Here, I am collecting samples with teammates; we were volunteers with a marine biology research project. We were called the ‘goats;’ we spent our time on sharp, slippery rocks to get to the tide-pools. The cool kids did the diving and underwater tasks.
I do a podcast called: Conversations with…
One series is Conversations with…scientists in which I talk with researchers about their work, their approach to science, their mentoring, their lives.
Sometimes it’s a conversations with one scientist, as in the case of Carol Robinson, professor of chemistry at the University of Oxford, Dame Commander of the Order of the British Empire.
Another are podcast features with a number of scientists. Bye-bye Bunny is about antibodies in our bodies, about COVID-19 and antibodies, about recombinant antibodies and other types of research antibodies and about the prospects for making research antibodies animal-free.
One episode is with Hui Yang from the Institute of Neuroscience at Shanghai Institutes for Biological Sciences.
There ‘s a sneak peak of the 2020 American Association for Cancer Research annual meeting part II with the current society president Elaine Mardis from Nationwide Children’s Hospital and with the incoming president Antoni Ribas from UCLA.
You can listen to any of these podcasts on Apple podcasts, Google Podcasts, Stitcher, Spotify, Breaker, on transistor.fm. And a few podcasts are right here.
Method of the Year: spatially resolved transcriptomics
The Method of the Year, chosen by Nature Methods, is about approaches to understand how genes are expressed in a tissue or a cell and to capture where they are expressed. It’s called spatially resolved transcriptomics. And here is my story, here’s an excerpt:
If a researcher is making a smoothie, it might be snack time. Or it could be the moment to prepare a sample for bulk RNA sequencing, in which tissue is homogenized and analyzed to yield averaged gene expression from the mRNAs in a tissue’s cells — its transcriptome. …Working with single cells is more like digging into a fruit salad than a smoothie, says Hongkui Zeng, who directs the Allen Institute for Brain Science. …“Fruit tart is spatial transcriptomics,” says Bosiljka Tasic, an Allen Institute researcher who was interviewed jointly with Zeng. “You know exactly where each piece of fruit is and what is the relationship of each piece of fruit to the other,” she says….
Am writing a lot about COVID-19 and the virus that causes this infection costing so many lives and disrupting our everyday around the world.
Primer detectives is a story about reliable coronavirus assays. But lots of trouble-shooting has to happen with these PCR-based assays. And staying ahead of a pandemic is tough. One can never catch up time lost. I looked into some issues with the CDC assay and some others.
Coronavirus jolts labs to warp speed is a piece about the many ways labs are accelerating their work to make headway on this coronavirus. They rush to expand resources for collaboration, swap data and findings in genomics, assay-building, in structural biology. The spike protein of the virus holds some secrets about this virus’s infectiousness.
Think simple is also about assays for this virus. Labs and companies are developing simpler assays, which might make large-scale roll-out easier.
Here is a video I did about one of the systems presented in this piece. I call this type of video Quick-Look, a nano-documentary.
Coronavirus encounter is about an emerging structural biologist from Singapore whose career development through a fellowship in Germany had to take a detour due to COVID-19. His experience is likely one example of many around the world.
For Metropolis of Science, a project developed by Columbia University’s Graduate School of Journalism’s Marguerite Holloway, I did a piece about the Yellow Fever Fence in New York City.
“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.
Yellow Fever repeatedly ravaged New York City. It’s a sad reminder that infectious diseases do not just come and go.
“When yellow fever ravaged New York in 1822, the city’s Board of Health put up a picket fence to quarantine a section of lower Manhattan. Residents were ordered to leave. If they were unwilling, the authorities forcibly removed them. Those who were too poor to leave were taken to a temporary asylum.”
The project is part of Columbia University’s Center for Science and Society.
These days many people seem to tune out science and care little about facts. I made these gifs and use them on social media to highlight science I find notable.
The Vertebrate Genomes Project
Here are some videos I shot and produced about The Vertebrate Genomes Project. That’s the plan to sequence all vertebrates on Earth. There are around 66,000 vertebrates.
There’s an animation about the first group of reference-grade genomes.
Since that video was produced, the research team has generated many more genomes than these first 15. Will update the animation. Information about the project’s progress can be found here.)
And here’s a mini-documentary about the Vertebrate Genomes Project
Here is a story in Nature “The Big Challenges of Big Data”
“Biologists are joining the big-data club. With the advent of high-throughput genomics, life scientists are starting to grapple with massive data sets, encountering challenges with handling, processing and moving information that were once the domain of astronomers and high-energy physicists.”
Machine learning is not magic
Here is a story in Nature Methods on machine learning, called Machine learning, practically speaking.
‘Artificial intelligence’ (AI) is hard to beat as an enigmatic term. It draws your attention and make you think of all-powerful machines.
Within the AI field, many projects involve machine learning (ML), in which a computer can learn iteratively from data and make predictions. That can be super-helpful in so many areas. The story is about a form of ML called deep learning. Biomedical researchers want to use deep learning to analyze all kinds of data and better understand health and disease.
For example, machines can learn to see assess whether tissue slides that the system has not ‘seen’ before show features of luminal A breast cancer. But it’s not easy to have machines learn in this realm. The story is about the labs trying to do so.
Erin Dewalt did this wonderful illustration for the story. It’s modern and retro, which corresponds well to ML. Which is new and it has been around for decades, too.
When computational pipelines go ‘clank’
These two stories, available here and here, are about what it takes to build and maintain computational pipelines. Yes, pipelines can go ‘clank’ and they can plunk but interviewees talk a little about how to avoid that or to fix it when it does.
There’s text, animation and a podcast. And some animated puns that harken back to another story I did on benchmarking software tools. Again, some fun, informative interactions with scientists and collaboration with the oh-so-talented managing designer Erin Dewalt.
An Iron Man and cancer researcher
This is a piece about a scientist at Baylor College of Medicine. Ken Scott is an Iron Man, a dad, a husband, a scientist, a religious man and a cancer patient. I started writing about him after I had interviewed him for a story and he shared his cancer diagnosis with me. I wrote for him and his family. Then I asked him if it would be ok to write about him in a more public way. He and his wife said yes and I am grateful for that.
The story starts like this:
As a kid, Ken Scott once rode his bike off the roof of his family home. In a later experiment, he attached a model rocket to the bike that melted his seat and his rear caught on fire. Ken grew up to marry his high school sweetheart, raise two kids, become a scientist. He trains hard; he has jogged up to 10 miles at a time wearing a backpack loaded with 100 pounds of logs. He competes in the Iron Man in which participants swim 2.4 miles, bike 112 miles and run 26.2 miles.
You can read the piece on Medium here.
For The Daily Beast, I wrote
New Mayan Discovery: The World Isn’t Ending!
…“That is correct, the world will not end,” says William Saturno, the Boston University archaeologist behind a new paper that could help put to rest the long-held myth that the ancient Mayans predicted a 2012 apocalypse—a belief still held by 10 percent of the world’s population, according to Reuters. “A cycle is ending, but a new one begins, according to the Mayans, who regard their calendar as a series of infinite cycles,” he says.
Read the full story here, which also includes a bit about an excavated room that was likely space where a Mayan nerd—a calendar-keeper, astronomer, and scribe—puzzled away.