships. Knowing that A and B are related does not tell you if A and B are more closely related to each other than they are to C, for instance.

Secondly, Darwin’s tree only considered the possibility of branches – it never considered the possibility that branches may merge or that relationships other than branching out could exist. For instance, bacteria have at least three ways of obtaining genetic material through a method other than replicating:

• Transformation: a bacterium absorbs genetic material from its surroundings
• Conjugation: a bacterium exchanges genetic material with a neighboring bacterium
• Transduction: a virus inserts genetic material into the bacterium’s genetic code

Third, evidence linking two species in terms of an evolutionary tree is difficult to interpret. The challenge is that evolution occurs over millions of years – what we can see are end-results and fossils. What we don’t see is that evolution can change “directions” or affect different genes and characteristics differently over time.

So, what do we do? How do we present the richness of information encoded in an evolutionary tree, but updated with a contemporary understanding of evolutionary biology and genetics, and yet presented in a way which is actually useful and meaningful to scientists?

Enter Tree 2.0. Scientists (including Michael Sanderson’s group at the University of Arizona who developed the Paloverde software to visualize dense “tree of life”’s) have apparently partnered with web technology super-specialists Google and Adobe (HT: New York Times) to develop a new way of visualizing and storing the massive amounts of information needed to fully characterize the tree of life.

While very little in the way of details of the partnership have emerged, I think this is a clear example of where advances in computational and visualization technology can play in helping biologists better understand evolution, on three levels:

• First, sophisticated software can be used to help scientists crunch through the myriads of genetic data that needs to be understood in order to synthesize a proper evolutionary tree; it’s simply too difficult for humans and non-automated systems to sift through data from thousands of species at once to pick out all the relevant relationships; we posted before about how algorithms used to detect cheating may help in picking out evolutionary relationships – we probably need many more to detect and assemble the total tree of life structure
• Second, new technology and standards are needed to store the information within the tree to depict the types of relationships which can emerge between species (e.g. horizontal gene transfer, how certain genes have converged between species while others have diverged, etc)
• Third, visualization technology akin to what is used by Google Earth to depict rich and complex information quickly can help scientists quickly query and use to advance our understanding of biology – not to mention it would just look cool and be something everyone could easily browse

I can’t wait for what comes out of the collaboration with Google – and I do believe that this is the best birthday present Charles Darwin could ask for – even if he has to wait a little after his 200th birthday to get it.

(Image credit – Darwin’s tree: Wikipedia) (Image credit – Circle Tree of Life: Hillis and Bull laboratory)