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.
My podcast is: Conversations with…
In Conversations with…scientists I speak with researchers about their work and their lives, about their field and about the role of science in society. It’s research made personable.
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. There is an episode with Paola Oliveri, developmental biologist at University College, London.
Others are podcast features and they include a number of scientists in academia, non-profit research institutions, universities and at companies.
Bye-bye Bunny, for example, is about antibodies in our bodies, about COVID-19, about different types research antibodies and about the prospects for making research antibodies animal-free.
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.
The CRISPR Children.
I always wondered what happened to the ‘CRISPR babies,’ born in China and to an uproar in 2018 as the first children with genomes edited before their birth. How might their edited genomes affect their lives?
My story about them in Nature Biotechnology has been three years in the making. It’s accessible here or here. I did some blog-posts to go along with the story and podcasts. More podcasts on this subject are underway.
Here is some reading material. And here are some podcasts.
This one is with physician-scientist Kiran Musunuru of the University of Pennsylvania, who is also co-founder of Verve Therapeutics. He is also author of the book:
And here is a podcast with Rudolf Jaenisch from the Whitehead Institute for Biomedical Research. In February 2018, He Jiankui, who had done the experiments, came to see Rudolf Jaenisch.
…”He came in February. The announcement was in November, he came in February, the experiment had been done, I think, he wanted to get approval from labs, Here, I think he went to other labs. Of course, it was absolutely not acceptable. I didn’t realize the guy had already done it, I thought he was maybe thinking about this and that I could talk him out of this.”…
Machine learning, quantum computing, they’re not magic
‘Artificial intelligence’ (AI) is hard to beat as an enigmatic term. And quantum computing is right up there, too, in the way it draws attention. Without good training data machine learning algorithms can disappoint.
For my Nature Methods story Machine learning, practically speaking, I asked biomedical researchers about how they use machine learning. For example, machines can learn to assess whether a tissue sample that the system has not previously ‘seen’ indicates breast cancer.
For my story Biology begins to tangle with quantum computing and in a piece called Bits of quantum bits, I asked scientists about how they use quantum computing and what they think it’s promise is. And I looked into the mysterious disappearance of Ettore Majorana.
Erin Dewalt did this wonderful illustration for the machine learning story. It’s modern and retro, which corresponds well to ML, which is new and 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.
COVID-19 has cost so many lives and disrupted our everyday around the world.
For Scientists set out to connect the dots on long-COVID, I explored what might underpin the bewildering array of symptoms some people experience after they recover from COVID-19. They might have breathing problems, heart palpitations, joint pain, damage to their lungs, heart or kidneys, they might have ‘brain fog.’
I also did three podcasts to go along with this long-COVID piece.
One is about genetic diversity and long-COVID. It’s a conversation with Nadia Rosenthal, scientific director of The Jackson Laboratory. The podcast and transcript are on this page.
Another is about long-COVID and brain fog. It’s a conversation with Avi Nath, intramural clinical director at the US NIH National Institute for Neurological Disorders and Stroke (NINDS). The podcast and transcript are on this page.
And there’s a podcast with a more business angle about modeling long-COVID on this page.
Primer detectives is about coronavirus testing and I looked into some issues with PCR assays, including the one from the CDC, which was giving inconclusive results.
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.
Here are the podcasts on long-COVID.
This one is based on a conversation with Nadia Rosenthal, the scientific director of The Jackson Laboratory.
“The field is racing. And yet I’m not seeing that much that’s really budging our understanding of what’s going on in these various cases where people are really having very different responses,” says Nadia Rosenthal.
Most of the studies on animal models of COVID look at time points that are acute, like three days, six days, nine days, maybe 21 days maybe, and although mice have a compressed lifespan, the virus is basically running the same show.
And so you really need to take these mice out for months to understand whether we have the right models for long COVID and the study of long COVID.”
You can hear this podcast here:
And you will find a transcript here:
This podcast on long-COVID is based on a conversation with Avi Nath from the US National Institutes of Health National Institute of Neurological Disorders and Stroke.
“Now, the virus may be gone, but the music lingers on. But what is lingering: is it the immune system that is lingering or is it parts of the virus that are lingering?”
You can hear this podcast here:
And you will find a transcript here.
This podcast on long-COVID is based on a conversation with Terina Martinez, a field application scientist at Taconic Biosciences.
“We are all on the brink, hopefully, of reaching some better population immunity because of the vaccine program. But the research doesn’t stop because of the vaccines. I think that because we have this whole group of people who have long COVID we need models that will help us understand what’s going on there, because, you know, giving someone another vaccine, is it going to stop their long COVID.”
You can hear this podcast here:
And you will find a transcript here.
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.
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.”
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.