Here, one of my brilliant MD PhD students and I study one of the “information” arguments against evolution. What do you think of our study?

I recently put this preprint in biorxiv. To be clear, this study is not yet peer-reviewed, and I do not want anyone to miss this point. This is an “experiment” too. I’m curious to see if these types of studies are publishable. If they are, you might see more from me. Currently it is under review at a very good journal. So it might actually turn the corner and get out there. An a parallel question: do you think this type of work should be published?

I’m curious what the community thinks. I hope it is clear enough for non-experts to follow too. We went to great lengths to make the source code for the simulations available in an easy to read and annotated format. My hope is that a college level student could follow the details. And even if you can’t, you can weigh in on if the scientific community should publish this type of work.

Functional Information and Evolution

http://www.biorxiv.org/content/early/2017/03/06/114132

“Functional Information”—estimated from the mutual information of protein sequence alignments—has been proposed as a reliable way of estimating the number of proteins with a specified function and the consequent difficulty of evolving a new function. The fantastic rarity of functional proteins computed by this approach emboldens some to argue that evolution is impossible. Random searches, it seems, would have no hope of finding new functions. Here, we use simulations to demonstrate that sequence alignments are a poor estimate of functional information. The mutual information of sequence alignments fantastically underestimates of the true number of functional proteins. In addition to functional constraints, mutual information is also strongly influenced by a family’s history, mutational bias, and selection. Regardless, even if functional information could be reliably calculated, it tells us nothing about the difficulty of evolving new functions, because it does not estimate the distance between a new function and existing functions. Moreover, the pervasive observation of multifunctional proteins suggests that functions are actually very close to one another and abundant. Multifunctional proteins would be impossible if the FI argument against evolution were true.