Sloppiness vs Reproducibility

I’m not a big fan of reproducibility projects. Shoddy papers shouldn’t be tolerated, but the truth is that sometimes rigorously done research isn’t reproducible — and when that happens, science gets interesting. It should go without saying that a peer-reviewed paper isn’t a guarantee of truth. If done properly, a paper is a record of a rigorous attempt to discover something about the world, no more, no less. What we believe about nature should reflect the accumulated evidence of many researchers and many papers, and that means the scientific literature should reflect our latest tentative, bleeding-edge thinking, even at the risk of being wrong. It’s counterproductive to hold up publication until some other lab reproduces your result, or to retract papers that don’t hold up, unless they had clear methodological flaws or artifacts that should have been caught in review.

Two recent articles capture what I think is the right attitude on reproducibility. First, as David Allison and his colleagues write, as a community of researchers, editors, and reviewers, we’re not doing as well as we should be when it comes to meeting high standards for best statistical and other methodological practices:

 In the course of assembling weekly lists of articles in our field, we began noticing more peer-reviewed articles containing what we call substantial or invalidating errors. These involve factual mistakes or veer substantially from clearly accepted procedures in ways that, if corrected, might alter a paper’s conclusions.

There is no excuse for this kind of sloppiness.

On the other hand, here is Columbia’s Stuart Firestein:

The failure to replicate a part or even the whole of an experiment is not sufficient for indictment of the initial inquiry or its researchers. Failure is part of science. Without failures there would be no great discoveries.

So yes, let’s clean up science by rooting out obvious “invalidating practices” that all too often plague papers in journals at all tiers. But let’s not be naive about how science works, and what the scientific literature is supposed to be. To paraphrase what  I wrote recently, if some of our studies don’t turn out to be wrong, than we’re not pushing hard enough at the boundaries of our knowledge.

Revisting the blink comparator and The Rural Alberta Advantage

Today is the anniversary of the discovery of our sentimental favourite dwarf planet, Pluto. On February 18, 1930 Clyde Tombaugh, working at the Lowell Observatory in Flagstaff, found the first evidence of a planet beyond Neptune. This seems like the perfect day to revisit an old post about a song that reminded me of the equipment he used. This is an edited and updated version of a Finch and Pea post from February 11, 2012.

With rich dark wooden curio cabinets and a narrow book-filled balcony accessed by a steep staircase, the Rotunda at the Lowell Observatory in Flagstaff feels like a natural home for the distinguished scientist. I visited the Lowell in 2011 for the National Association of Science Writers meeting, and it was everything that I had always imagined being a scientist would be when I was a kid. Feeling the warm glow of scientific discoveries past, there was one thing in the room I couldn’t take my eyes off: the glass plates and elegant brass eyepiece of the blink comparator used to discover Pluto. Continue reading “Revisting the blink comparator and The Rural Alberta Advantage”

GMO wild organisms: As if GMO crops weren’t controversial enough…

The big biotech controversy of last year was over the ethics of using CRISPR to edit human embryos – something which a team of Chinese scientists did last April. The possibility of designer babies led to a major scientific summit meeting, hosted by the National Academy of Sciences, during which the attendees concluded that “It would be irresponsible to proceed with any clinical use of germline editing” until safety concerns are allayed and society comes closer to an ethical consensus.

While the world was fretting about edited embryos, scientists introduced an even more ethically fraught biotechnology: gene drives, a tool to genetically modify organisms in the wild. Gene drives have the potential to do a lot of good, by controlling disease vectors like malaria-bearing mosquitos. But if you thought GMO crops were controversial, just wait to see how people react to GMO wild organisms.

I cover the new CRISPR-based gene drive technologies in my latest Pacific Standard column. Here’s the tl;dr version: Gene drives can do a lot of good, but because they are simple to make, and because their consequences aren’t confined by political borders, we’re going to have a hell of a time ensuring they’re used responsibly.

Future Travel Plans

There was a time when travel was sleek and sophisticated (and inaccessible). Frank Sinatra sang about flying. I remember finding an old PanAm in-flight service menu my grandfather ha kept in his attic. There was real food that you might actually want to eat. The newest installments in the NASA/JPL Visions of the Future poster series invite us to imagine travel across our solar system and the galaxy with nostalgia for the optimism of mid-20th Century travel and hope that the future of space exploration is sexier than The Martian.

Music of the Spheres

This was something I wrote for the “review” assignment of my writing course.

2016-01-20 17.44.32There is a time and a place for complex atonal music, and perhaps the drinks reception of a genomics conference at the Excel Centre was not it. Through the chatter it wasn’t always easy to hear what the string quartet was doing, and meeting attendees were confused about the performance. “I thought they were still tuning”, said one of the guests.

There was a good reason the Kreutzer Quartet was playing here, at the Festival of Genomics, surrounded by exhibit stands for DNA sequencing companies and clusters of geneticists. Their performance was a crucial part of an art piece by Charlotte Jarvis, which explored the possibilities of encoding complex information in DNA.

Jarvis and Goldman introducing the Kreutzer Quartet.
Jarvis and Goldman introducing the Kreutzer Quartet.

The work, Music of the Spheres (named after a Byron poem), combines music, science, and a bubble machine. It requires some effort on the part of the audience to grasp how all the components fit together.

The core of the work is a three-movement musical composition, written by the Kreutzer Quartet, and inspired by DNA. The musicians performed the first and third movements live during a drinks reception at the Festival of Genomics, on January 20th. They used asynchronous glissando scales to express the coiling strands of DNA, and tapped the strings with the wooden part of their bow (col legno) to suggest the sound of large machines handling genetic information.

Movement 2, however, was not performed – at least not by the string quartet. This middle movement was converted into DNA code according to a system developed by Nick Goldman at the European Bioinformatics Institute. He initiated this collaboration with Jarvis to illustrate the enormous potential of using DNA code to digitize large amounts of information: in this case, a recording of the Kreutzer Quartet playing the middle movement of their genetics-inspired piece. This segment of custom-designed DNA was then created and mixed into a soapy solution. So it wasn’t the string quartet playing the middle movement of the piece, but a bubble machine. While the musicians rested, Jarvis switched on the machine, and the music travelled in the air – unheard, but tangible and visible. If you were to capture a bubble, isolate the DNA and sequence it, you might be able to get the data for the recording back out of its unconventional storage format.

2016-01-20 17.48.45This was not the first performance of Music of the Spheres. It had previously been set up in a large empty building, a gallery along the coast, and Hornsey Town Hall. The string quartet can’t be everywhere, but the bubbles are always there, and form the core part of the work. In fact, Jarvis turned on the bubble machine a few times during breaks at the Festival of Genomics. Without the string quartet, this created an effect of simple party entertainment, not out of place at this conference, which also featured a lively talk show and a treadmill challenge. People engaged with the bubbles by photographing them, popping them, or shielding their coffee cups from soapy surprises. Many of them were unaware that each bubble contained fragments of DNA encoding a piece of music.

2016-01-20 15.29.00

But while the bubbles alone were a good match for the hectic venue, the live performance unfortunately was not. It seems a shame that the talented Kreutzer Quartet came all the way here to perform for a crowd that could barely hear them and was more interested in catching up with colleagues over a drink.

Music of the Spheres is a work that makes us think about the potential of DNA as a data storage method. It requires thoughtful reflection, and is best experienced against a quiet backdrop – not one of clinking wine glasses and murmuring conversations.