Feed-forward motifs in transcription factor networks evolved to filter out spurious signals? ‘Just-so’ no longer

Biosystems Analytics

Mechanistic computational models, particularly rule-based stochastic models, are a vital complement to wet-lab experiments (and a vital chunk of our work at Amber Biology), but can also provide insights into evolutionary processes. In a paper just published in Nature Communications, the team, which included Kun Xiong, myself, Mark Siegal and Joanna Masel, asked whether a particular 3-node feed-forward loop motif (specifically the type 1 coherent FFL, or C1-FFL, widely hypothesized to have evolved to filter out spurious signals, actually evolved for that purpose. Due to it’s overrepresentation in the transcriptional networks of many species, and it’s demonstrated function in filtering out these signals many researchers have previously accepted a kind of ‘just-so’ account of the feed-forward motif. To test this hypothesis properly, we built a detailed stochastic model of the dynamics of transcriptional networks, and then allowed the network to evolve under selection for the function, and without…

View original post 103 more words

Advertisements

Resisting cheaters will be the big challenge for “platform cooperativism”

The promise of the Internet as a means to “level the playing field’ has seriously gone off the rails. A two-day conference at The New School that just wound up this last weekend, explored the emergence of platform cooperativism.  Platform cooperativism aims to return the democratic promise of the Internet away from the rapacious, heavily-leveraged extractive models of the so-called “sharing economy” such as Uber and AirBnB, and towards models of true user ownership and governance.  As pointed out in a set of 5 summary essays that appeared in The Nation, these are not (mainly) technical challenges but legal and political ones.  An example is FairCoop:

FairCoop is one among a whole slew of new projects attempting to create a more democratic Internet, one that serves as a global commons. These projects include user-owned cooperatives, “open value” companies structured like a wiki, and forms of community-based financing. Part of what distinguishes them from mainstream tech culture is the determination to put real control and ownership in the hands of the users. When you do that, the platform becomes what it always should have been: a tool for those who use it, not a means of exploiting them.

Many of these efforts will face an uphill battle, and as pointed out by Astra Taylor at the conference (she follows Douglas Rushkoff’s presentation in the video link), will probably be fiercely resisted by the newly entrenched platforms of Google, Facebook and the like.  But we can also say the same thing about those platforms many of which were just small upstarts back in the 1990s. The real challenge is one that is familiar to evolutionary biologists in game theory: building systems that reduce the chance of “invaders” or “cheaters” (in this case, rapacious VC firms and super-capitalism in general) from swamping a population of mutually beneficial co-operators (or turning those cooperators into cheaters). It doesn’t have to be, and could never be, perfect: you’ll never reduce the population of cheaters to zero, but at least keep them from taking over your population completely.

Read more about platform cooperativism at The Nation

Volvocine algae relationship status: “It’s complicated”

Biosystems Analytics

800px-Mikrofoto.de-volvox-4Volvox are green algae that can form large and amazingly beautiful colonies of up to 50,000 cells, and have been widely studied as a model for the evolution of multicellularity, but they also have a huge diversity of mating systems.   Matthew Herron has a great post over on his blog, Fierce Roller (which focuses on the the biology of volvocine algae and evolutionary mathematical models amongst other things), about the unusual and complicated world of Volvox sex, direct from the the Volvox 2015 conference.   For those of us who work mostly on model organisms, it’s good to be reminded that these organisms are just the tip of the proverbial evolutionary iceberg, and that there are many great practical and conceptual discoveries awaiting all over the tree of life.

Volvox, and the volvocine algae in general, are well known as a model system for the evolution of multicellularity and cellular…

View original post 158 more words