A Few Arguments for Open Science

graphic by Greg Emmerich

In science, I am sometimes challenged to justify my affection for open source software and open access publishing. The warm, fuzzy feeling, of community ownership and control, is not sufficient to convince people to switch to open source models. Here I reiterate some arguments that open science is morally and ethically favorable.

Scientific knowledge, especially publicly funded knowledge, should be returned freely to society. Sadly, current solutions for allocating funding conflict with this ideal. To fund research, we enforce artificial scarcity using the concept of 'Intellectual Property'. Artificial scarcity allows us to adjust the value of knowledge to match the costs associated with its creation. Intellectual property concerns are similar in academia, industry, and the arts, but I restrict reflection to the area which most affects me : Science.

Academia runs on reputation, and requires accurate attribution of intellectual property. This discourages behaviors that benefit science at large. Collaboration is avoided out of fear that it could cause one to lose ownership of ideas. Data are not shared if there is a possibility that said data cold yield more publications. Useful intermediate results that are too small to publish are kept secret. Techniques may be kept 'trade secrets'. These behaviors are bad for science, but academics are pressured into them to survive. Similar can be said for all industries : protecting a product ensures that the market rewards those who make the original investment, but this problem is not one of free-markets. All economic models must solve the problem of funding the most capable individuals.

Can open science resolve this conflict? Not yet, but it suggests a few immediately useful steps. Resource allocation is simplified when resources are abundant.

• Open science lowers the cost of research by reducing artificial scarcity.
• Open access publishing frees researchers from large, expensive, library subscriptions. 
• Open source scientific software frees researchers from expensive proprietary software. 
• Open source operating systems and software reduces the cost of computing. 
• Open source hardware and small scale fabrication technologies reduce material costs.

When grants no longer support library subscriptions and matlab licenses, the same amount of money can support more researchers, and more research. For theorists, this can mean reducing the cost of research to the cost of living, and university affiliation is no longer a feudal necessity. With these simple steps, we can confine competition for resources to covering the cost of living and physical material costs of experiments.

The remaining costs of competition can be lessened by following an open science etiquette. Share data freely. Let people know what you're working on, if not the details. Publish often so that useful results are not withheld. If you find someone working on a similar problem, collaborate and discuss how to redirect efforts to reduce overlap. Clearly state the nature of contributions to a manuscript. Give attribution liberally, and acknowledge sources of inspiration explicitly. Take advantage of self publishing and non-peer reviewed repositories like arxiv, which, while they do not provide a stamp of legitimacy to the research, preserve attribution. Encourage people to build upon your work, and accept that they have many of the same ideas, goals, and competencies, as you. When someone does an experiment you had planned, be excited that you get to see the results earlier, and talk to the authors to look for possible collaborations and ways to reduce future overlap. There are many interesting problems to solve before we can eliminate anti-collaborative pressures in science.

Open science may be a social good, but can it also be a selfish good? Publishing open access can lead to broader dissemination of your results, bolstering reputation. Releasing code under open licenses provides and opportunity to demonstrate competence, and demonstrates your value to the scientific community. Using open source languages for scientific computing make your code available to students, educators, and outsiders, who would otherwise be unable to use your code. Source code licenses that preserve attribution can improve reputation and awareness of your work. Using open document formats for collaboration creates positive feedback to improve free productivity tools, which will lead to lower costs in the long run.

There is much more to be said on this topic, here and elsewhere. Democratization of science is something that I think about daily and is an ideal that I strive to uphold in my own research as much as I am able.

Musings on the Post-Human Condition

Back in April I wrote a short story for ARC’s fiction contest, that while it didn’t win, was a lot of fun. They have a second contest up about the post-human condition, which has got me thinking seriously about where we’re going, and what we’ll become.

I’m going to start with two axioms
1) A post-human upgrade is about more than seeking a competitive or aesthetic edge, it is about the type of community that you want to belong to.
2) Late-stage capitalism is fucked, along with the ecosystem and 90% of the current population, and everybody with more than three brain cells knows it.

With those premises, what kind of world shakes out?

One option is space colonization, getting off this rock entirely. Now, there are a surprising number of weird cryptic billionaires backing private spaceflight, but this isn’t about sub-orbital hops for tourists, this is about saving humanity, and if you run the number of kilos to orbit per year times the number of years left before the global economy goes kablooie, it’s obvious that there isn’t enough lift for everybody who wants to be saved. Space colonization is inherently incredibly dangerous, and you need the best colonists to have a chance: experts in a variety of technical fields, in peak physical condition, fitting effortlessly into teams, working best under pressure, and with the self-discipline of a Zen master. NASA does this by selecting the best of the best military pilots and starry-eyed scientists, and running them though a brutal training lottery to earn a dwindling number of spaceflight seats, but our program is run by tech CEOs, and they do things differently.

The only best way to run the system would be a meritocratic lottery.  Prospective applicants put themselves under constant technological surveillance to demonstrate that they have the Right Stuff emotionally to make it in the tight confines of a space colony. They master abstruse scientific fields, discipline their bodies with exercise and technology, and talk politics with their fellow Emigrants, trying to build up enough of a rep to qualify for a seat on a rocket out of here. And of course there’s no way a mere human could earn their way in, which is why these people enhance their brains with drugs and cybernetics, harden their body against radiation, reduce their caloric and oxygen intake, and otherwise demonstrate their commitment to the program. The whole system is orchestrated by Sergey Brin, Jeff Bezos, and James Cameron, as they tweak the social scoring parameters on the whole system to cultivate an elite race that can thrive in the empty vastness of space.

It’s easy to imagine what these people look and act like. They spend all their time cooped up learning how to repair solar panels in vacuum and run a closed cycle life-support system, and when they get out of their rooms they argue with their friends about utopia and the end of the world. They think everything on Earth is going to shit, so they don’t care about material possessions or friendship, but they’re also all ambitious and socially adept and self-effacing, possessing a brittle layer of charisma over the zealous flame of the true believer. You can spot them on the street in an instant, thin and pale in their simple black clothing with the logo of the colony they hope to join, expensive electronics discretely recording everything they do, and the same haunted, hunted, look. Immortality awaits them, if they can please their masters.

The second route is to think seriously about what it will take to be in the 10% that survives the collapse of civilization. Part of it is physical: they need to be able to eat anything or nothing at all, because our agricultural system needs cheap oil and constant irrigation and a stable climate to work, and all of that’s going to change. Resistance to disease is critical because refugee camps breed epidemics. Plague is one of the Four Horsemen for a reason. Civilized psychology gets people killed when the savages take over; toughness and a willing to kill those who will try and kill you become virtues. The most important component is social. When the government breaks down, people turn to their primary loyalties, and unlike Somalia or Iraq, most people in the Western World are a long way from authentic tribalism. Losers will try and fake it with fandoms, or their job, or ethnicity, or some other dumb 20th century identity marker, but at the end of the day the survivors will need an unbreakable bond of trust with those who will be watching their back.

They’re out there, running through the woods and practicing martial arts and stockpiling weapons and tools for the end of the world. They pick subtle enhancements sensory and physical enhancements to give them an edge in combat and wilderness survival. They build trust with a combination of the oldest and newest methods, using orgies and designer drugs to bind each other into fighting packs closer than any family. By day, they go about their lives like anyone else, the only difference a certain gleam in their eyes as they calculate what sudden violence could get them in while standing in line at the supermarket, but when night comes, they’ll be ready. They will be the wolves, and everybody else will be the sheep.

Still trying to work out precisely what the story is; who the characters are, and what the tension pivots on, but I have until July 8. As if I don’t have enough on my plate…

Guerrilla Science

Observing various scientific “controversies” over the past few years, I’ve seen a pattern repeated again and again between the scientific mainstream and dissenters. Whether it’s about global warming, a link between vaccines and autism, the safety of GMO crops, or any other issue, the conversation looks pretty much like this.

Scientists: “We have developed the following hypothesis due to a preponderance of evidence, and the scientific consensus says we should enact the following policies.”
Dissenters: “Well, that’s just your theory. What about this evidence which argues something entirely different?”
Scientists:  “That evidence is methodologically and theoretically flawed, and we have dismissed it for scientific reasons.”
Dissenters: “No, you’re dismissing it because you’ve been bought off by Big Pharma/Monsanto/Al Gore!”
Scientists: “Well, you’re anti-science, and you aren’t responsible enough to participate in this debate. Come back when you’re willing to accept the truth.”

And then the two camps go their separate ways: The dissenters to fringe websites where they catalog the corruption of mainstream science and develop their alternative bodies of evidence, and the scientists to letters pages of scientific journals, where they write pleads for better science education and communication, so that science can drive out all the frauds out of the public sphere and we can have rational policies again, like we did in the good old days.

The other thing that I’ve observed while following these controversies is that mainstream science is losing. The American political system has become entrenched around the truth or falsity of anthropogenic global warming, despite an overwhelming scientific consensus that it is happening and it is a problem. Fewer people completely vaccinate their kids each year, even though the original Wakefield study has been totally discredited and disease rates are on the rise. And fears of GMO have become a permanent part of European politics, and a rising force in America and China.

This leads to one of two conclusions: either despite all the calls by respected scientists for more communication and education efforts by the scientific community have been falling short and should be increased, or the conventional framing of the problem is essentially wrong and misleading. I believe it is the latter; that the arena of public scientific debate has changed in recent decades, that the dissenters are “guerrilla scientists” who like guerrilla fighters use asymmetric strategies to avoid the superior strength of their foe, and that to win, mainstream science must find an equally adaptable counter-strategy.

To explain this idea, I’m going to need to talk about science and guerrilla warfare. Please bear with me.

As a PhD student in science and technology studies, one of the biggest questions that we face is “What is science?” There are lots of good definitions: facts about the natural world, systemic knowledge, a method for generating said facts and knowledge and ensuring their reliability using experiment and observation, but all of these definitions conceal the process of how science is made; how specific claims become true facts or false hypothesizes. To understand that process, we need to go inside science, inside scientific writing, and inside the lab. Bruno Latour has developed some of the most powerful lenses on the actual practice of science in his books Laboratory Life and Science in Action.

For Latour, science is a rhetoric; a way of convincing other people to believe your claims. The form of the modern scientific paper has been careful developed to be as convincing as possible. A successful scientific paper integrates itself in a network of previous scholarship, explains how it will extend the results of previous scholars, presents a method that can be duplicated by others, shows results (typically in graphical form), and then discusses those results. I’m going to use as my example a paper by the other author of this blog, “A model for the origin and properties of flicker-induced geometric phospenes”, but any other paper would work just as well.

The paper begins by summarizing the previous work in the field, starting in 1819 and moving through the 1970s and into the present day. The introduction establishes the paper vis-à-vis previous work on the visual system, and a question about the origins of flicker in either the retina or the visual cortex. The method section describes using the Wilson-Cowan equation for modeling flicker in a simulated neural network, how to implement that equation in a computer program, the images that are produced by the model, and finally a discussion of how those images might relate to what happens in the brain and what we can perceive when we close our eyes and press on our eyeballs (or use ze goggles).

At every turn, the paper preemptively parries those who would try to doubt it. “You think that this problem is unimportant. Here are people who have worked on it before me.” “You doubt my math? Write your own program and check my results.” “You disagree with my choice of the Wilson-Cowan equation? Here are 1040 papers that also use it. Do you disagree with all of them?” The paper is structured and linked such that to disagree with it either requires opposing a much larger and more authoritative body of scholarship than “things that Mike Rule, Matt Stoffregen, and Bard Ermentrout say”, or going into their lab, checking that all their machines work, that the graphs in the paper are actually reproducible, and essentially duplicating their effort and expertise.

This post-modernist view of science can be disconcerting at first; what about objective physical reality? What about the search for truth? Has science just become another kind of blind faith, based on appeal to past authority?  No. What Latour tells us is that scientists do not know a priori what is ‘real’ and ‘true’. Those words are only applied to hypothesis after an intense process of purification and examination by the community of scientists that rules out every other possible explanation.

The picture of science that Latour develops is an interlocking network of claims about the natural world, linked into a mutually reinforcing pattern with more accepted claims at the center and weaker claims at the fringes. Science as a totality is like a fractal star fort, defensible from any angle.  But this picture is partial and passive.

The life of science is in active disputes, for example, “What is the structure of DNA circa 1953?” Disputes are opposing versions of reality, and they are only settled by the destruction and absorption of alternative facts and theories into the final ‘science truth’. Actor-Network Theory describe this process as one of enrollment wherein scientists enlist facts, instruments, and people as allies in their cause, with the aim of building the strongest rhetorical network.

Looking at this, it struck me that the contest is much like a battle, with the scientist deploying his or her enrolled facts like a general committing his soldiers. There are many points of congruence between these models: critical questions and strategic points, the ability to generate new results and supply, predictive power and firepower, but they key point is that in science as in war there are rules.

Science has its own kind of Geneva Convention. Not an explicit treaty, but social norms that describe how science should be done, and how the contest should be decided. I’m not going to provide a complete set of norms, but a some of the more important ones might be: results must be reproducible; judge the idea and not the person; cite your sources; do not present others’ work as your own; remain open-minded; accept the accolades of your peers humbly. A scientist whole held onto a clearly discredited theory would not be respected, and it is considered bad form to pillage a rival’s lab and enslave their postdocs.

In action, the difference between mainstream scientists and dissenters is that dissenters don’t play by the rules. Dissenters care more about their personal commitments than the structure of science as a whole. They do not cede the field gracefully if their facts are overturned. And they accept a wider variety of evidence as a basis for their claims, including social, moral, economic, and political factors. They may not be good scientists, their theories are frequently shoddy and mystical, but it is important to recognize that they are engaged in essentially the same kind of work as mainstream scientists: making cause-and-effect claims about the natural world. Calling dissenters ‘anti-science’ implies that scientists should ignore and belittle them as unworthy of serious critique. Calling them guerrillas suggests a very different approach for understanding their aims and engaging with them.

Guerrilla warfare is political warfare. In conventional war, the goal is defeat of the enemy through decisive battle, and strategy is the art of staging the decisive battle on favorable terms. The aim of guerrilla warfare is to demonstrate the political illegitimacy of the people in charge while building popular support for revolution. Strategy is focused on swift strikes to demonstrate the ineffectiveness of the governance and provoke reprisals against the people, the preservation of the guerrilla’s own forces, and the use of time to wear out the enemy’s will to resist. While conventional military firepower is still important in guerrilla war, it is of secondary importance compared to psychological and political factors. In guerrilla warfare, the winner is the side that everybody believes has won; not the side that maintains control of the battlefield afterwards.

Guerrilla warfare is a complicated subject, and no two conflicts are alike, but some common patterns can be drawn. Lt Col John Boyd developed a theory of warfare based on learning systems, and he noticed that as a force slides towards defeat, it becomes isolated and insular, it stops taking in information from the outside world, and is eventually confined to irrelevance. Information and morality are central; as the American military learned in Vietnam in the 1960s and in Iraq in 2003 and 2004, firepower is useless if targets cannot be located, and support can only be gained through demonstrating moral strength and sensitivity. To beat guerrillas, the government must demonstrate its superiority through active policies that improve the lot of the people while avoiding internal corruption. Successful counter-insurgency strategies, such as the Iraq Surge implemented by General Petraeus, aims to isolate guerrillas, to draw wavering fighters back into the government’s camp, and to find and kill the most hardcore commanders who could not be converted.

Combining these two theories, Latour’s Actor-Network Theory and Boyd’s OODA Loop, the shape of the problem and its solution begin to emerge. Scientific guerrillas exist because scientific expertise is a key buttress of democratic decision-making. 21st century American culture is such that a policy must appeal both to the will of the people and an external reality as informed by expert, i.e. scientific, opinion. But science, to put it bluntly, is hard. It requires a long and grueling apprenticeship and then access to expensive and specialized laboratory equipment. And worse from a political perspective, science is not democratic. No matter how many geeks wished that the OPERA neutrinos were truly faster-than-light, that result stubbornly remains an experimental error. It’s far easier to don the guise of expertise when it’s needed to support a policy position than it is to genuinely discover the truth according to the strict rules of science.

In this context, saying that the dissenters need to play by mainstream standards of evidence is like saying that we just need Al Qaeda to put on uniforms, gather around Tora Bora, and have that decisive battle we’ve been waiting for. It’s a fantasy, because it involves convincing guerrillas who are winning to fight a conventional battle that they will surely lose. Science education, science funding, and more public understanding of science are equivalent to sending in more troops, more weapons, more airstrikes. It can stabilize the situation, but it is unlikely to actually defeat the guerrillas.

I worry that science is becoming isolated in a Boydian sense. Scientific papers only cite other scientific papers; most scientists work and live in enclaves around major research universities. There are extremely good reasons for this, from a conventional perspective it generates stronger science, but it has also made science more brittle, less relevant, and less politically legitimate.

Like it or not, scientists have become embroiled in a wide variety of guerrilla disputes on major issues, and I’ve not seen a robust strategy for countering the guerrillas. I love and respect science; it’s the best tool for understanding and improving the world that we have, but it is under attack in ways that most people can’t even see, and is not effectively defending itself. Guerillas can be beaten, but it will require an active strategy of integrity, candor, and two-way communication. The stakes could not be higher. As Henry Kissinger said on the Vietnam War in 1969, “The guerilla wins if he does not lose; the conventional army loses if it does not win.”