Some of the profiles I have done
Sequencing: Ship-Seq sails the seas
Neurobiologist Leonid Moroz likes being out at sea. He likes having all the amenities there, too. Such as high-throughput sequencers. And his complete team.
“Although organisms can be taken from the sea to the lab, they often need ocean depths or a certain temperature to survive. And when samples are prepared for travel, they need optimized conditions to not degrade. Three decades of dealing with dead organisms, degraded samples, delayed shipments and customs snafus have led Moroz to try something new: Ship-Seq. “We cannot bring the sea to the lab, but we can bring a whole lab to the sea,” he says.”
Here is how he set up Ship-Seq. (Hint: sequencing quality goes up on the high seas.)
1 x 141-foot boat
1 x generous entrepreneur
1 x ship’s crew
1 x mobile molecular biology lab equipped with lab benches, a sequencer, reagents
1 x manufacturer of a high-throughput sequencer willing to donate an instrument
1 x satellite link to a supercomputer
1 x lab staff and scientist/wife willing to be scientist-sailors
1 x diving equipment
1 x funding National Institutes of Health (NIH), National Science Foundation (NSF), National Aeronautics and Space Administration (NASA)
3 x support from non-profit organizations: Florida Biodiversity Institute, Florida Museum of Natural History, the International Seakeepers Society
1,000 international units of patience
Several remedies for seasickness
Nature Methods, March 2020
She joined the Berkeley faculty in 2016 and splits her time between the physics and molecular and cell biology departments. She realizes she has always wanted to apply knowledge from one field in another. “I’m just very curious about things, like anything,” she says and it drives her inter- and cross-disciplinary activities. “It’s not something I have to strive for, it’s just something that I really enjoy to be doing,” she says. She reads voraciously about, among other subjects, pop culture, politics and history.
Nature Methods, February 2013
He likes his shirts and biosensors bright. Loren Looger, who leads a research group at Howard Hughes Medical Institute’s Janelia Farm Research Campus, lights up message transfer in the brain. And he wants to go even further than tracking excitatory messages.
“Proteins are pretty [expletive] awesome,” says Looger. “They are everywhere, doing everything,” handling many biological jobs from lending Spinosaurus its size and a cheetah its speed to helping organisms survive and adapt. To harness that versatility, he engineers proteins with methods that are “equal parts conceptual, modeling based and recreating Darwinian selection in the lab.”
Nature Methods, May 2020
Robinson gets ideas on runs. Because of COVID-19, she now likes winding down the week with virtual social catchups. She would enjoy imaginary virtual tea with Marie Curie, whom she likes because Curie was ahead of her time as a woman in science. Another invitee would be Joseph John Thomson, who separated two low-molecular-weight isotopes in the first mass spec experiment. “Now I’d like to say, ‘you know, look what you started’,” says Robinson.
Nature Methods, June 2016
Richard D. Cummings
…Growing up in rural Alabama, Cummings was drawn to the piano at the ripe age of five. “If you wanted any other noise other than bees humming and birds singing, you had to make it yourself,” he says.
Some technology stories
Nature Methods, March 2018
Putting microfluidics in other people’s hands
They’re tiny, they can be DIY, they’re shareable. Except they’re not so easy to share. A number of labs want to change that with community-organizing.
…University of Groningen researcher Matthias Heinemann faces a nail-biter situation. He has only one silicon wafer with which to make microfluidic devices. It’s nine years old, which, in wafer years, is a geological time frame.
With age, it has become slightly damaged, so it’s only half a wafer that five people in his lab share. They rely on it for making devices for their daily experiments. It’s the only one that leads, via soft lithography, to well-working microfluidic devices. “My nightmare is that if this would now break, then half of my lab gets stuck,” he says. He would like to share copies of the wafer with external scientists. But he doesn’t have those…
Big data – computing – biology
Nature, 13 June 2013
The big challenges of big data
Biologists are joining the big-data club, and not just so they can act like they have things to talk about with physicists who juggle big data all the time. Biologists are pushing data mountains around; swapping and comparing big genomics data on various clouds, deciding whether to bring the data to the tools or the tools to the data. Some wet-worlders become in silico worlders.
Data-sharing in science and medicine
Nature Biotechnology, June 2012
My data are your data
Sharing is easy, scientists do it in their sleep. Actually, they don’t always want to share.
Newsweek/The Daily Beast, May 10, 2012
New Mayan Discovery: The World Isn’t Ending!
The Mayans predicted that the world would end back in 2012. It didn’t come to pass and according to findings from this dig, it wasn’t gong to happen
Newsweek/The Daily Beast, April 24, 2012
James Cameron and Investors Seek to Lasso and Mine an Asteroid
Lassoing an asteroid could be big business, it might just be a wild ride into space.
The details on how to lasso an asteroid are still being worked out. Earlier this month, the Keck Institute for Space Studies (KISS) at California Institute of Technology/NASA Jet Propulsion Laboratory in Pasadena, Calif., published a study authored by a team of space scientists from across the country about the technology and know-how needed to identify, robotically capture, and haul in an asteroid that is about 22 feet across (seven meters) and weighs about 550 pounds (500 metric tons) and bring it closer to Earth for mining purposes.”
Culture – Computing
The New York Times, August 3, 2003
Technology: In DSpace, Ideas Are Forever
The libraries at the Massachusetts Institute of Technology are earnestly bookish (2.6 million volumes and 17,000 journals) but increasingly digital (275 databases and 3,800 electronic journals). And just as e-mail dealt a blow to snail mail, digital archives are retooling scholarly exchange. A number of universities, from the California Institute of Technology to M.I.T., are creating ”institutional repositories” designed to harness their own intellectual output. M.I.T.’s archive, perhaps the most ambitious, is called DSpace (www.dspace.org).
Scholarly Storage: Traditionally, journals make research public after peer review, which can take months, sometimes years. Archives like DSpace, however, collect unpublished work — documents of any length, lecture notes, photos, videos, computer simulations, blueprints, software — in all disciplines and make most of it available to anyone as soon as it’s received.
Energy – Transportation
New Scientist, 3 October 2008
Steam power takes to the road again
To the engineers and steam buffs gathered in the auditorium, most of the images in Roger Waller’s video were familiar enough – the gleaming bulk of a black locomotive standing in Waller’s workshop, a small loco climbing a precipitous mountain railway, an elegant paddle steamer crossing the blue waters of a Swiss lake. What caused a ripple of surprise, though, was a short sequence near the end. It showed a small green car with a round silver tank zipping along a Swiss road, its twin exhausts puffing out clouds of white vapour.
Waller is a modern steam pioneer. Along with a team at his engineering company DLM in Schaffhausen, northern Switzerland, he has spent the last decade redesigning and modernising steam locomotives to make them far cleaner, and more profitable, than “old steam”.
Some stories about biomedicine
High-security labs – medical research
Nature January 16, 2014
High-security labs: Life in the danger zone
Some microbes are deadly. Working with them in a research environment takes many precautions. And scientists have to find a way to maintain instruments that cannot be removed from the lab, once they are placed under bio-containment. A new high-security lab is opening up in Frederick, Maryland, a stone’s throw from the storied US Army Medical Research Institute of Infectious Diseases (USAMRIID). The proximity is intentional.
Genomics – computing – medicine
Nature August 27, 2015
The DNA of a nation
The 100,000 genomes in the 100,000 Genomes Project are not quite sequenced and analyzed yet. Here is a glimpse behind the scenes on some of what it takes to organize the project. Data need to be secured, reliable software pipelines must be put in place and tested. And plenty of experts are needed on hand for manual analysis, genomic deep-diving and general quality control.
The project’s idea is to help people, at first people with rare diseases and cancer. But at one not so distant point, whole genome sequencing might be a common element in the medical records of all of the UK’s National Health Service patients. And along the way it might all spark a genomics industry in the UK.
Genomics – health and disease
Nature Methods, February 2018
Meet some code-breakers of noncoding RNAs
DNA makes RNA makes protein. That’s dogma. But actually RNA does not always make protein. There are many, many noncoding RNAs. This is a story about some of them.
Health and disease are likely shaped by the push-and-pull of numerous noncoding RNA regulators, says Isidore Rigoutsos, a researcher at Jefferson University….
NcRNAs have intrigued Uwe Ohler at the Max Delbrück Center for Molecular Medicine since his postdoc days working on alternative splicing and miRNAs. Computational biologists need to look beyond a single regulatory mechanism and gaze across different data sets, he says. NcRNAs have been, he says, “constantly good for a surprise.”…
Vocal learning – comparative genomics
What makes birds and bat the talk of the town. Also here.
Nature Methods, July 2018
Songbirds and bats learn to vocalize from parents and peers, much as people do. Their vocal learning abilities are striking. Here is Stella the starling. Here is the beat-boxing, chatterbox, Disco the parakeet. Here is the lyrebird who can copy all sorts of other birds. This bird can also learn from his or her environment: how to do camera-shutters, chainsaws and car alarms. Studying songbirds and bats can help labs understand how we learn to speak and how we process speech.
Nature, November 13, 2014
A deep look at synaptic dynamics
Synapses in the brain are busy messaging intersections. Neurotransmitters of various sorts are released, but then what. How are these vesicles refilled with neurotransmitters? There are multiple hypotheses about how that might occur.
Die Welt, 14. November 2014
So wird die Hirnforschung zu einem großen Spiel
Die Crowd packt bei der Neurobiologie mit an, um harte Herausforderungen zu lösen. Mitwirken kann jeder/jede. Voraussetzung ist lediglich Neugierde.
Thwarting cancer-cell biology
Nature Methods, April 2018
How to pull the blanket off dormant cancer cells
Cancer cells grow and grow. Sometimes, though, they go to sleep. It helps them avoid death-by-chemo. By studying cancer cell dormancy labs hope to better understand this resilience. And maybe cancer cells can be killed in their sleep. A committed cancer community is strategizing about that.
Nature, July 24, 2014
Cell communication: Stop the microbial chatter
Bacteria are chatterboxes. They communicate with one another, in large groups, and even across species. This exchange helps them survive and also helps them become more resistant to antibiotics. But by undermining all this chatter, scientists hope to treat infections in new ways. To do so, they are developing new ways to eavesdrop on microbial communication.
Nature Methods, January 2017
The return of culture
Did culture, the act of coaxing growing microorganisms on plates, ever leave microbiology? It never left but it’s true that sequencing and computational techniques sort of took over, in a compelling productive way. But researchers want culture back
The Lancet June 8, 2012
FDA reform plan edges closer to realisation
A bill that gives the US Food and Drug Administration much new heft in addressing drug shortages as well as drug and device approvals has cleared House vote
The Metropolis of Science explores the history of science and technology in New York City. Here’s my entry.
Yellow Fever Fence
Yellow fever outbreaks first hit New York in 1668 and hit the city again and again. “Coffins, coffins of all sizes!” is what boys shouted through the city streets, touting the pine coffins for the many dead. The four-dollar price tag was too steep for many people. Nightly, a dead cart carried corpses to the pits of Potter’s Field, now the site of Washington Square Park. In 1822, New York City officials closed off a portion of lower Manhattan in an effort to combat repeated outbreaks.
Metropolis of Science is a web-based web based mapping project led by Marguerite Holloway at Columbia University.
A software platform in the making: SeeSaw.
SeeSaw weighs news and comments, showing the community of readers the spectrum of reporting and views on a topic.
Here are a few projects I am developing.
When people post comments about stories they read, see, or hear, the lists can get unwieldy. SeeSaw weighs the comments’ content and tone and delivers icons to readers that reflect these thoughts and emotions.
We are developing SeeSaw and hope to have a beta up and running soon.
Wikis are great because they can draw on contributions from a large crowd. Right now, these wikis are hosted at Columbia University, so only members of the Columbia community can see them and comment. But I hope to grow these wikis beyond that realm to the world at large and find reasonably priced hosting for them. If you have tips/ideas, please let me know.
A blog that follows the discussion about the illegal medical experiments on Guatemalans in the 1940s.
I have a few more ideas, please stay tuned. These projects are all just seedlings, but I hope they grow to be useful to many people.
I enjoy kinetic typography. Here’s a little experiment I did. No copyright infringement intended.