Russell's Blog

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Computing as a liberal arts degree

Posted by Russell on August 11, 2013 at 7:42 a.m.
I never really fit into any of the various educational programs I've attended. I've spent a lot of time thinking about what's wrong with them, because I know, of course, that there isn't anything wrong with me.

I see five big problems with higher education :

  • We draw too bright a line between "technical" and "non-technical" degrees
  • We design courses around departments instead of topics
  • We do a terrible job of integrating hands-on experience
  • We structure courses and evaluations in a strictly linear, pipeline-like way
  • We do an criminally bad job of caring for students' mental and emotional health
Biology students learn about cell culture and PCR, but they rarely have a chance to actually do these things. Computer science students learn about microprocessors, but never build one. Engineering and physics students learn about ballistics, but never actually get to try it in any meaningful way. Labs are always almost always afterthoughts, and connect poorly to the rest of the curriculum.

I would like to see at least a few colleges scrap the idea of traditional bachelors of science degree, and instead offer a liberal arts style degree focused on science and technology. I would like to see them mix in a heavy dose of practical trade-school style instruction. Get students into machine shops and out into the woods, and let them get their hands dirty. The spine of every kind of degree should be structured around history. Only history can lend any sort of coherent narrative to a big topic. Last of all, there absolutely must be some way of avoiding the classes-grades-classes-grades treadmill. The hectic academic schedule of classes and grades promotes toxic mix of self-loathing and narcissism and severely punishes any sort of reflection. There are better, easier ways of organizing instruction and evaluating students.

This is my curriculum for a liberal arts degree in technology and computing. Someone with this degree would be prepared to begin a masters degree in an engineering or technical field, but it is not intended to provide any sort of "workplace" training (although it doesn't discourage it). It would also serve as a strong base from which to purse a Ph.D. in a wide variety of topics, and would better prepare students to operate as independent researchers. In that sense, it's a liberal arts degree, not a bachelors of science. Personally, I think this would be vastly superior to any existing undergraduate science or engineering degree, both for people who go on to pursue advanced degrees and people who do not. Really successful undergraduates wind up constructing an experience something like this for themselves. Everyone would be better served if we simply made it official.

Evaluations would be based on the student's portfolio. Each of the sixteen classes would be designed around the creation of tangible artifacts that would go into the portfolio. The quality and imagination of the artifacts would determine the grade for the unit, and would be set by a panel of faculty assembled for the review. Faculty reviews of each portfolio would be archived and made available to the student. Artifacts may be replaced by the student at any time and the portfolio resubmitted for evaluation. Graduation occurs upon a positive evaluation of a complete portfolio.

The curriculum might take a bit longer than four years to complete. I would address this by offering admission to students around sixteen or seventeen years old, and select faculty with the necessary skills for mentoring adolescents. Regardless of age, the admissions process would include a formal psychological evaluation to establish the emotional preparedness of the student to engage in the program. I would would also include mandatory counseling for all students throughout the program; student who are doing emotionally well would use it as career counseling and to help them grapple with their intellectual and aesthetic priorities.

I would also encourage students to take vacations and breaks, and advise and organize these breaks through the counseling services. For struggling students, these would be no-fault opportunities to collect themselves and address personal issues. For others, they would be opportunities for internships, travel and other projects. Organizing evaluations around student portfolios would benefit both struggling and excelling students; breaks in instruction could be used to shore up specific weak spots, or to create artifacts of superlative quality.

The portfolio structure would also make it less risky to include younger students. If it is determined that a student is not emotionally prepared for college, he or she can be placed into an associated high school but continue attending the program part-time, and then re-join as a full time student once they graduate from high school. The portfolio structure would also prevent young students from rushing through the program without reaching the appropriate level of emotional and intellectual maturity deemed necessary by the faculty. It would provide a fair mechanism for the faculty to push precocious students to direct their efforts at achieving quality rather than speed.

I've also included a few topics and activities that most university programs would probably deem inappropriate, particularly related to weapons and warfare. I've done this because I think too many engineers and scientists fail to truly appreciate the destructive aspects of technology and do not develop a mature understanding of how their work is used. There is simply no getting around the fact that much of our technology is directly connected to the business of fighting and killing.

To address this, the program would require students to build, use and study weapons and their uses. This would include using stone tools to make spears, and then learning how to hunt with them, using basic metalworking to build simple firearms, and then conducting target practice on a ballistics range, and building vehicles such as sailboats and drones and using them to conduct mock battles. The scenarios would be designed to evoke questions about history and ethics, and the coursework would include studies on those topics. To make this work, the faculty would need to include military historians. This is an aspect that is totally missing from extant engineering and science curricula.

Freshman Year : Origins

History 1, Origins of Computing : A review of counting systems from different cultures, how "everyday" mathematics was actually carried out by ordinary people in ancient Greece, Rome and China. A review of early record keeping and writing technologies from Cuneiform to punch cards.

Literature 1, Origins of the Written Word : A review of the historical and linguistic development of early writing systems and technologies from each continent.

Theory 1, Foundations of Logic and Philosophy : Deductive and inductive reasoning in mathematics and rhetoric, with applications to geometry, number theory and argument.

Practicum 1, Mathematics, Writing Systems and Technologies of the Ancient World : Students will learn and perform the basics of many of the key technologies of the ancient world :

  • Stone toolmaking
  • Working bronze and copper
  • Ironworking and steel toolmaking
  • Writing in clay, papyrus, stone, wood and metal
  • Jeweling
  • Weaving
  • Weapons
  • Glass blowing
  • Ceramics
During freshman year, all transactions with the university will be carried out using contract devices of the ancient world. Meal plans will be tabulated with tally sticks, tuition and aid and Work Study with Cuneiform in clay, and books supplies and sundries using abacus and ancient Chinese coinage.

Sophomore Year : Empiricism

History 2, Birth of Computing : The invention, use and theory of the Jacquard loom. Charles Babbage and the first mechanical computers. Ada Lovelace and the concept of stored programs. Use of early mechanical computing in industry, navigation, civil society and warfare. Galileo, Newton and Darwin and the birth of Empiricism.

Literature 2, The Spread of the Written Word : The origin of modern writing systems, scripts, materials and technologies. The scroll, the codex and the library; the printing press and the Gutenberg Bible; movable type, the Enlightenment and the American and French revolutions; the cryptographic systems of the Napoleonic Wars; the development of scientific reasoning in the Enlightenment and before.

Theory 2, Foundations of Algebraic Reasoning and Empiricism : Set theory and the synthesis of algebraic systems, with applications to algebra, calculus and physics. Physics will emphasize thermodynamics, and treat kinetics and mechanics in the context of heat engines. Introduction to empirical reasoning and with emphasis on the design of controlled experiments.

Practicum 2, The Technologies of the Early Modern Age : Students will construct and and operate the technologies of the early modern age :

  • Casting type and printing
  • Drafting and technical drawing
  • Machining in steel and brass
  • Making and breaking early cryptographic systems
  • Mechanized textile manufacturing
  • Techniques of mass production
  • Printing at large scales
  • Theory, construction and operation of steam engines
  • Firearms
  • Sail power
Students will transact their business with university using double entry ledgers.

Junior Year : Science & Engineering

History 3, The Science of the Three World Wars : The impact of steam power on naval and land battles of World War I; the birth of aviation; The Manhattan Project; the cracking of Enigma and Purple; the first modern computers and their uses; the computing of the Apollo Project; balistic missiles and space exploration; the Soviet computer industry; the invention of transistor and the integrated circuit; the Age of Moore's Law; the United States v. Microsoft Corporation; Linux and the Free Software movement.

Literature 3, Science Fiction and Fact : A review of the science fiction of the 19th, 20th and 21st centuries; case studies on the works of Jules Verne, Issac Asimov and William Gibson. A review of popular science literature and science journalism; Thomas Huxley, Issac Asimov, Carl Sagan. An introduction to the scientific literature; the case of Newton vs. Leibniz, Einstein's 1905 papers, Watson & Crick and Roseland Franklin; modern controversies in the literature. Seminars on research methods and archival practices.

Theory 3, The Language of Computing : The Turing and von Neumann concepts; the principles of computer languages; algorithms and data structures; numerical methods in mathematics and physics; statistics, statistical mechanics and quantum mechanics.

Practicum 3, Modern Computing Technologies : Students will construct and operate a selection of key contemporary technologies, with an emphasis on computing :

  • Lasers, optics and radio
  • Imaging
  • Microprocessor design
  • Mechanized and digital typesetting technologies
  • Semiconductor manufacturing
  • Computing languages
  • Building compilers and interpreters
  • Device drivers
  • Networking
  • Digital signal processing
  • Operating systems internals
  • Real time computing
  • Industrial design and CAD/CAM
Students will transact their business with the university using networking technologies. The university will provide a machine readable interfaces to services, and the students must construct their own software solutions to interact with them.

Senior Year : Here & Now

History 4, Contemporary Issues in Science, Technology and Society : Climate change; poverty and development economics; alternative pathways for economic development; medicine and disease; renewable energy.

Literature 4, Communicating in Writing, Speech and Art : Practical instruction on rhetoric, writing style and visual design.

Theory 4, Topics in Science and Engineering : Focused seminars on technical topics to support Practicum 4.

Practicum 4, Capstone Project : Students will work individually or in small teams with faculty mentors on projects of their own design.

The university will endeavor to minimize direct administrative contact with students during senior year, and instead mediate through their faculty mentors.

Arduino in the lab, example 9,345,234

Posted by Russell on June 10, 2013 at 6:23 p.m.
Last week, my friend Emily at Pivot Bio was debugging some crazy protocol she's working on, and she was wondering if her incubators were maintaining correct temperature. So, we decided to find out.

For my own project, I happen to have a bunch of Arduino hardware. So, I threw together a quick solution based on Adafruit's thermistor tutorial (I have a bunch of thermistors sitting around). Here is Emily's setup, complete with masking tape junctions and protoboarded electronics :

A few hours later, and she's got a pretty good answer to one of science's oldest and most important questions : "Is this thing even working? WTF, man?" Here's the data collected at 1Hz with a one minute moving average :

I'm not sure what those wobbles around hour two are from. Hopefully someone just opened the door or something. Arduinos really are the Swiss Army Knife of the laboratory!

Nominating openSNP for the ASAP Award

Posted by Russell on June 05, 2013 at 1:28 p.m.
So, there is this awesome new thing called the Accelerating Science Award Program (ASAP), which recognizes individuals who have used, applied, or remixed Open Access scientific research to create something new and cool. I can't think of a better example of remixing Open Access science than openSNP.

Here is my nomination.

Information About the Innovative Use

Describe the innovative use of scientific research published through Open Access you would like to nominate.

openSNP uses Open Access scientific research in several ways :

  1. It is itself and Open Access, user contributed dataset.
  2. It provides information about particular genetic variants through an innovative mashup of user contributed data with several other resources :
    1. SNPedia, a user created Open Access dataset that functions as a namespace for individual genetic variants (SNPs, or single-nucleotide polymorphisms) and a clearinghouse for references to the scientific literature relating to each SNP. Example and publication.
    2. PLOS, a major Open Access scientific publisher, is automatically scanned for references to each SNP. References and readership statistics are aggregated on for each SNP. Example.
    3. Mendeley, a social bookmarking and sharing site for scientific literature, is automatically scanned for papers containing references to each SNP. References and readership statistics are aggregated for each SNP. Example.
    4. The Personal Genome Project, an Open Access effort to improve genome annotation, is automatically scanned for data relating to each SNP. References are aggregated for each SNP.
    5., the NIH-sponsored site for the National Human Genome Research Institute, is automatically scanned for data relating to each SNP. References, associated traits, and statistical confidence intervals are aggregated for each SNP. Example.
  3. BioDAS, a Open Access, distributed annotation protocol, is used to generate contextual, annotated visualizations of each SNP from DAS servers running worldwide, including those provided by the European Bioinformatics Institute, Ensembl, the Sanger Institute, UCSC, WormBase, FlyBase, TIGR, and UniProt.

Describe why you believe this work should be recognized.

openSNP serves more than one community. It is a community where the public can come to learn about and discuss their own health issues. Within that community, it allows people who are brave enough to step forward and share their genetic and health data for the benefit and education of the rest of the community. The community has been designed to encourage sharing of data with other users, which includes the scientific community. These activities have created a dataset that allows researchers to conduct genome wide association surveys (GWASs) inexpensively and largely free of the complexities usually associated with research involving human subjects.

There are other efforts that aim to accomplish similar objectives, but the creators of openSNP have taken what I feel is the most intellectually honest position. They accomplish this in two ways. First, they offer no pretense of privacy to people who elect to share their personal genomic data, and instead provide a clear warning of the real and potential hazards. Second, for those who choose to share their data despite this warning, they maximize the public good it can achieve by making it truly accessible. Data contributed to openSNP is indexed, annotated, linked, referenced, sorted and shared in as many ways as possible, making the contributions of participants as meaningful as possible.

Last of all, the creators of openSNP and its many contributors have elected to share everything they have produced under the least restrictive license possible. The entirety of this effort has been donated to the Public Domain. I strongly believe that this commitment to the common good deserves to be recognized.

For this reason, I think it is important not only to recognize Bastian, Helge, and Helge, but also the 1019 other people who have contributed personal data to openSNP. Bastian has also contributed his own genotype.

P.S. -- Others involved in openSNP may include Fabian Zimmer and Julia Reda.

Information About the Original Research

Please provide links or citations/references/DOIs to the articles, manuscripts, or datasets pertaining to the original scientific research published through Open Access on which the nomination for the innovative use is based, so that we may locate these online.

There are probably hundreds of thousands of publications referenced, indexed or linked from openSNP, far too many to enumerate here. Please see the links I have provided as various examples under "Information About the Innovative Use."

Bastian, Helge and Helge, as well as Fabian Zimmer and Julia Reda, are preparing a manuscript for submission describing openSNP. It is another measure of their commitment to Open Science that the progress with this manuscript can be viewed (and forked, and contributed to) among their public GitHub repositories.

LA Natural History Museum doesn't grok citations

Posted by Russell on March 18, 2013 at 8:25 a.m.

Earlier today, I received a request to use one of the photographs I've posted on Flickr. I get a lot of these requests, and I always find them a bit annoying; I release all of my photographs (and writing, including this blog) under a Creative Commons Attribution license.

I would be delighted if people emailed to say, "Hey, thanks for letting me use your photo! Here's a link to what the thing I'm using it for." Even that isn't strictly necessary, since I always notice the inbound referrals from the attribution links. The whole point is that you don't need to ask permission because you already have it, provided you give proper attribution. So, as usual, I tried to explain this concept, and got an interesting answer.

Hi Russell,

Thanks for your email. That's neat to hear that you have a connection to the Museum.

Yes, I did notice that your photo was offered under a Creative Commons license. In the case of this particular video, however, we are crediting contributors by name only (ie "Credit: Russell Neches". That is one of the reasons why I contacted you directly, to see if you would be willing to waive the standard CC attribution requirements.

If it is ok to only credit using your name, please let me know. Your credit will appear on the image itself. We are also looking to label each photo with the location where the image was taken. Based on the tag, I assume the Opossum image is from Pasadena. Please correct me if I am wrong.

Look forward to hearing from you.

Thanks again,

Sam Easterson

Sam Easterson
Senior Media Producer, Nature Lab
Natural History Museum of Los Angeles
900 Exposition Blvd.
Los Angeles, CA 90007

Wait, he wants me to waive the CC-BY license just so they can avoid actually linking to the original photo in the credit? That doesn't make a bit of sense. Yes, I want credit for my work, but that's not why I licence under CC-BY. Even if something is in the public domain, nobody has the right to plagiarize from it, and an author can and should expect their public domain works to be properly credited. You can copy it, and you can cut it into bits, rearrange the bits, paint the whole mess orange and trade for a silly hat. However, you cannot claim you created the original, because, well, you didn't. That would be fraud.

The reason I use CC-BY instead of Public Domain is because it requires anyone using my work to provide useful attribution information. This is basically the same standard of attribution used in science. Scientists have to cite the work of others in such a way that the reader can actually identify and obtain the cited material for themselves. It's about access, not just credit.

So, I try to explain...

Ah, I see. Well, I suppose I should explain myself then.

The reason I release my photos under CC-BY rather than Public Domain is because I believe it is important that the practice of traceable attribution be extended to new circumstances. It is important because it is often very important that people be able to ascertain where a particular piece of media came from. For example, they may wish to find related materials, or they may wish to independently verify its authenticity. This is why standard citation formats in research papers are so important. Giving credit is necessary, but not sufficient. The reader must able to actually access the source material, or they aren't really in a position to exercise judgment.

Now, I understand that this can be awkward when you're outside the traditional media formats where there is an acknowledged code of conduct for citations. There isn't yet a "standard" way to include citations in a slideshow, or in a dance performance, or in an opera, or in a sculpture. It's easy to imagine how doing it badly could mar the work.

Nevertheless, I think it needs to be attempted. The Natural History Museum is the sort of institution that is most likely to actually get it right and to set trends that others will follow. Everything in the museum has to meet pedagogical, scientific and aesthetic goals. It's one of the things that makes science museums so awesome.

I think developing some best practices for incorporating traceable citations into a mixed media installation is perfectly in keeping with that. After all, you're not using these images to sell toothpaste. You're using them to teach the public about science and nature. One of the most important practices in science is making sure the audience has direct access to the sources. Science regards the audience as peers, not as consumers.

Now, I'm not designing the exhibit, so I'm not going to insist on any particular design solution for providing links. I'm sure you can think of something that will work wonderfully, and won't be much trouble.

I can also imagine how an exuberant use of citations could make the exhibit like what you're describing extremely awesome. For example, a smartly-designed footer on each image with a scientific name, common name, time, location and a QR code link. Patrons could say, "Ooo! What's that?" and snap a photo with their phones, and be taken to a page with lots and lots of details about the organism and the source image. That's not necessarily what you should do, but perhaps you see what I mean about why citations are important? They make media more awesome!

As for the furry fellow in the picture, I found these guys in Eaton Canyon after their mother had been killed by a coyote. The ranger gave the babies to me, I suppose, because she didn't want them to be eaten by hawks in front of a school group on the hiking trail. They stayed at my mom's house in Pasadena for a few weeks until they were big enough to eat and do opossum-y things, and then I released them back into Eaton Canyon. The photo was taken in her backyard.


I was hopeful that this would click. There tons of easy things they could do to house the links. They could make a page on their website somewhere that said "attributions page for exhibit X" with a list of photos and attribution links. It would just take a few minutes, and it would be useful.

But alas, no.

Thanks for your email Russell. I very much appreciate your thoughts.

Unfortunately, in this case, I'm not going to be able to accommodate your request.

I'm sorry that I won't be able to include your image in the slideshow after all. My apologies for taking up your time.



Think about this here. He says, "I'm not going to be able to accommodate your request." Remember who's requesting what here. He really means, "I'm not going to be able to comply with the terms of your license."

So, I'm pretty disappointed. I don't care if they use my photo or not. I get thousands of views already. My photos get used for lots of things, including a couple of elementary school science textbooks in developing countries. The publishers didn't have any problem putting a link next to my name.

No, I'm disappointed that the Los Angeles Natural History Museum doesn't seem to understand why citations are important.

My papers, for Aaron Swartz

Posted by Russell on January 14, 2013 at 7:49 a.m.
This past Friday, I was enjoying a dinner party with some friends in Brooklyn. Elsewhere in Brooklyn, Aaron Swartz, a fellow I have long admired, hanged himself after two years of being stalked, bullied and harassed by those we employ to Serve and Protect. He was being prosecuted for downloading a bunch of academic papers. Papers to which he had legal access, and whose content was overwhelmingly funded by taxpayers. His "crime" was that he downloaded a lot of them, although the publisher imposed no particular limit on how many he could download, and that he downloaded them from a network he perhaps didn't have permission to use. The "victims," JSTOR, the publisher, and MIT, the owner of the network, were not the least interested in pursuing either a civil or criminal case against Aaron.

Perversely, the Department of Justice and the Secret Service thought otherwise. The US Attorney's Office was about to go to trial with charges that would have resulted in thirty years of imprisonment were Aaron convicted, but I can't imagine that Aaron hanged himself because he was afraid.

Aaron was a patriot and a humanitarian. He was dedicated to the work of delivering a dose of integrity to the institutions of democracy, even as those very institutions crushed him for... for what, exactly? Sport and amusement, it seems. The People's case against Aaron Swartz, as represented by US attorney Carmen Ortiz, only makes sense if the People are sadistic bullies. It's hard not to wonder if Carmen Ortiz was planning to run for elected office, and if so, it's impossible to see Ortiz' case against Aaron as anything other than a cold-blooded gambit for future campaign donations from the media and publishing industries. Aaron's destruction was to be a signal that Carmen Ortiz is tough on piracy. Grist for the mill of our perfectly-legal political corruption.

That's not paranoia. That's politics in America. Aaron was deeply committed to healing the necrotic tissues of America's democracy. Over the last two years, reading about the case against him absolutely boiled my blood, but it must have broken Aaron's heart. Perhaps he despaired that America can be saved from the rot, or could no longer withstand the pain and humiliation of being so ill-treated by the republic he cared so much about.

As my tribute to Aaron, I've downloaded all of my own papers and posted them here. Since joining Jonathan Eisen's lab, I've been publishing in Open Access journals, and so the two most recent papers are perfectly legal for me to post here. The first three were written before I worked for an advisor who understood what is really at stake in scientific publishing, and so they are not open access. Here they are anyway. For Aaron.

  1. Functional biogeography of ocean microbes revealed through Non-Negative matrix factorization.
    Xingpeng Jiang, Morgan G. I. Langille, Russell Y. Neches, Marie Elliot, Simon A. Levin, Jonathan A. Eisen, Joshua S. Weitz, and Jonathan Dushoff. PLoS ONE, 7(9):e43866+, September 2012.
  2. A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq.
    Elizabeth G. Wilbanks, David J. Larsen, Russell Y. Neches, Andrew I. Yao, Chia-Ying Wu, Rachel A. S. Kjolby, and Marc T. Facciotti. Nucleic Acids Research, February 2012.
  3. The convergence of analytic high- equilibrium in a finite aspect ratio tokamak.
    R. Y. Neches, S. C. Cowley, P. A. Gourdain, and J. N. Leboeuf. Physics of Plasmas, 15(12):122504+, 2008.
  4. Stability of highly shifted equilibria in a large aspect ratio low-field tokamak.
    P. A. Gourdain, J. N. Leboeuf, and R. Y. Neches. Physics of Plasmas, 14(11):112513+, 2007.
  5. Stability of highly shifted equilibria in a Large-Aspect-ratio tokamak.
    P. A. Gourdain, S. C. Cowley, J. N. Leboeuf, and R. Y. Neches. Physical Review Letters, 97(5), August 2006.