Cataloging a year of blogging: complexity in evolution, general models, and philosophy

Last month, with just hours to spare in January, I shared a linkdex of the 14 cancer-related posts from TheEGG in 2016. Now, as February runs out, it’s time to reflect on the 15 non cancer-specific posts from last year. Although, as we’ll see, some of them are still related to mathematical oncology. With a nice number like 15, I feel that I am obliged to divide them into three categories of five articles each.…

Continue reading


Cataloging a year of cancer blogging: double goods, measuring games & resistance

Happy year of the Rooster and 2017, This month marks the start of the 7th calendar year of updates on TheEGG. Time to celebrate and summarize the posts of the year past. In 2016 there was the same number of posts as 2015, but instead of being clustered in a period of <7 months, they were more uniformly distributed across the calendar. Every month had at least one new post, although not necessarily written by…

Continue reading


Antoni Gaudi and learning algorithms from Nature

Happy holidays. A few days ago, I was exploring Barcelona. This means that I saw a lot of architecture by Antoni Gaudi. His works have a very distinct style; their fluid lines, bright colours, myriad materials, and interface of design and function make for very naturesque buildings. They are unique and stand in sharp contrast to the other — often Gothic revival and Catalan Modernisme — architecture around them. The contrast is conscious; when starting…

Continue reading


Fusion and sex in protocells & the start of evolution

In 1864, five years after reading Darwin’s On the Origin of Species, Pyotr Kropotkin — the anarchist prince of mutual aid — was leading a geographic survey expedition aboard a dog-sleigh — a distinctly Siberian variant of the HMS Beagle. In the harsh Manchurian climate, Kropotkin did not see competition ‘red in tooth and claw’, but a flourishing of cooperation as animals banded together to survive their environment. From this, he built a theory of…

Continue reading


Chemical games and the origin of life from prebiotic RNA

From bacteria to vertebrates, life — as we know it today — relies on complex molecular interactions, the intricacies of which science has not fully untangled. But for all its complexity, life always requires two essential abilities. Organisms need to preserve their genetic information and reproduce. In our own cells, these tasks are assigned to specialized molecules. DNA, of course, is the memory store. The information it encodes is expressed into proteins via messenger RNAs.Transcription…

Continue reading


Three mechanisms of dark selection for ruxolitinib resistance

Last week I returned from the 6th annual IMO Workshop at the Moffitt Cancer Center in Tampa, Florida. As I’ve sketched in an earlier post, my team worked on understanding ruxolitinib resistance in chronic myelomonocytic leukemia (CMML). We developed a suite of integrated multi-scale models for uncovering how resistance arises in CMML with no apparent strong selective pressures, no changes in tumour burden, and no genetic changes in the clonal architecture of the tumour. On…

Continue reading


Dark selection and ruxolitinib resistance in myeloid neoplasms

I am weathering the US election in Tampa, Florida. For this week, I am back at the Moffitt Cancer Center to participate in the 6th annual IMO Workshop. The 2016 theme is one of the biggest challenges to current cancer treatment: therapy resistance. All five teams participating this year are comfortable with the evolutionary view of cancer as a highly heterogeneous disease. And up to four of the teams are ready to embrace and refine…

Continue reading


Don’t take Pokemon Go for dead: a model of product growth

In the last month, some people wrote about the decay in active users for Pokemon Go after its first month, in a tone that presents the game as likely a mere fad – with article on 538, cinemablend and Bloomberg, for example. “Have you deleted Pokémon Go yet?” was even trending on Twitter. Although it is of course certainly possible that this ends up being an accurate description for the game, I posit that such conclusions are rushed. To…

Continue reading


Social algorithms and the Weapons of Math Destructions

Cathy O’Neil holding her new book: Weapons of Math Destruction at a Barnes & Noble in New York city.In reference to intelligent robots taking over the world, Andrew Ng once said: “I don’t work on preventing AI from turning evil for the same reason that I don’t work on combating overpopulation on the planet Mars.” Sure, it will be an important issue to think about when the time comes. But for now, there is no…

Continue reading


Drug holidays and losing resistance with replicator dynamics

A couple of weeks ago, before we all left Tampa, Pranav Warman, David Basanta and I frantically worked on refinements of our model of prostate cancer in the bone. One of the things that David and Pranav hoped to see from the model was conditions under which adaptive therapy (or just treatment interrupted with non-treatment holidays) performs better than solid blocks of treatment. As we struggled to find parameters that might achieve this result, my…

Continue reading