Scientific Methods

Scrapbook for Method Quarterly, a magazine about science in the making. methodquarterly.com

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With my degree in hand and an idealistic dream of making some groundbreaking contribution to TB research in mind, I arrived amidst the chaos of the official opening of the state-of-the-art research facility that had been drawn up by Dr. Walker and the K-RITH steering committee in 2009. The shiny new building quickly filled with brand new laboratory equipment, brilliant scientists from all over the world, precious samples from patients suffering from TB and HIV infection, and a few idealistic recent college grads like me. Between the smart people, the millions of dollars, and the myriad fascinating scientific questions to be answered, it seemed like all of the ingredients were in place for realizing the ambitious vision born six years prior at HHMI. Zuri Sullivan | Seeing the Future of African Science

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In late 1905, two biologists from Clark University — Oris Polk Dellinger and David Gibbs — worked in a continuous relay for six days and five nights to observe several Amoeba proteus in their “daily lives.” Recording their hourly movements, Dellinger and Gibbs tried to discern whether the amoeba’s life patterns fell into the rhythmic ebbs and flows of work and rest — tied to the search and attainment of food — that were the basis for all known animal life. Observed under a microscope, diagrammed in their zig-zagging movements, and photographed landing their prey, the biologists found that the amoeba too exhibited these characteristic patterns. Viewed in the context of their behaviors, Dellinger and Gibbs concluded, the amoeba must be considered a rightful member of the animal kingdom. Much anthropomorphizing ensued. The following quotes and images can serve as a summary of their 1908 paper, “The Daily Life of Amoeba Proteus.“ Azeen Ghorayshi | The Daily Life of Amoeba Proteus

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This kind of making sense of the material world with these radically different representations that come from diverse organisms is critical for making sense of these complex urban ecosystems. They give us this immediate feedback cycle, where we’re not just looking at some sort of blank array of distributed low power sensors. The vision of the “smart city” is that we’ll have these sensors everywhere, electronic sensors that will somehow make sense of things. But we can see that with the battery of what we use to make sense of water quality — dissolved oxygen, turbidity, pH, salinity — even water quality experts can’t tell you what that means. But if the mussels can survive, if they can thrive, or if they don’t thrive, or if their flapping in panic, or if they’re clammed shut and not singing—I trust a mussel more than the data! There can’t be any decimal point errors or recalibration issues when their lives depend on it. So this idea that we can make sense through and with these diverse representations and these non-human organisms and is really part of the story of how you make sense of things in order to act on them, to improve and change our relationship to natural systems. The goal is to redesign this relationship so that we actually can increase biodiversity and increase water quality, using living infrastructure to make these places more habitable. Conversations with Natalie Jeremijenko | "Turning data spectatorship into data full-contact sports"

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Stranger still are those scientists who appear to have known things long before they could possibly know them. Stories of such people are incredibly rare and must be treated with caution. Like that popular misconception, the Eureka Myth, narratives of visionary foreknowledge tend to be apocryphal, presenting discovery as a result of individual insight rather than a process of investigation, calibration, and collaboration. But among the noise, do real visionaries — those who appear to ‘see’ the scientific future — really exist? Simultaneous discovery and visionary foreknowledge hold a special place in the imagination because they appear to defy logic and reason. But humans, not machines, conduct science. And as such, discovery can be organic and surprising, unpredictable and messy. Discoveries are made, not found. If these stories really are true, how and why they happen — and whether they constitute an intrinsic part of scientific research or are a condition of temporally specific contexts — are important questions. But they also make for fascinating stories. Sam Golding | Visions of the Lone Scientific Genius

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A fruit fly develops very quickly. Just three hours after the egg is fertilized, the original single cell has divided 14 times, yielding about 6000 cells. The embryos at this stage look like tiny footballs, with all of their cells on the surface and yolk in the middle. The cells look similar, but they actually already know what part of the body they will become. The DePace Lab | Protocol: Visualizing Gene Expression

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Consider also the “moonshot,” a phrase used today by Google X, the division of Google that explores inventions that would satisfy some larger human dream — not unlike how the Wrights satisfied the urge to fly, and the Apollo missions were the final push of a chain of inquiry stemming back to the earliest astronomers. The phrase means risk, a distant goal, and uncertain payoff outside of a wider, scientific glory. And yet in Google’s context, the phrase now describes self-driving cars and broadband-by-balloon. While both are certainly technological feats, it is difficult to say whether they would usher in a new era of human history. What does the “moonshot” mean to us today, when we are still struggling to get back to the moon? Why aren’t Google X’s “moonshots” actual, literal moonshots? Adam Rothstein | The Greatest Thing Since Sliced Bread: Snowclones and the History of the Next Big Thing

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But it’s not just what climate scientists say that’s important, it’s what they do—in the field, in the lab, and in conversation with other scientists. The allegations of fraud made against climate scientists during Climategate made it clear that members of the public hold widespread assumptions about what is “normal” scientific practice. But except for climate scientists themselves, very few people actually know about the process of climate science “in action”—how scientists build climate models, how they interpret data, and how they interact with other relevant groups in society. Meritxell Ramírez-i-Ollé | The Social Life of Climate Science

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A polemical cottage industry runs on religion, naturalism, and the war between their houses. All the same, many men and women worship on weekends and return, come Monday, to telescopes, spectrometers, and flow cytometers. Often this requires some clever compartmentalization: imagine particles caught in crisscrossed electromagnetic fields of the kind used to isolate antimatter, as if allowing science to touch faith would produce an especially energetic kaboom. In that spirit, William Saletan pointed out in Slate last year that while Young Earth Creationism can’t pass scientific muster, some Young Earth Creationists do leave belief at the laboratory door. But for other researchers, faith is never especially far from the front burner. The most striking are probably those who practice—for a living—both Catholicism and astronomy: the stargazers of the Holy See. Grayson Clary | The Pope's Planetologists

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“I was trying to find ways to compare other people’s structures,” Jane said. “The entire first year or two [at Duke] was just learning how to do those drawings. So it was very gradual. I’m not an artist. I can’t draw other things all that well.” Since proteins are too small to be photographed directly, representations of them are often based off of earlier representations. One strategy their lab used was to paint the backbone of the wire model with a special paint that glowed under UV light. With the lights switched off, they took photos, and those photos ended up being a key inspiration for Jane’s later ribbon drawings of protein backbones. Focusing just on the backbone, it became a lot easier to show the folds and curls of the protein. But it was still not easy. “A lot of good illustration is, as you probably are aware, taking things away so that you’re left with the essential picture,” said Dave. “The issue, of course, is that you might cut off something vital and that it might never be recovered.” “The big deal is to really look at the drawing critically and ask whether it really shows what you mean it to show,” Jane said. “You have to try to forget all of what you know and try pretend that it’s new.” Diana Crow | Atom by Atom: Building Protein structures

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On the press preview day of the Collider exhibition in the Science Museum London, a journalist asked Peter Higgs about how he himself visualizes the Higgs boson. Higgs responded that he doesn’t visualize it at all. That’s because the Higgs boson isn’t really a ‘thing’ in the way that a non-particle physicist might understand the term. Rather, it is a perturbation, a ripple in an energy field. In 1964, Peter Higgs proposed that fundamental particles get their mass by interacting with an ever-present energy field. To prove the existence of the Higgs field, it has to be excited to create detectable ripples. If the Higgs field is an invisible sea, the Higgs boson is a wave on the surface that requires very expensive equipment to be able to ‘see’. Chihwei Yeh | Seeing is Believing: Constructing the Image of the Higgs Boson

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Issue 2: Visions What does the Higgs boson look like? If you followed any of the news of the boson’s announcement in 2013, you probably saw a lot of brightly colored curlicues exploding against a black background. But as Chihwei Yeh notes in this issue of Method Quarterly — on “Visions” — there is actually no boson in these images. The Higgs boson is a perturbation in an energy field, visible to particle physicists only through the statistical ripples it leaves behind. For the particle physicist, to see is to create. The miles of accelerator tunnels at CERN create subatomic perturbations to make them detectable; CERN’s graphic artists then create the images that begin to make these perturbations graspable in the imaginations of people outside of the lab. Even at a much more familiar scale, scientific vision requires more than just seeing. From ecologists observing natural systems, to astrophysicists scanning the skies, to molecular biologists peering into the eye of a microscope searching for the neon green glint of a fluorescent tagged protein, the work of seeing requires technology, methods, and a vision of what to look for. Perhaps because of this, scientists are also — often with too little or too much doubt cast — ordained with a sort of visionary foresight. How do scientists consider the future — in their assumptions, forecasts, and hallucinations? Whose visions guide these predictions, and whose don't? And how do they decide what to look for? In this issue of Method, we look at the ways in which scientists try to observe the world, and how disputes and changes over the ways we choose to see things can in turn alter how we envision the future. We have the astronomers at the Vatican observatory, who — free from the confines of the grant system — are asking some of the farthest reaching scientific questions about what exists in space. We trace the changing tools x-ray crystallographers used to model the twists, curls, and folds of proteins — and how that in turn transformed the way they viewed these microscopic structures. We examine what a new vision for South African science must do to see the human impacts of disease, beyond just its biochemistry.  And we ask what the phenomenon of simultaneous discovery says about the myth of the lone scientific visionary. And much more.  

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Issue 2 | VISIONS The scientific process makes the invisible visible. How did science change as scientists built new tools for seeing? How do scientists consider the future-in their assumptions, forecasts, and hallucinations? Whose visions guide these predictions, and whose don't? How do they decide what to look for? Available now, online and in print.

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Maybe Achenbach and everyone else that writes about science denialism knows this, and this is why they act so surprised when “well educated and affluent” people stop vaccinating their children. Why would the affluent –the people that science serves best– start questioning the validity of science? After all, it is the poor that were used as guinea pigs for medical research. It was poor southern black people that were mislead into believing they were being treated for a disease, not rich Bay Area yuppies. I would venture to make an educated, maybe even socially scientific, guess that while the rich can afford to construct purity narratives that put vaccines in the same category as pesticides and preservatives, the rest of us still react positively to the ethics of care that vaccines engender: the common good over profit. It is the kind of care that encouraged Jonas Salk to sell the polio vaccine at cost. Vaccines are one of the few medical technologies that don’t follow the pill-every-day-for-the-rest-of-your-life business model. You aren’t renting your health with a daily supplement; you are doing something to yourself that keeps others safe as well. You take on the pain and burden of getting the shot so that those too weak to take it aren’t put in harm’s way. If you stop thinking of the affluent as the only people capable of making an informed and collective decision, and start thinking of them as selfish actors that can’t imagine their bodies working the same way a poor person’s body works, the education paradox disappears.

Why Do Many Reasonable People Trust Science? » Cyborgology

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"The interesting question from an STS perspective, and the hinge which cheating allegations revolve around, is whether or not the atmospheric conditions at the AFC championship game could have caused a football to deflate what the NFL call “a significant amount.” The question is a thorny one because it is entirely unclear who counts as an expert on football deflation, where one might turn to find an expert opinion, or even what criteria might be appropriate in determining who is, or is not, an expert on football deflation. Worse, how might one find a deflation expert who does not have a rooting interest for or against the Patriots at this late date? In short, who may enunciate the truths of football deflation?" Deflategate, or Ballghazi, and the Conundrum of Expertise (or: why anthropologists should write about football) | CASTAC Blog

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"Starting with a pear, Zaciu has been drilling and carving holes into fruits and vegetables, inserting a light bulb, and then photographing the glowing produce in a darkened room. The results are gorgeous, from the liquid magma of the cauliflower to the delicate, protoplasmic green waves of a tightly furled cabbage." Pear Bulb | Edible Geography

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"My interest in distribution models as well as the virus’s built-in visual potential is what originally brought me to the computer virus. Like traditional illnesses, computer viruses travel through networks of communication or trade, meaning that they can be mapped and rendered graphically across set geographies. Much of my project in the last few years has centered on taking these immaterial actors that reside within cultural networks as a starting point, attempting to reverse-engineer forms of expression or communication from them. I borrow from the historical vernacular of abstraction to render the work as abstract paintings. It allows me to talk about viruses using the language of painting rather than the technical jargon of computer programming or the hyperbole of mass media. In this way, abstraction functions as a lens, an interface." Bomb — Artists in Conversation | James Hoff

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“We have come to look at feminist critique as we would any other experimental control. Whenever one performs as experiment, one sets up all the controls one can think of in order to make as certain as possible that the result obtained does not come from any other source. One asks oneself what assumptions one is making. Have I assumed the temperature to be constant? Have I assumed that the pH doesn't change over the time of the reaction? Feminist critique asks if there may be some assumptions that we haven’t checked concerning gender bias. In this way feminist critique should be part of normative science. Like any control, it seeks to provide critical rigor, and to ignore this critique is to ignore a possible source of error.”

The Importance of Feminist Critique for Contemporary Cell Biology