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…

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The Institute for Globally Distributed Open Research and Education: IGDORE

Biosystems Analytics

Over on the Ronin Institute blog, I recently conducted an interview with  Rebecca Willén of the Institute for Globally Distributed Open Research and Education (IGDORE) one the Ronin Institute’s  Fellow Travelers: organizations share some common goals, approaches or philosophy with the Ronin Institute.

Rebecca Willén

In this interview, I asked Rebeccca about the motivations for founding IGDORE, discuss what “New Academia” is all about and our changing academic cultures . [This is a edited version of our conversation. Full disclosure: I am an affiliated researcher with IGDORE].

Tell me a bit about IGDORE?

IGDORE stands for the Institute for Globally Distributed Open Research and Education. It’s an independent institute I founded in 2016, directly after I had finished my PhD.  It’s a virtual research institute, just like Ronin. We have one non-virtual facility and that is on Bali in Indonesia.

What motivated you to…

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The Ronin Institute at Performing the World in NYC

Biosystems Analytics

Reposted from my Ronin Institute blog post

Performing the World (PTW) is a biennial conference with a focus on building communities, social change and performance. This year it is being held in New York City on September 21-23. Here’s the description from the conference website:

Since the first PTW in 2001, the conference has been a gathering place to explore and celebrate performance as a catalyst for human and community development and culture change. PTW is now a global community of hundreds who creatively engage social problems, educate, heal, organize and activate individuals, organizations and communities, and bring new social-cultural-psychological and political possibilities into existence.

Building on the conversations started in the related CESTEMER meeting  last year, several Ronin Institute Research Scholars will be holding a session “Performing New Models of Scholarship at the Ronin Institute” at 5:15pm on Saturday afternoon. I’ll be joining Research Scholars 

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Revisiting the gig economy: a Labor Day post

Biosystems Analytics

Reposted from my Ronin Institute blog post

The Ronin Institute’s Research Scholars are drawn from many different career stages, levels of experience and backgrounds, and given that we don’t advocate a single model of a career in scholarship (in contrast to the traditional academic pipeline), it isn’t surprising that Research Scholars explore many different means to support their scholarship (we are still analyzing the results of the independent scholarship survey we did last year, but this much is clear). For many Research Scholars who are also freelancers, especially those in the sciences, one common means of support is being hired for short or long-term projects by academic institutions, private companies or non-profit organizations. This may be in in full-time or part-time capacity as an independent contractor or consultant. Ideally these projects utilise the scholars’ unique research background and skills and the experience and skills gained during consulting activities will…

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Scientific “ecosystem” paper now published in F1000 Research

Biosystems Analytics

I’ve previously blogged about our PeerJ Pre-print on moving away from the dominant metaphor of the scientific enterprise as “pipeline” leading to professorial positions in universities, towards a metaphor of diverse “ecosystem”. The paper has now been published in F1000 Research and has already garnered one peer review:

Lancaster AK, Thessen AE and Virapongse A. A new paradigm for the scientific enterprise: nurturing the ecosystem [version 1; referees: 1 approved]. F1000Research 2018, 7:803
(doi: 10.12688/f1000research.15078.1)

One the major points of the paper is that we need to move away from the currently closed system that emphasizes artificial scarcity (e.g. in journal spots), towards a system that emphasizes abundance, and we feel that publishing in journals that use post–publication and transparent peer review (like F1000 Research) helps us “walk-the-walk” as we build those new ecosystems.

Table 1 from the paper reinforces this point: illustrating the contrasting language between…

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Nurturing the scientific ecosystem: new preprint

Biosystems Analytics

The debate about the future of the independent scientific career has become arid and sterile, focusing almost entirely on accessing tenure-track jobs in universities (often collectively referred to as the academic “pipeline”). An unstated assumption of much of the discussion is that “early career” scientists who wish to become “independent” must either adapt to this rigid pipeline or “leave science” (or move to yet another career “pipeline”) and that a permanent position in the academic hierarchy should be the ultimate goal.  It is also taken almost as axiom that all changes must be driven by senior leaders in a top-down manner within existing scientific institutions. This seems unlikely given that the status quo disproportionately benefits those in senior positions, as well as extremely slow, given the glacial pace of institutional change.

We need a vastly enlarged conception of the future of science. Myself and Ronin Institute colleagues, Anne Thessen and Arika…

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Beyond the “alt-ac”

Biosystems Analytics

Reposted from my Ronin Institute blog post

As scholars, we are constantly negotiating our relationships to our field(s) of study and to our job titles. In the sciences, a PhD can remain a “physicist” whether in a professorial job in a university, national lab, or industry

But what of the humanities? If an anthropologist with a PhD is not employed as an academic in a university, are they any less an anthropologist? For many traditional academics it is almost inconceivable to remain a scholar without being either in a tenure-track position, or on the road to one. The number of people willing to take poorly paid adjunct positions to stay on the treadmill is testament to the persistence of this idea, and even in the sciences the culture is slow to change as we’ve noted previously. Twitter and the blogosphere is overflowing with discussions of “alt-ac”.

In a…

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