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Another month, another preprint. This time a new draft (and much improved, with new results) draft of my work on the complexity of evolutionary equilibria in static fitness landscapes:

http://www.biorxiv.org/content/early/2017/09/12/187682

The biological goal here is to question the common assumption in evolutionary theory that local peaks can always be found quickly in fitness landscapes (and it is only

The methodological goal here is to connect classic models in evolution to work in theoretical computer science. In particular, to the combinatorial analysis of simplex algorithms, the complexity class of polynomial local search, and approximation algorithms. The resulting proofs aren't difficult by #cstheory standards, so you could use them as motivations in upper undergraduate classes. But since they use techniques and arguments that are not common in theoretical biology, they're saved for the technical appendix.

I am grateful to many helpful comments from various scientists over the years. Among those that are on Google Plus: +Julian Xue, +Eric Bolo, +Frederic Guichard, +Marc Harper, +Sergey Kryazhimskiy, +Andy M, +Dan Nichol, +Prakash Panangaden, +Jacob Scott. I appreciate any further feedback you guys, or anyone else, has on this work.

The results and approach might also interest +Russ Abbott, +John Baez, and +David Eppstein

http://www.biorxiv.org/content/early/2017/09/12/187682

The biological goal here is to question the common assumption in evolutionary theory that local peaks can always be found quickly in fitness landscapes (and it is only

*global*peaks that are difficult because of local blocks). I show that even simple fitness landscapes can hide exponentially long adaptive walks. And that there is sometimes no ways to avoid getting stuck on them. This can then be used to provide some alternative explanations to recent empirical literature; including using approximation results to connect the fitness traces of Lenski's long-term evolution experiment.The methodological goal here is to connect classic models in evolution to work in theoretical computer science. In particular, to the combinatorial analysis of simplex algorithms, the complexity class of polynomial local search, and approximation algorithms. The resulting proofs aren't difficult by #cstheory standards, so you could use them as motivations in upper undergraduate classes. But since they use techniques and arguments that are not common in theoretical biology, they're saved for the technical appendix.

I am grateful to many helpful comments from various scientists over the years. Among those that are on Google Plus: +Julian Xue, +Eric Bolo, +Frederic Guichard, +Marc Harper, +Sergey Kryazhimskiy, +Andy M, +Dan Nichol, +Prakash Panangaden, +Jacob Scott. I appreciate any further feedback you guys, or anyone else, has on this work.

The results and approach might also interest +Russ Abbott, +John Baez, and +David Eppstein

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I've had a hard time keeping up with social media recently, spending more time on twitter than G+ or my blog. Also, I guess I've been writing some papers. Together with Jeffrey Peacock, +David Basanta, +Andy M, and +Jacob Scott, we've recently released one of them on bioRxiv:

"Cancer associated fibroblasts and alectinib switch the evolutionary games that non-small cell lung cancer plays" http://www.biorxiv.org/content/early/2017/08/21/179259

The goal is to introduce a method for directly measuring effective evolutionary games. We then used this method for looking at games played by non-small cell lung cancer and noticed that treatment and fibroblasts can change the qualitative kind of game being played. This is pretty fun, since it gives us an empirical examples of the EGT approach to thereapy: don't treat the player, treat the game. I've sketched this approach before in a slightly different setting on #TheEGG: https://egtheory.wordpress.com/2016/03/26/game-treatment/

The figures below are two from the preprint. The first has all the raw data and the second has the inferred games. The procedure for doing this is both experimentally and mathematically straightforward, and we hope that more people will try it in their favourite experimental system.

Let's build an experimental catalog of evolutionary games!

"Cancer associated fibroblasts and alectinib switch the evolutionary games that non-small cell lung cancer plays" http://www.biorxiv.org/content/early/2017/08/21/179259

The goal is to introduce a method for directly measuring effective evolutionary games. We then used this method for looking at games played by non-small cell lung cancer and noticed that treatment and fibroblasts can change the qualitative kind of game being played. This is pretty fun, since it gives us an empirical examples of the EGT approach to thereapy: don't treat the player, treat the game. I've sketched this approach before in a slightly different setting on #TheEGG: https://egtheory.wordpress.com/2016/03/26/game-treatment/

The figures below are two from the preprint. The first has all the raw data and the second has the inferred games. The procedure for doing this is both experimentally and mathematically straightforward, and we hope that more people will try it in their favourite experimental system.

Let's build an experimental catalog of evolutionary games!

8/27/17

2 Photos - View album

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+Vox pretends to be a competitor for Wikipedia, while in reality setting up the exact branding of "opining as authoritative explanation" that the few legitimate branches of post-truth are railing against. It is a great highlight of non-participatory neoliberal managerialism. A choice quote from this long article:

It is a fine line to walk between legitimate deference to experts and entrenching of a neoliberal managerial elite. And when we defend experts, we need to make sure that we are aware of the fine balance that we need to strike. Unfortunately, I see many of my fellow scientists missing this mark. Or worse, yet, not even trying to land it. Although I also don't know how to find just the right balance, and would be interested in feedback from folks like +John Baez, +Forrest Barnum, +David Basanta, +David Robert Grimes, and +Michael Nielsen.

To go with this topic is another nice recent article on the necessity of credibility from Nathan J. Robinson of Current Affairs:

https://www.currentaffairs.org/2016/12/the-necessity-of-credibility

Here he discusses more broadly the connection between truth and power, and calls out the +Washington Post. It was nice to see Foucault mentioned, but would have been good to also discuss Herman & Chomsky.

Apparently Robinson has also written about Vox, but I haven't had a chance to read this article, yet:

https://www.currentaffairs.org/2016/11/explaining-it-all

I'll save that for later. /via Frank Pasquale & Scott Smith.

*"[Vox] is the ideological grandstanding of the technocrat and of the professional-managerial class, whose differences with you, ordinary citizen, are not political—no, no, no—but based on expertise. He “knows” what you don’t and “explains” what you “fail to understand,” so that you, too, like him, will see what he sees and agree that it is obvious common sense. You don’t need persuasion to support free trade. You just need a PowerPoint-style review of the facts—or at least, of those facts that your helpful pedagogic explainer class deems to be relevant."*It is a fine line to walk between legitimate deference to experts and entrenching of a neoliberal managerial elite. And when we defend experts, we need to make sure that we are aware of the fine balance that we need to strike. Unfortunately, I see many of my fellow scientists missing this mark. Or worse, yet, not even trying to land it. Although I also don't know how to find just the right balance, and would be interested in feedback from folks like +John Baez, +Forrest Barnum, +David Basanta, +David Robert Grimes, and +Michael Nielsen.

To go with this topic is another nice recent article on the necessity of credibility from Nathan J. Robinson of Current Affairs:

https://www.currentaffairs.org/2016/12/the-necessity-of-credibility

Here he discusses more broadly the connection between truth and power, and calls out the +Washington Post. It was nice to see Foucault mentioned, but would have been good to also discuss Herman & Chomsky.

Apparently Robinson has also written about Vox, but I haven't had a chance to read this article, yet:

https://www.currentaffairs.org/2016/11/explaining-it-all

I'll save that for later. /via Frank Pasquale & Scott Smith.

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The GRIM test is meant for measures that return integers. It proceeds by testing if the reported mean times the reported number of participants results in an integer, and if it doesn't then if the closest integers could have been properly rounded to the reported mean. In other words, it is a basic arithmetic check.

The thing that blows my mind is that about half of the psychology studies that had integer measures sampled from leading journals for this paper can't pass this test. How do people even make these mistakes? Why even do statistics at this point if the numbers are just for show?

/cc +Adam J Calhoun, +Adam Elkus, +Sergio Graziosi

The thing that blows my mind is that about half of the psychology studies that had integer measures sampled from leading journals for this paper can't pass this test. How do people even make these mistakes? Why even do statistics at this point if the numbers are just for show?

/cc +Adam J Calhoun, +Adam Elkus, +Sergio Graziosi

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A few years ago, I asked a question about if Bertrand Russell understood Godel's incompleteness theorem. It had seemed to me that he had written little or nothing about it, yet Godel is seen as the final nail in the coffin for logicism. Shortly after I asked, +Niel de Beaudrap and others pointed me to evidence that Russell did engage with Godel's work, but under some misinterpretations.

Yesterday, George Chen gave a new answer which pointed to that I asked the wrong question. I should have asked: "Did Godel understand Russell's work? Or did he slay an imaginary Principia?" Chen suggests it is the latter, and that Godel did not properly understand or engage with Russell's theory of types. Unlike Wittgenstein and Ramsey, who critiqued Russell while showing an understanding of his work.

Very interesting. And gives me a greater respect for and more interest in Bertrand Russell. I might have to read more about this and summarize in a blog post for #TheEGG.

Yesterday, George Chen gave a new answer which pointed to that I asked the wrong question. I should have asked: "Did Godel understand Russell's work? Or did he slay an imaginary Principia?" Chen suggests it is the latter, and that Godel did not properly understand or engage with Russell's theory of types. Unlike Wittgenstein and Ramsey, who critiqued Russell while showing an understanding of his work.

Very interesting. And gives me a greater respect for and more interest in Bertrand Russell. I might have to read more about this and summarize in a blog post for #TheEGG.

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Tonight on #TheEGG, I finally finished my review and comments on +Cathy O'Neil's

There were a few more comments I wanted to make, mostly on rhetorical strategy (heavy focus on single person anecdotes) and lack of strong anti-capitalist statements, but I decided that the post was getting too long both by word count and my delaying.

Maybe I will follow up with more later. How does this square with your reading of the book +David Basanta?

I would also recommend this book to +Alexander Yartsev and +Sergio Graziosi.

*Weapons of Math Destruction*. The book was a joy to read, and I hope it reaches many.There were a few more comments I wanted to make, mostly on rhetorical strategy (heavy focus on single person anecdotes) and lack of strong anti-capitalist statements, but I decided that the post was getting too long both by word count and my delaying.

Maybe I will follow up with more later. How does this square with your reading of the book +David Basanta?

I would also recommend this book to +Alexander Yartsev and +Sergio Graziosi.

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Today on #TheEGG, I built a minimal model of treatment resistance that allows for the benefit of drug holidays. Might be of interest to +Alexander Anderson, +David Basanta, +Jacob Scott, and +Robert Vander Velde.

Apparently, this is my 200th post on TheEGG (of a total of 239) and it comes the day after the blog turned 5 years old!

Apparently, this is my 200th post on TheEGG (of a total of 239) and it comes the day after the blog turned 5 years old!

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After lots of egging on, mostly from +David Basanta and +Jacob Scott, I have returned to twitter. If you are a fellow tweep then please help me refind the great community I remember from before. Who should I be following?

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Last night on #TheEGG, I explored some metaphors for philosophical argument. In particular, I touched on argument-is-war, argument-is-therapy, argument-is-gift-exchange, and my favorite: argument-is-midwifery. This is a much delayed follow up to a post by +Catarina Dutilh Novaes on the topic.

/cc +Sergio Graziosi, +Abel Molina, +Alexander Yartsev

/cc +Sergio Graziosi, +Abel Molina, +Alexander Yartsev

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I forgot to share this this when it was hot off the press, but last week +David Basanta, +Jacob Scott, +Robert Vander Velde, and I released our latest preprint on the evolutionary games of cancer.

Here we introduce the double goods game for modeling acidity as a public good for all cancer cells, and oxygen from vasculature as a club good for non-glycolytic cancer cells. In this preprint, we focus on the case of linear goods, showing that our game has an internal equilibrium that one might not expect from previous analyses of the games in isolation. The dynamics in this case are (almost) identical to the optional public goods game (with the glycolytic cells as loners, and the slope of the acidity benefit function as their reward). The three possible dynamics regimes also have important consequences for treatment, in particular when it comes to scheduling concerns like timing, duration, and order.

If you prefer blog posts then this recent post has an overview of much of the content of the paper:

https://egtheory.wordpress.com/2016/07/14/double-goods-dex/

If you still don't feel comfortable citing blog posts in your papers, but wanted to cite some of my work from TheEGG, then look at the appendices of this recent paper. What you want to cite might be there.

For those that prefer arXiv to the bioRxiv: http://arxiv.org/abs/1608.00985

If you have any comments on the work then please let me know. Either in the comments here, on the blog, or through email.

Here we introduce the double goods game for modeling acidity as a public good for all cancer cells, and oxygen from vasculature as a club good for non-glycolytic cancer cells. In this preprint, we focus on the case of linear goods, showing that our game has an internal equilibrium that one might not expect from previous analyses of the games in isolation. The dynamics in this case are (almost) identical to the optional public goods game (with the glycolytic cells as loners, and the slope of the acidity benefit function as their reward). The three possible dynamics regimes also have important consequences for treatment, in particular when it comes to scheduling concerns like timing, duration, and order.

If you prefer blog posts then this recent post has an overview of much of the content of the paper:

https://egtheory.wordpress.com/2016/07/14/double-goods-dex/

If you still don't feel comfortable citing blog posts in your papers, but wanted to cite some of my work from TheEGG, then look at the appendices of this recent paper. What you want to cite might be there.

For those that prefer arXiv to the bioRxiv: http://arxiv.org/abs/1608.00985

If you have any comments on the work then please let me know. Either in the comments here, on the blog, or through email.

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