As I sit here on the redeye flight to an airport named for an assassinated president, most of the televisions embedded into the headrests of the passengers who remain awake are tuned to cable news, and most of cable news is tuned to Charleston. The face of the man who brought this latest slaughter among us sneers from among the shadowed ranks the darkened cabin. I want to look away, but there is nowhere to turn where his face will not suddenly leap out at me.

The screens strobe between cut after cut of pundits talking to each other in split-screen. White face after white face, explaining. Black faces, silent. A montage of the victims, also silent. More white faces, explaining. Occasionally, a black pundit is asked a question. White faces receive the response, and continue explaining. Commercial break. White actors pitch drugs for chronic conditions and financial services; it’s hard not to infer the expectation of a white audience. A high-production-value sequence begins. A white face explains in simple words, emphasized with animated typography and diagrams, what a hate crime is. A Sesame Street segment from our nightmare world.

Like a lot of people my age, I don’t get my news from the television. I don’t own one, and I don’t have cable service. What am seeing right now is obscene, and shocks me.

A man walked into one of the most historically important black churches in the United States. He was welcomed in by the people he found there. He talked with them for an hour. Then he slaughtered them, leaving one alive to tell the rest of us what his reason was. Those are some of the facts. Now, the television is crammed with white people explaining it.

There is an obvious conflict of interest. Human beings are seldom able to see themselves as anything but the good guy. When you stand on the diagram of culpability, it is human nature to experience an overpowering impulse to kick sand over any line that links you to evil. It will shape how you see things and how you explain them. This impulse is called shame. Those who fall under its shadow cannot be trusted to behave normally.

By his own words, the murders were carried out on behalf of all white people. If you are not black, please be quiet right now. It is not your turn to explain. It is your turn to listen and, if you can withstand it, to reflect.

As a biologist with a 3D printer, one of the questions I get most often about 3D printed parts is, “Can you autoclave these things?” As it turns out, no, not really. There are only a handful of thermoplastics that can survive the autoclave process, and most of them are not very good for 3D printing. With few exceptions, only polypropylene and blends of polypropylene hold up to repeated autoclave cycles, and polypropylene is, unfortunately, very a difficult material to print. It shrinks a lot when it cools, which causes a lot of warping during printing, and it is very difficult to get molten polypropylene to bond strongly to cooler, solid polypropylene.

It turns out that this is all unnecessary. Fused deposition modeling (FDM) 3D printing involves shoving a rod of thermoplastic into a hot nozzle until it melts and squirts out the nozzle. For most popular 3D printing plastics like ABS and PLA, the nozzle temperature is somewhere between 180C and 260C, and the plastic stays at that temperature for around a minute, depending on what the toolpath looks like. It’s actually a lot like Pasteurization, except way overkill. Get it? Overkill?

Anyway, here’s how FDM 3D printing compares to various Pasteurization (in black) and autoclave (in red) protocols :

enter image description here

Earlier this year, I was wondering about this, and my friend Emily Tung convinced me to just try it. So, on her advice, I heated up the nozzle of my 3D printer to 220C and placed a beaker of sterile liquid LB media under it. I then extruded some plastic until the blob fell into the media. I then incubated it, along with a positive an negative control, at 37C until… well, until nothing. Only the positive control (a short length of raw plastic feedstock) grew anything.

enter image description here

I tweeted this little experiment as it went along, and suddenly I had two collaborators, Kaitlin Flynn in Michele Swanson lab at the University of Michigan, and Luis Zaman in Richard Lenski’s lab at Michigan State University. Kaitlin immediately started suggesting different growth conditions I should try, and Luis, who also has a 3D printer, replicated all of my experiments and invented new variations to try. Because Kaitlin didn’t have a 3D printer of her own, Luis and I 3D printed a bunch of little test parts for her to try out, and mailed them to her. In her spare time, Kaitlin tried culturing the parts under all sorts of different conditions, including with mouse macrophages.

The results are detailed in our new paper On the intrinsic sterility of 3D printing, which is now available as a PeerJ PrePrint as of yesterday.

The tl;dr is that yes, 3D prints are sterile after printing. They are not sterile after touching them with your fingers or dropping them on the floor.

I’ve been thinking a lot (and writing a little) about road safety for several years. The catalyst for this was an accident that nearly killed my sister while she was riding her bicycle in Norman, Oklahoma. The driver was on the wrong side of the road, but couldn’t tell because of the mind-bendingly poor quality of Norman’s street design. Not long after I came to Davis, I witnessed a pretty nasty accident on Russell Boulevard, and wrote about it here. The response to that blog post got me involved in the long-simmering debate over a proposed re-design of the Fifth Street/Russell Boulevard corridor. To me, the debate seemed to hinge on a factual question regarding the frequency and severity of accidents, and so I did some data analysis of city-wide accident reports to satisfy my own curiosity. Well, maybe more than just my curiosity. It’s pretty damned personal to me.

I suppose my data-centric approach made it possible for me to open a dialog with the Davis Chamber of Commerce. Once the business community and activists were able to communicate their concerns to one another, it turned out that the substantive disagreements were not very disagreeable after all; the Chamber’s biggest concern was that in the original design, as proposed, the left turn pockets were too small. I signaled that the activists wanted a general concept: A two-lane design with bike lanes and left turn pockets. As long as the Chamber was willing to roll with that, the details were mostly a matter of law and necessity. Within the general two-lane concept, whatever variations were legal and physically possible would likely be acceptable to the pro-redesign camp. The preliminary design was approved shortly after, with the support of the Chamber. Later on, this lead to my appointment to the City of Davis Safety and Parking Advisory Commission, and later to the new Transportation Advisory Commission. If only all political fights would boil down to misunderstandings, and if only opposing parties could get what they want by arranging the details just so. Alas!

As a commissioner, I’m proud to have been involved in several modest improvements to the street design in Davis. We’ve scrutinized speed limits and moved lane strips around. We were also among the many quarters that called for the City’s swift re-design and signalization of the Russell/Lake intersection and the similar Pole Line/Moore intersection after the death of UC Davis law student Megan Glanville. In the background, though, the Fifth Street Project has preoccupied us throughout my term as a Commissioner.

Well, if you’ve been downtown in the last few days, you’ve probably seen the new signals, the new lines and crosswalks. Fifth Street is no longer a four lane road on which it is suicidal to bicycle and dangerous to cross. It is now a normal, two lane road with left turn pockets and bike lanes. It’s actually quite wonderful.

The new Fifth Street

Expect traffic to move a little more slowly on the new street, but with fewer and abbreviated complete stops. The time it takes to get from one side of downtown to the other should be a few seconds less, despite the slower speed – even in heavy traffic. You will have to slow down, but you will spend less time waiting. It should feel a little bit less “busy.” Of course, it won’t be perfect. Road designs are always compromises. This new design is simply a compromise that better fits the needs of the people who use it.

I am proud that I can finally say, “Go ahead, ride your bike on the new Fifth Street now.”

Welcome to the new Vort.org! After much fussing about, I’m finally migrating away from my old blogging platform and officially re-launched. I’ve built a new blogging tool specifically designed for science. It’s called Erlenmeyer. Erlenmeyer is still a work in progress, but even in its current larval instar it is already quite nice to use, especially if you have something to say like

\[ \underbrace{\nabla p}_{\cal{O}(\beta)} + \underbrace{\frac{\nabla B^2_{\mathrm{T}}}{2}}_{{\cal O}( 1 )} + \underbrace{\frac{\nabla B^2_{\mathrm{P}}}{2}}_{{\cal O}( \epsilon^2/q^2)} + \underbrace{\frac{B^2_{\mathrm{T}} \nabla R}{R}}_{{\cal O}(\epsilon)} + \underbrace{B_{\mathrm{P}} \cdot \nabla B_{\mathrm{P}}}_{{\cal O}(\epsilon^2/q^2)} = 0 \]

Erlenmeyer has built-in citation management, so blog posts can seamlessly include a proper bibliography, generated automatically. For example, the equation above comes from a paper I wrote a few years ago. [1] Erlenmeyer also supports a syntax highlighting in a large number of languages.

def findregions( data, N ) :
    """
    Return all the regions of an array that exceed N.
    """
    pos = filter(lambda(a) : a[1] == abs(a[1]), zip(range(len(data)),data-N) )
    if len(pos) == 0 :
        return []
    pos = numpy.array( zip(*pos)[0] )
    regions = []
   for k,g in itertools.groupby( enumerate(pos), lambda(i,x):i-x ) :
        l = map( operator.itemgetter(1),g )
        regions.append( {'start':l[0],'stop':l[-1] } )
   return regions

There’s still a lot of work to do, but at this point, the best way to make sure that it gets done is learn to eat my own dogfood.. There have been a lot of things I’ve wanted to blog about, but I was so annoyed with my software that I didn’t bother with it. So, this is both a return to blogging and a return to web development – now with more Science!

References

1. Neches RY, Cowley SC, Gourdain PA, Leboeuf JN (2008) The convergence of analytic high-β equilibrium in a finite aspect ratio tokamak. Phys Plasmas 15: 122504. Available: http://dx.doi.org/10.1063/1.3008049.

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.

Here is a conundrum. Suppose you want to measure growth rates of bacterial cultures in an aerobic environment, on LB, in 96-well plate format. So, you buy some plates from your favorite supplier, and program them dispense some LB into the wells with a multichannel pipetter, inoculate from whatever your source is, and pop it into your plate reader and start the program.

Now, what do you do if your plate reader was installed upside down? Your media will spill out and get all over the expensive bits inside the machine, and your PI will become sad and despondent. You could perhaps put the plate in upside down too, and that might solve the problem. What if the instrument randomly changes its orientation as the experiment proceeds? Or worse yet, what if the instrument is permanently in free fall? What then, kemosabe?

One would think, I suppose, that NASA has a thing for that. And you would be correct, to a point. The problem is that the thing in question is not ready yet, and the experiment is going ahead without the thing. So, here is your mission, should you choose to accept it : Design a cup that doesn’t spill when it is open.

I must admit I toyed with the idea of 3D printing an array of Klein bottles, but settled on fabricating plates out of acrylic and PDMS. I’m relying on the strong hydrophobicity of PDMS to prevent liquid from entering the ventilation ports.

The International Space Station needs to maintain very strict controls on volatile compounds off gassed from they bring aboard, which means rules out a lot of useful things, like pretty much every glue you can think of. So, another advantage of PDMS is that it is food safe. In fact, it is an ingredient in many cosmetics and foods, including McDonald’s Chicken McNuggets. Now, the idea of eating silicone elastomer, the same material used in the front shock absorber on my mountain bike, may not sound appetizing, but it there is pretty good evidence that it is at least not demonstrably harmful. So, that should hopefully keep us well clear of toxicological issues.

I’ll wrap up with a poem from my childhood.

Three jolly sailors from Blaydon-on-Tyne
They went to sea in a bottle by Klein.
Since the sea was entirely inside the hull
The scenery seen was exceedingly dull.
– The Space Child’s Mother Goose, Frederick Winsor & Marian Parry

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.

Russell

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.

Sincerely,

Sam

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.

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.
   doi:10.1371/journal.pone.0043866
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.
   doi:10.1093/nar/gks063
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.
   doi:10.1063/1.3008049
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.
   doi:10.1063/1.2807024
5. Stability of highly shifted equilibria in a Large-Aspect-ratio tokamak.
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