Vort.org, now with Erlenmeyer

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.

Posted by Russell Neches

on 17/06/2014 at 23:50 under a Creative Commons Attributuion License.

Computing as a liberal arts degree

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 :

• 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

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.

Posted by Russell Neches

on 11/08/2013 at 07:42 under a Creative Commons Attributuion License.

The saga of the space plates

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

Posted by Russell Neches

on 29/04/2013 at 04:30 under a Creative Commons Attributuion License.

LA Natural History Museum doesn't grok citations

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.

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.

Posted by Russell Neches

on 18/03/2013 at 08:25 under a Creative Commons Attributuion License.

My papers, for Aaron Swartz

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.
P. A. Gourdain, S. C. Cowley, J. N. Leboeuf, and R. Y. Neches. Physical Review Letters, 97(5), August 2006.
doi:10.1103/PhysRevLett.97.055003

Posted by Russell Neches

on 14/01/2013 at 07:49 under a Creative Commons Attributuion License.

Makers do not make weapons

Last Tuesday, I started writing an article about Thing 11770 on Thingiverse, a MakerBot Industries for sharing 3D printable objects. Thing 11770 is a reinforced 3D printable lower receiver for an AR-15 assault rifle. This is the part of the gun that feeds bullets from the magazine into upper receiver, which handles the cycling of the spent round and the insertion of the new round. With the right combination of upper and lower receiver, fresh rounds are cycled into the weapon using a portion of the kinetic energy from firing the previous round. When the trigger is pulled, this process happens continuously, firing one bullet after another. That is what it means to be an “automatic” weapon. Thing 11770 is particularly interesting because, legally speaking, the lower receiver is the gun itself. It is the engine that makes the gun a gun, rather than a movie prop. And you can 3D print it. And it works.

At very the moment I was hemming and hawing over how to articulate my feelings about this development, someone used an AR-15 to murder twenty seven people, including twenty children, ages six and seven at Sandy Hook Elementary School. Now I know exactly how I feel.

I love 3D printing. I love the maker movement. I love the idea of people building home-brew versions of all sorts of devices, and inventing entirely new classes of devices. 3D printing has played, and will continue to play, an important role in that.

When I was fourteen, like many boys at that age, I thought missiles and fighter planes and tanks were pretty awesome. I read a lot of Tom Clancy books, and I indulged in my interest by dragging my family to the Wright Patterson Air Force Base Museum, the Smithsonian Air & Space Museum, the California Science Center’s Air & Space Museum, and the Intrepid Air, Sea & Space Museum. At Wright Patterson, I visited the F-117 Nighthawk as many times as I could. The author of Thing 11770 calls himself “Have Blue,” the codename for the Nighthawk demonstrator aircraft.

When I was sixteen, I went to boarding school, where I learned vector calculus and farming. I learned how to grub potatoes out of the freezing ground in the driving rain, how to make maple syrup, how to lay in beets and squash and onions for the winter. I stood on a windy mountain top and learned how to find the orbital ephemera of a comet. I learned how to milk cows, how to care for cows when they are sick, and how to make the most delicious yogurt and mozzarella cheese you could possibly imagine. I learned how to repair a tractor engine with a mallet and a wrench. One freezing night, I found myself covered in blood and shit and urine and fear as I helped bring a new life gasping and staggering into the world.

Farming also means slaughtering and butchering. One morning, I walked into the barn. I was handed a weapon. I was asked to take a life.

I found that I could not.

Not ever.

The instant my shoulders took up the weight of the strange, snub nosed machine, it felt like the weight of the metal hung from my heart, stretching and distorting it. I wanted the weight of it to tear me apart, but I knew it was a weight I could carry, if I wanted to. I quietly handed the gun back to the farm manager, and walked out into the thawing snow, and spent the rest of the black pre-dawn puking into the mud behind the water tower.

Many people have wondered why I do not eat meat. This is why. For the rest of my life, I will feel the weight of that terrible little machine.

There are reasons to make, to have and to use guns. To defend your country, yes. To humanely put down an animal before butchering it, perhaps. For vainglory? For entertainment? No.

Tools are sacred things. We are a tool-using species; our tools are projections of our hopes and aspirations. When we are filled with joy, we pick up our tools and hammer the air into music. We need to understand and to be understood, and so we shape our voices into language. We send our tools delicately probing into the bodies of our loved ones, seeking out cancers and blood clots and infections. We invest huge amounts of effort building and maintaining tools that allow us to speak to one another across great distances. We hurl our tools across the void to other planets to satisfy our craving for knowledge. When we grieve, we take up our tools and carve the names of those we have lost into the living rock of our planet. Our tools are our souls. They are our defining characteristic. Love may be what makes us alive, but our tools are what make us human.

A gun is a tool. It is a simple tool. Any man or woman or child can use one. A gun is not much more complicated than a can opener, and not nearly as sophisticated as cordless screwdriver. Like all tools, a gun reveals something fundamental about its maker, its wielder and its abuser. This is true for all weapons.

As a strong supporter of the maker movement, of free and open source software, of open science, I want people to have as much freedom as possible to make and remake and experiment. I also believe very, very strongly in the responsibly we have to one another. I believe that we each have a responsibility not make things that hurt and kill and destroy.

I am not yet prepared to call for a law to prohibit Have Blue from posting functional 3D printable assault rifle parts on the internet. The law is a blunt instrument, and would cause a great deal of collateral damage. However, I am prepared to say that Have Blue is a fucking asshole. I am prepared to call Justin Halford, who created the original CNC model, a fucking asshole. I am prepared to say that anyone who considers themselves a “gun enthusiast” and is older than about sixteen needs to grow the fuck up. The maker community should not tolerate this behavior. Meditate on the meaning of the word antisocial for a moment. What could be more antisocial than gleefully proliferating machines whose principal function is murder?

The maker community should not tolerate these designs, or the ideas and opinions of their designers until they show evidence of behaving like adults. It’s clear that the CNC Gunsmithing community has a lot of talented, clever people. It’s clear from reading his blog that Have Blue is neither ignorant nor stupid.

So, I’m calling you folks out. There are twenty children dead in Connecticut. Their bodies were ripped apart by the very machines you are “democratizing.” As far as I know, nobody has used your designs to kill anyone. If you continue down this path, some future version of Thing 11770 will be used to murder little children. It’s just a matter of time, and probably a lot less time than you think. However, there is still time to take a stand. Do the right thing. Take down the designs. Apologize for what you’ve done. Find a new project. Use your talents for something good. This will not stop people from murdering children with 3D printed guns, but perhaps you can buy us some time before that day comes. You know that this is true.

If making home-brew assault rifles is really what you want to do, there is perhaps one venue where this might actually make sense. Freight your CNC machine to Istanbul, and smuggle it into Homs or Aleppo. Help the Free Syrian Army get rid of Bashar Assad. Oh wait, what’s that? You don’t want to get shot? Fancy that.

It takes courage to admit you are wrong. Show us some courage.

Update : It appears that MakerBot has decided to remove Thing 11770 from Thingiverse. If you follow the link to the item, the files have been removed and a message says, “This Thing is currently under moderation for violating the Thingiverse Terms of Service. Files and images for this Thing are currently unavailable.” I’m glad it’s no longer up, but I am disappointed in how this was handled. I’m disappointed that MakerBot left it up for so long, but I’m also disappointed that Have Blue didn’t just take it down himself.

Posted by Russell Neches

on 17/12/2012 at 18:58 under a Creative Commons Attributuion License.

A new Prometheus

One year ago, UC Davis law student Megan Glanville was killed a stone’s throw from my front door. She was crossing the street for a morning run. It was foggy. The driver didn’t see her.

Since then, the intersection where she died has been redesigned. It is now a three-way stop with modern LED lighting. Watching over the scene, there is a new flashing red beacon.

This sort of infrastructure is easy to take for granted. As a Commissioner for the City of Davis, I suppose I pay closer attention to these things that most people do. I’ve payed particular attention to this little piece of city infrastructure because I pass through it several times a day.

Something has changed there since the red beacon went up. Up and down the boulevard, for almost a mile, there are crossings to access the bicycle path. Drivers now stop and let me cross. They never did that before. I am not exaggerating when I say that wherever the beacon’s light falls, the feel of the street has changed. It’s no longer the tail end of a lonely country road. It’s a neighborhood street, and people act accordingly.

I would like to think that drivers feel the significance of the flashing beacon. I would like to think that they have noticed that the intersection has been redesigned. I would like to think that they know that Megan Glanville died there. In all likelihood, they are oblivious to these things. They stop and smile and waive me through anyway.

Why?

Good design matters. That’s why.

The rocky ledge runs far into the sea,
And on its outer point, some miles away,
The Lighthouse lifts its massive masonry,
A pillar of fire by night, of cloud by day.

Even at this distance I can see the tides,
Upheaving, break unheard along its base,
A speechless wrath, that rises and subsides
In the white lip and tremor of the face.

And as the evening darkens, lo! how bright,
Through the deep purple of the twilight air,
Beams forth the sudden radiance of its light
With strange, unearthly splendor in the glare!

Not one alone; from each projecting cape
And perilous reef along the ocean’s verge,
Starts into life a dim, gigantic shape,
Holding its lantern o’er the restless surge.

Like the great giant Christopher it stands
Upon the brink of the tempestuous wave,
Wading far out among the rocks and sands,
The night-o’ertaken mariner to save.

On a superficial level, a flashing red beacon is a utilitarian thing. If you look more closely, you will see that it is also a thing of beauty. It is an avatar of the compulsion we all feel to protect, to warn, to guide. The humble beacon is one of the better angels of our nature, sculpted with massive limbs of galvanized steel and eyes of electrically exuberant gallium phosphide. It sends our message out into the world, again, and again, and again.

be careful

be careful

be careful

be careful

be careful

Posted by Russell Neches

on 08/12/2012 at 02:33 under a Creative Commons Attributuion License.

Why doesn't your lab have a 3D printer yet?

Electrophoresis setups are like Tupperware. You can never find the right lid when you need it, and someone always seems to be borrowing the doohicky you need.

Here in the Eisen Lab, it turns out we’ve been using Marc Facciotti’s electrophoresis stuff for years. He keeps his stuff organized, and, well… that’s not been our strong suit lately. John, our lab manager, has been gently but inexorably herding us towards a semblance of respectability in our lab behavior. As part of this, he decided that it was time for us to get our electrophoresis stuff straightened out. So, he ordered a bunch nice of gel combs from one of our suppliers. They cost $51 each (see the “12 tooth double-sided comb”, catalog number 669-B2-12, for the exact one pictured below). We bought six of them with different sizes and spacing, for a total exceeding$300.

While I appreciate that companies need to make money, this is a ridiculous price for a lousy little scrap of plastic. $300 for a couple of gel combs is cartel pricing, not market pricing. Fortunately, we happen to have a very nice 3D printer. It is very good at making little scraps of plastic. So, I busted out the calipers and tossed together some models of gel combs in OpenSCAD. A few minutes of printing later, and the$51 gel combs are heading back to the store.

Here’s the code for the six well 1.5mm by 9mm comb :

f=0.01;
difference(){
difference(){
union(){
cube( [ 80, 27, 3 ] );
translate( [ 5.25, 14.3, f ] ) cube( [ 68, 9.3, 7.25 ] );
}
for ( i = [ 0:5 ] ) {
translate( [ 17.1+i*11.0, -f, -f ] ) cube( [ 1.75, 12, 5 ] );
}
}
union(){
translate( [ -f,   -f, -f ] ) cube( [ 7,  12, 7] );
translate( [ 73+f, -f, -f ] ) cube( [ 7,  12, 7] );
translate( [ 0,    -f, 1.6] ) cube( [ 80, 12, 8] );
}
}

Pretty easy to grasp, even if you’ve never seen SCAD before.

So, how much did this cost?

I ordered this plastic from ProtoParadigm at $42 for a kilogram. That’s about four pennies a gram. Each of these gel combs cost about 21 cents to print. That’s 1/243rd the price. The 3D printer cost €1194.00 ($1524.62), which is less than the laptop I use for most of my work. The savings on just these gel combs has recuperated 18% of the cost of the printer.

It’s also important that I was able to make some minor improvements to the design. The printed combs fit into the gel mold a bit better than the “official” ones. I also made separate combs for the 1.0mm and 1.5mm versions, and the labels are easier to read. If I wanted, tiny tweaks to my SCAD file would let me make all sorts of fun combinations of thicknesses and widths that aren’t available from the manufacturer. So, these gel combs are not only 1/243rd the price, but they are also better.

If you read the media hype about 3D printing, you will undoubtedly encounter a lot of fantastical-sounding speculation about how consumers will someday be able to print living goldfish, or computers, or bicycles. Maybe so. Maybe not. However, right now, you can print basic lab supplies and save a pile of money.

Buy your lab manager a little FDM printer and hook them up with some basic CAD training. Yes, the printer will probably mostly get used to make bottle openers and Tardis cookie cutters. So what? Your paper-printer, if you will excuse the retronym, mostly gets used for non-essential stuff too. I’d wager that for every important document printed in your lab, a hundred sheets have gone to Far Side cartoons and humorous notices taped up in the bathroom. It’s a negligible expense compared to the benefits of having a machine that spits out documents when you really need them, and the social value of those the Far Side cartoons probably sums to a net positive anyway.

Conclusion : If you have a lab, and you don’t have a 3D printer, you are wasting your money. Seriously.

In the time it took write this post, I printed \$150 worth of gel combs, and it cost less than a cup of coffee.

Updates : Here is the tweet I originally posted about this article, before the URL for it vanishes into Twitter’s memory hole. Here’s an encouraging post from the Genome Web blog, and a nice article by Tim Dean at Australian Life Scientist. My article here seems to have spawned a thread on BioStar. Also, it made Ed Yong’s Missing Links for November 24 over at Discover, and Megan Treacy did a really spiffy article over at Treehugger.

Many people have asked, and so I decided to see how well these kinds of 3D printed parts do in the autoclave. I tried it out with a couple of bad prints, and they seemed to hold up just fine after one or two cycles. Very thin parts did warp a bit, though, so I recommend printing parts you plan to autoclave nice and solid. Here is a before and after of a single-wall part (less than half a millimeter thick). I was expecting a puddle.

Posted by Russell Neches

on 20/11/2012 at 06:30 under a Creative Commons Attributuion License.