Above, 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.
Here is my new podcast: Conversations with…
There will be a series of Conversations with…scientists
Here is my first episode with and about Carol Robinson, professor of chemistry at the University of Oxford. She has also been appointed Dame Commander of the Order of the British Empire.
You can listen to it on iTunes, Google Podcasts, Stitcher, Spotify, Breaker and on transistor.fm
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.
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 about one of the systems presented in this piece.
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.
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.
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 this video was produced, the research team has generated many more genomes than these first 15. Am updating the animation…)
And here’s a mini-documentary about the Vertebrate Genomes Project
Some other stories:
Here is a piece about the microbiology of the oceans. Microbiologists want to be heard on the subject of climate change. In a consensus statement, a community of scientists writes: “underappreciating the importance of microbial processes both on land and in the oceans, “we fundamentally limit our understanding of Earth’s biosphere and response to climate change and thus jeopardize efforts to create an environmentally sustainable future.”
The consensus statement ‘Microbiologists’ Warning to Humanity’ is here and so is a petition. Rick Cavicchioli, from Australia’s University of New South Wales, has been spearheading this effort.
Microbiology of the oceans is fascinating and there’s so much left to find out about what determines the distribution of microbial species, for example, and roles the microbes play.
There’s also increasing collaboration between biological oceanographers and physical oceanographers. Oops, let’s not forget chemical oceanographers. Read more here: When microbiologists plunge into the ocean.
Here’s a striking Landsat 8 satellite image showing phytoplankton swirls in the sea north of Canada’s Yukon Territory. Whoo, these are some swirls. And here’s a blog post with more pics.
(Credit: NASA Goddard Space Flight Center OceanColor Web)
Machine learning is not magic
Here is a story 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.
In genomics, there are a lot of software tools but without benchmarks , you don’t really know how well the tool does in which situation. I checked in with some benchmarkers, they’re cool and they have a lovely sense of humor, too.
Here is on benchmarking pun. And there are more in the story. Again, a marvelous collaboration with scientists and the oh-so-talented Erin Dewalt, who drew this. And thank you, Kasper!
Here is a story about an emerging technology called single-cell proteomics. Researchers can now routinely sequence genomes, and they can sequence RNA. Some labs are working on ways to be able to tally, and in high-throughput, how many proteins there are in a cell.
Knowing the genome and the RNA has enabled molecular biology in all sorts of ways. But according to a growing community of scientists in this new field, knowing which proteins are in a cell and how many of them there are, well that’s another big step toward understanding cells. And understanding the differences between healthy cells and those afflicted with disease.
Sure, there remains a divide both scientific and cultural about genes and proteins. But science can get a bit skewed when labs have to infer proteins from cellular mRNA levels. And maybe they will soon be able to avoid that.
For this story Erin Dewalt again did a fabulous illustration.
This illustration came about as I interviewed people and heard what a powerful dream this concept of single-cell proteomics was to them.
So I drafted an illustration in Illustrator. And, as is my habit, I showed it to a number of colleagues to finesse the concept. Many were involved. The result is this conceptual illustration and this story called: A dream of single-cell proteomics.
Sugars–cells use them in all sorts of ways
I also do podcasts. One of them is on this blog page and called Sugar Rush. You can also listen to the podcast on SoundCloud or right here.
And yes, I wish it were about candy, which I love. It is about sweetness, but not about the type we eat but the type that coats our cells. Sugars coat all cells in the human body.
I spoke with a number of scientists working to understand the role these sugars play. Pam Marino at NIH, Gordan Lauc of the University of Zagreb, Chris Taron at New England Biolabs.
Some science behind the rogue science of editing the genes of human embryos and bringing them to term.
Here is a story about embryo-editing. Yes, it sounds creepy. There are scientists who are editing the genomes of human embryos. And in one case –perhaps more?– the babies were brought to term. This story is about one such rogue scientist….and it’s a look beyond rogue scientists.
It looks at DNA-repair mechanisms and discusses if they might work differently early on in development. It’s about the opportunities that might rest with gene-editing, what it will take to deliver gene-editing constructs efficiently. It’s about lowering the risk of mosaics. It’s hard to edit all the cells in a developing embryo. And then there’s the CRISPR-Cas system itself.. how might one stop it from editing after the first edit.
From the good news department:
New Mayan Discovery: The World Isn’t Ending!
For the Daily Beast I wrote about a Mayan Discovery.
…“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.
James Cameron and Investors Seek to Lasso and Mine an Asteroid
Also for The Daily Beast I did a story about asteroid mining. James Cameron is advising a company called Planetary Resources. Asteroids have bounty to offer, says John Lewis, professor emeritus at the University of Arizona’s Lunar and Planetary Laboratory, also an adviser to Planetary Resources, and author of a book, Mining the Sky, Untold Riches From the Asteroids.
Read the full story here.
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 New Scientist, I wrote about Swiss engineer Roger Waller, a modern steam pioneer. He and his team update and redesign steam engines on railway routes. And they have built a steam car.