Blogging community of computational and mathematical oncologists

A few weeks ago, David Basanta reached out to me (and many other members of the mathematical oncology community) about building a community blog together. This week, to coincide with the Society for Mathematical Biology meeting in Montreal, we launched the blog. In keeping with the community focus, we have an editorial board of 8 people that includes (in addition to David and me): Christina Curtis, Elana Fertig, Stacey Finley, Jakob Nikolas Kather, Jacob G.…

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How does the Weddell Polynya affect Antarctic ice shelves?

The Weddell Polynya is a large hole in the sea ice of the Weddell Sea, near Antarctica. It occurs only very rarely in observations, but is extremely common in ocean models, many of which simulate a near-permanent polynya. My new paper published today in Journal of Climate finds that the Weddell Polynya increases melting beneath the nearby Filchner-Ronne Ice Shelf. This means it’s important to fix the polynya problems in ocean models, if we want…

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Closing the gap between quantum and deterministic query complexity for easy to certify total functions

Recently, trying to keep with my weekly post schedule, I’ve been a bit strapped for inspiration. As such, I’ve posted a few times on a major topic from my past life: quantum query complexity. I’ve mostly tried to describe some techniques for (lower) bounding query complexity like the negative adversary method and span programs. But I’ve never really showed how to use these methods to actually set up interesting bounds. Since I am again short…

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The gene-interaction networks of easy fitness landscapes

Since evolutionary fitness landscapes have been a recurrent theme on TheEGG, I want to return, yet again, to the question of finding local peaks in fitness landscapes. In particular, to the distinction between easy and hard fitness landscapes. Roughly, in easy landscapes, we can find local peaks quickly and in hard ones, we cannot. But this is very vague. To be a little more precise, I have to borrow the notion of orders of growth…

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Twitter vs blogs and science advertising vs discussion

I read and write a lot of science outside the traditional medium of papers. Most often on blogs, twitter, and Reddit. And these alternative media are colliding more and more with the ‘mainstream media’ of academic publishing. A particularly visible trend has been the twitter paper thread: a collection of tweets that advertise a new paper and summarize its results. I’ve even written such a thread (5-6 March) for my recent paper on how to…

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Description before prediction: evolutionary games in oncology

As I discussed towards the end of an old post on cross-validation and prediction: we don’t always want to have prediction as our primary goal, or metric of success. In fact, I think that if a discipline has not found a vocabulary for its basic terms, a grammar for combining those terms, and a framework for collecting, interpreting, and/or translating experimental practice into those terms then focusing on prediction can actually slow us down or…

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Fighting about frequency and randomly generating fitness landscapes

A couple of months ago, I was in Cambridge for the Evolution Evolving conference. It was a lot of fun, and it was nice to catch up with some familiar faces and meet some new ones. My favourite talk was Karen Kovaka‘s “Fighting about frequency”. It was an extremely well-delivered talk on the philosophy of science. And it engaged with a topic that has been very important to discussions of my own recent work. Although…

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Hiding behind chaos and error in the double pendulum

If you want a visual intuition for just how unpredictable chaotic dynamics can be then the go-to toy model is the double pendulum. There are lots of great simulations (and some physical implementations) of the double pendulum online. Recently, /u/abraxasknister posted such a simulation on the /r/physics subreddit and quickly attracted a lot of attention. In their simulation, /u/abraxasknister has a fixed center (block dot) that the first mass (red dot) is attached to (by…

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Notation and Beginners

You’re interested in learning a new mathematical topic. After reading some popular articles that speak in broad terms about the subject, you are energized to go on a deeper dive and learn the details. You open up a textbook, pencil in hand and ready to expand your horizons. You start going through the introductory chapter, motivated with the dream of working through the whole textbook. You make a little progress, but you find yourself pausing…

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Span programs as a linear-algebraic representation of functions

I feel like TheEGG has been a bit monotone in the sort of theoretical computer science that I’ve been writing about recently. In part, this has been due to time constraints and the pressure of the weekly posting schedule (it has now been over a year with a post every calendar week); and in part due to my mind being too fixated on algorithmic biology. So for this week, I want to change things up…

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