Open Science and Its Discontents

My first post on the Ronin Institute blog:

Open science has well and truly arrived. Preprints. Research Parasites. Scientific Reproducibility. Citizen science. Mozilla, the producer of the Firefox browser, has started an Open Science initiative. Open science really hit the mainstream in 2016. So what is open science? Depending on who you ask, it simply means more timely and regular releases of data sets, and publication in open-access journals. Others imagine a more radical transformation of science and scholarship and are advocating “open-notebook” science with a continuous public record of scientific work and concomitant release of open data. In this more expansive vision: science will be ultimately transformed from a series of static snapshots represented by papers and grants into a more supple and real-time practice where the production of science involves both professionals and citizen scientists blending, and co-creating a publicly available shared knowledge. Michael Nielsen, author of the 2012 book Reinventing Discovery: The New Era of Networked Science describes open science, less as a set of specific practices, but ultimately as a process to amplify collective intelligence to solve scientific problems more easily:

To amplify collective intelligence, we should scale up collaborations, increasing the cognitive diversity and range of available expertise as much as possible. This broadens the range of problems that can be easy solved … Ideally, the collaboration will achieve designed serendipity, so that a problem that seems hard to the person posing it finds its way to a person with just the right microexpertise to easily solve it.

Read the rest at the Ronin Institute blog


A spring surprise: computational analysis unearths potential prions in plants

Biosystems Analytics

With warm weather finally kicking in in New England, it was nice to get a Spring surprise in the form of a new paper on prions seeing the light of day.  Prions are particular kind of protein that propagate by imbuing an altered shape, or “confirmation”, on other proteins of the same type.  They essentially act as a kind of protein “zombie”, and there has been some speculation that they may support a kind of “memory function” due to their ability to transmit state across generations.  Prions were first discovered in the context of diseases like scrapie and variant Creutzfeldt–Jakob Disease (vCJD) but have shown up in all kinds of unexpected places, such as yeast and possibly – providing the aforementioned Spring suprise – plants.  Scientific American has a nice blog post on a recently-published study  from the Whitehead Institute, authored by Sohini Chakrabortee, Can Kayatekin, Greg…

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The limitations of Big Data in life science R&D

Biosystems Analytics

Big Data has become an increasingly large presence in the life science R&D world, but as I have blogged about previously, increasingly larger datasets and better machine algorithms alone, will not leverage that data into bankable knowledge and can lead to erroneous inferences.  My Amber Biology colleague, Gordon Webster has a great post over on LinkedIn leavening the hype around Big Data, pointing out that analytics and visualizations alone are insufficient for making progress in extracting knowledge from biological datasets:

Applying the standard pantheon of data analytics and data visualization techniques to large biological datasets, and expecting to draw some meaningful biological insight from this approach, is like expecting to learn about the life of an Egyptian pharaoh by excavating his tomb with a bulldozer

“-omics” such as those produced by transcriptomic and proteomic analyses are ultimately generated by dynamic processes consisting of individual genes, proteins and other molecules…

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Table of contents preview for Python for the Life Sciences

Biosystems Analytics

book-coverOur Amber Biology book Python For The Life Sciences is now nearing publication – we anticipate sometime in the early summer of 2016 for the publication date. As requested by many folks we are releasing the first draft of the table of contents.  If you’re interested in updates you can sign up for our book mailing list.  You can also checkout a preview chapter on Leanpub.

Python at the bench:
In which we introduce some Python fundamentals and show you how to ditch those calculators and spreadsheets and let Python relieve the drudgery of basic lab calculations (freeing up more valuable time to drink coffee and play Minecraft)

Building biological sequences:
In which we introduce basic Python string and character handling and demonstrate Python’s innate awesomeness for handling nucleic acid and protein sequences.

Of biomarkers and Bayes:
In which we discuss Bayes’ Theorem and implement it in Python, illustrating in the…

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Where is this cancer moonshot aimed?

Biosystems Analytics

Much has been made of the recent announcement of VP Biden’s cancer moonshot program.  In these days of ever tightening research funding, every little bit helps, and the research community is obviously grateful for any infusion of funds.   However, large-scale approaches to tackling cancer have been a staple of funding ever since Nixon announced his “War on Cancer” back in the 1970s, and any new approaches must grapple with the often complicated history of research funding in this area.  Ronin Institute Research Scholar, Curt Balch, has a interesting post over on LinkedIn breaking down some of these issues.

What seems relatively new in this iteration of the “war”, however, is a greater awareness of the lack of communication between different approaches to those working on cancer.  Biden has specifically mentioned this need and has pledged to “break down silos and bring all cancer fighters together”.  This…

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Hollywood’s take on Wall Street: The Big Systemic Corruption

The Big Short is just about the best film I’ve seen in quite a while. It’s as if Guy Ritchie and Michael Moore took some coke together and decided to make a film about the almost-complete financial meltdown of the world.  Based on Michael Lewis’ 2010 bestseller, it delves deeply into both the mechanics of the crash and the mentality that drove us there.  It doesn’t pander, isn’t emotionally overwrought and gives just about the best explanation that I’ve heard of a synthetic CDO thanks to Selena Gomez and behavioural economist Richard Thaler.


The casting is spot on with Steve Carrell giving an amazing career-defining performance.  It has a fast-based, but not overly hyper-kinetic style, and is leavened through with a kind of gallows-humour, as expected given director Adam McKay’s background in comedy.  It’s also a film that treats the underlying ideas seriously, but it also never feels too complicated and plot-driven, no mean feat for a director. 

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From The Secret River to Stan Grant’s debate

The current longest non-stop flight in the world is the Qantas route from Sydney to Dallas: 14.5 hours in the air in an Airbus A-380.  A couple of weeks ago I was sitting on  that Airbus flipping through the inflight entertainment system in that semi-catatonic state that all long-haul flights seem to induce, when I stumbled across an intriguingly-titled television series: The Secret River.  It turned out to be a two-part mini-series originally broadcast by the Australian Broadcasting Corporation based on a novel by author Kate Grenville.  The blurb promised an exploration of an emancipated convict in the early days of the colony of New South Wales, carving out a new life on the Hawkesbury River (the Secret River of the title).

I thought to myself, this seem promising, and settled back expecting a mildly diverting period piece about early Australian history that I had never seen dramatized.  I imagined it might be a little dry and slow, but would have great images of the bushland that I was familiar with growing up (the Hawkesbury is just a 20-30 minute drive away from where I grew up), I was interested to see how the producers recreated the early Australian colony, and at the very least it would while away about 3 of the remaining hours until touchdown in Dallas.  Instead I found myself watching a graphic and unsentimental depiction of the often brutal confrontation between the early European settlers and the indigenous people, the Australian Aborigines.Read More »