Python for the Life Sciences Interviews

Last year, Research Scholars Gordon Webster and Alex Lancaster published Python for the Life Sciences through Leanpub. Last month, Leanpub posted interviews with each of them.

Here’s a snippet of Gordon’s interview, published on Feb 17:

I mean, I think the one thing I would say is that – yes – that lay people do tend to think of scientists as being almost kind of like Mr. Spock – that is logical, and everything is kind of decision making, devoid of all that other human baggage like emotion and ambition and greed and all that stuff.

And the truth is, it’s really still very much a human activity. And the application of the scientific method – there’s this kind of ideal view of it, if you look at the books on the philosophy of science and Karl Popper and all this kind of stuff. There’s this very idealized, sort of Platonic ideal of what the scientific method is. But when you start to combine science and commerce, then all that human stuff, it still plays a role. And honestly, it plays a role even in academic research.

And here’s a piece from Alex’s interview, published on the 21st:

I started life thinking I would be an astrophysicist, basically. It was where I was originally when I was an undergrad. And actually I spent about a week in a radio telescope down in Canberra – a while ago now, shall we say? Another century. And I realized that that wasn’t really going to be it for me for the rest of my life. Astrophysics has changed a lot since, but there was a lot of sitting in very quiet, desolate places, pouring over data, and it sounds very glamorous on the outside – but the reality of the day-to-day just turned out that it didn’t really appeal to me.

So, trying to figure out what to do, I decided to finish my engineering degree, which I started with. But I was always interested in evolution from a very young age, I think [from] when I picked up Richard Dawkins’ The Blind Watchmaker, which was written sometime in the 80s. I was just fascinated with the idea of these biomorphs, which were these little creatures that he had built evolutionarily on a Mac. It was nothing to do with real biology, but it was very – basically you could construct these creatures from this very simple genetic code. And it sort of always stayed with me.

Check out the full interviews, and the book!

Updates to Landry’s Work on Metaphysics

Ronin Institute Research Scholar Forrest Landry‘s essays on Analytic Metaphysics are available at Recently, Forrest has updated some of those essays, converting them to dialog form. Details follow, but Forrest notes that he welcomes comment particularly on the new dialog on the Incommensuration Theorem. So, those of you with an Analytic and/or Metaphysical mindset, have at it!

This is basically the essay, rewritten in dialog form, of a means by which the Axiom Concepts can be arrived at.

This is almost an exact copy of the relevant section of the 2.0 book, converted into web format, so that if you need to refer or cite to someone just (and only) the formal statement of the Axioms, that there is some place on the web where this is easy to read (even on a mobile phone).

This is an almost completely reworked and re-sequenced view of the main aphorism content of the IM 2.0 book, with an emphasis on just either defining or including the base language generally used in various ways in other IM essays, content, etc.  Think of this section as being a fairly minimal and compact Glossary of all of the important IM terms.

The essay of the Incommensuration Theorem (ICT) has been completely re-written as a dialog and is presented freshly completed today.  The dialog covers a number of important topics, and connects them together in a fairly compact and independent manner.  This dialog, at this point, represents probably one of the most useful ‘deep theory results’ to perhaps be offering as a presentation to use on general interest items such as QM/GR reconciliation failure, the hard problem, generalization of Bell/Godel, etc.

Also converted into mobile web presentable dialog format is a basic statement of language correspondence between the modality terms as formally used, and their occurrence within more general public usage.  Technically this is part of the core Glossary.

This URL is being included for completeness, insofar as it is also version 3 content — things edited or updated since the release of the 2.0 manuscript.  Even though it was not written or updated recently, insofar as it defines an important reconciliation of how/why the Axiom II flow dynamics are so composed.  Be advised that this represents some of the most abstract and complex work on the site — not an easy read.

Duerr Chapter(s) in New Book on Curating Research Data

Just published by the American Library Association is Curating Research Data, a two-volume collection edited by Lisa Johnston. Research Scholar Ruth Duerr writes:

Karen Baker and I wrote the first chapter in Volume 1 – Chapter 1. Research and the Changing Nature of Data Repositories.  Karen and I both have a long history with all things data related.  We realized when the call for authors for this book went out, that the academic library community is pretty unaware of the more than 50 years that domain repositories and other such institutions have been dealing with data.  So we thought we’d write this chapter to bring the community up to speed.   It is nice that it was chosen as the first chapter in the section Part I. Setting the Stage for Data Curation. Policies, Culture, and Collaboration.

We also contributed a Case study to Volume 2, Section Step 4.0: Ingest and Store Data in Your Repository entitled “data and a diversity of repositories” just to make the reader aware of the various types of repositories out there…

So check it out!

Battle-Fisher Producing Documentary on Transhumanism

Congratulations to Ronin Institute Research Scholar Michele Battle-Fisher, who will be a co-producer on News2Share’s upcoming film Transhumanism: A Documentary. Here’s the concept trailer:

The project is currently raising funds on indiegogo. Check out the project page to learn more:

On a related note:

Banerjee on International Scientific Collaboration

Ronin Institute Research Scholar Soumya Banerjee has posted a preprint of an analysis of scientific collaboration networks, focusing on patterns of collaboration within and among different nations. He writes that

Our latest article looks at a scientific collaboration network and finds novel patterns and clusters in the data that may reflect past foreign policies and contemporary geopolitics. Our model and analysis gives insights and guidelines into how scientific development of developing countries can be guided. This is intimately related to fostering economic development of impoverished nations and creating a richer and more prosperous society.

More information on the work can be found via the following links:

Paper –

Talk –

Slides –

Code –

Ruth Duerr and Colleagues Win International Data Rescue Award

Congratulations to Research Scholar Ruth Duerr, who accepted the 2016 International Data Rescue Award in the Geosciences on behalf of a team of researchers from multiple institutions. From an article on the award in Eos:

This year’s winning project, “Revealing Our Melting Past: Rescuing Historical Snow and Ice Data,” is an effort to digitize the Roger G. Barry Archive at the National Snow and Ice Data Center (NSIDC) at the University of Colorado Boulder. The archive is a trove of snow and ice data in many formats, including prints; images on microplates and glass plates; ice charts from early expeditions to Alaska, the Alps, South and Central America, and Greenland; and handwritten 19th century exploration diaries and observational data.

“This is a project that is all about rescuing glacier photos that go all the way back to the late 1800s,” said Ruth Duerr, a project team member who represented the group at the award ceremony. “For science, it is giving you a 150-year record of individual glaciers around the world and how they have changed in terms of mass lost or gained; mostly lost,” said ESSI president-elect Duerr, a research scholar in science data management and software and system engineering at the Ronin Institute for Independent Scholarship, which is based in Montclair, N.J.

As also noted in that article,

The award was announced just 2 days after news broke that some other scientists are frantically copying unrelated U.S. government climate data out of their fear that the data could vanish during the Trump administration. That fear is based in the idea that some likely appointees are climate science skeptics.

So, congratulations to Ruth, and to everyone involved in the project! Check out the Eos article for some fantastic photographs that show the dramatic consequences of climate change over the past century.

Help Fund Scans of Dolphin Genitalia

Research Scholar Diane Kelly and her collaborators at Mount Holyoke College are raising money right now to fund CT scans of dolphin genitalia. From the project description at Experiment:

Our goal is to assess the depth of penile penetration during copulation and to explore which anatomical landmarks are in contact and where. The penises of adult males will be inflated with saline and inserted into the vaginas of adult females from the same species. The penises will be inserted as deep as possible to simulate copulation.

After the genitals are CT scanned together, they will be dissected to identify anatomical landmarks (Orbach et al. 2016), which will then be located on the CT scan images. The depth of penile penetration and the points of contact between the male and female genitalia will be identified and compared across species to explore broad patterns of genital coevolution.

So, maybe you’d like to help support some cool marine reproductive biology, or maybe your tastes, like those of Christian Grey, are singular. Either way, visit the project site for some inspiring science and horrifying images.

Ranalli on Thoreau

Ronin Institute Research Scholar Brent Ranalli has had two articles published recently in the Thoreau Society Bulletin. Both also appear on the Society’s blog. The first, co-authored with naturalist Cherrie Corey, seeks to identify the mystery mushroom that Henry David Thoreau describes in his journals as resembling a traditional New England “election cake.” The second uses literary sources to reconstruct Thoreau’s walking gait and asks what the gait reveals about the man.

Better Know a Ronin: Micky von Dassow

Mickey von Dassow is a biologist who is interested in exploring how physics contributes to environmental effects on development and recently joined the Ronin Institute as a Research Scholar.  Here is a edited version of an interview I did with him from last year (full version).

Mickey von Dassow

Can you describe your background?

My background is in biomechanics and developmental biology. My Ph.D. asked how feedback between form and function shapes marine invertebrate colonies. During my postdoc I worked on the physics of morphogenesis in vertebrate embryos, specifically focusing on trying to understand how the embryo tolerates inherent and environmentally driven mechanical variability. Since then I have been independently investigating interactions among ecology, biomechanics, and development of marine invertebrate embryos, as well as teaching courses.

Tell us more about Independent Generation of Research (IGoR) ?

IGoR is a wiki for sharing research ideas, skills, and resources among novice, amateur, and professional scientists. The goal is to make it easier for everyone to do scientific research, regardless of how they make a living.  One of the main motivations was that I often need devices that are just beyond my own skills to make, but which hobbyists with other skills could easily help me make. This got me thinking that I could do more and better science if there was an easy way for me to build collaborations with amateurs who have different skill sets. I also realized I would have much more fun doing science if I had a way to keep doing it whether or not I get the next grant or research job. Amateurs, such as Benjamin Franklin, Charles Darwin, or Grote Reber (the inventor of the radio telescope), used to be major contributors to scientific research. Today’s technologies should make it much easier for people to do science outside of a career, but we need ways to pool people’s talent and experience.

Where do you see “citizen science” going in the next 5 or 10 years?

I should say that IGoR is inspired by “citizen science,” but is a bit different from most citizen science. At the moment, most (but not all) citizen science seems to follow a model in which a few experts design a way to obtain a lot of data by getting many volunteers to do some low-skilled, repetitive task. However, there is a lot of interest in community-generated approaches (such as Public Lab, iNaturalist, OpenROV, and others), and approaches where there is real feedback between professionals and citizen scientists, involving creative and intellectual input from citizen scientists.

How does citizen science relate to the “open-science” movement?

As far as I can tell, the open-science movement seems to be focused mostly on open data and open publication models, but there are a lot of other strands to it. One strand that IGoR is definitely a part of is trying to move away from a status quo in which research is almost all done by people employed as researchers by big institutions. Open science, open source generally, citizen science, and the Maker/Hacker movement, all seem to be pushing against the divide between the professional and everyone else….

Are there particular kinds of research areas or projects that tend to fall through the cracks of traditional funding agencies (NSF, NIH etc.)?

Yes. Funding agencies and universities like high-tech science. If you use a big machine that goes ping to do it, you have a much higher chance of success than if you just need to watch something with your own eyeballs, even if the intellectual merit is the same or better. Funding agencies are also driven by fashion, so in biology anything “omics” is in, and organisms seem to be pretty much out for the moment. Finally, they are not good at funding brand new projects, or new or unknown researchers. For example, researchers often say you need to do the project before you can get funding for it, and then use the funding for the next step. This makes perfect sense: your best bet with limited money is the big lab, with lots of toys, piles of preliminary data, and oodles of publications to prove they can do the job. However, that makes it hard for new researchers, small labs, or people trying new directions. Cutting those researchers out reduces the diversity of research questions and perspectives.

My hypothesis for why “omics” and traditional model organisms dominate (even when there are better ones for particular problems) is positive feedback. If approach or field X is fashionable it will garner higher profile publications and more funding, so people doing X will have more opportunities, and other people will pay more attention to X, hence X seems even more exciting and an even better bet for funding or new hires. But, attention and funding are limited, so the more those go to X, the less they go to everything else. As I write this, it suggests that the answer is to make funding, and also publication visibility, a non-zero sum game. That gets back to finding new ways to support science, and to tell people about it, which encourage diversification of questions and approaches.

What kinds of changes in the institutional structures of science (e.g., peer review, publications, promotions etc.) would encourage more citizen science, open science or independent scholarship?

I think one of the biggest things that academic institutions could do is to teach students that independent scholarship is possible. There will never be enough funding for everyone who wants to do research (and is skilled at it) to make a living doing it. However, we all know that some of the deepest conceptual advances, notably Darwin and Wallace’s theory of evolution, came from people who were not employed as scientists. There are still many of important questions that can be addressed by an individual investigator on a shoestring budget.

So, if we value science (or scholarship generally), we need to create an environment in which research can be an avocation rather than a career. The most important parts of that are to make that choice socially acceptable within the scientific community, and to teach people – starting in undergrad and going through all career stages – how to make it work. There are many resources describing how to succeed in academia (or whatever other career one might choose); but, there are few, if any, guides to doing research successfully when one is not doing it for one’s job.

Are there other new models of doing research, outside of mainstream academic research institutions, that you have seen out there that inspire you?

Community labs are one that excites me a lot, and is an inspiration for IGoR. They could be great for getting novices, amateurs, and independent professionals working together to do substantive research; their main limitation is that they are few and far between. The Ronin Institute aims to create a more flexible approach to being an independent scholar, so that more professional-level scholars can do research. Even simple things like providing an institutional affiliation for applying for grants could be very helpful.

What’s your favourite organism?


Do I have to choose just one? Ctenophores might be it right now. The way they glide through the water with waves of iridescence running down bands of beating cilia, is incredibly beautiful. I love the fact that they coordinate a lot of their motion and sensation using interactions among cilia: a very different approach than most animals. They also have some very cool developmental features. For example, some of them can regenerate half or more of their body as adults, despite the fact that (for the most part) each embryonic cell forms a particular part of the body, and cannot be replaced when lost. There is a point in their development where they gain the ability to regenerate. However, I love lots of invertebrates, and I can’t look at ciliates without wondering why I don’t study them.

Read the full interview