Vivien Marx

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.

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….

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.

Yellow Fever came to visit New York many times. Here an account by James Hardie.

“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.

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.

Illustration by Erin Dewalt SpringerNature

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.

(Erin Dewalt)

When computational pipelines go ‘clank’

Pipeline plunk

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

composita/Pixabay

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.

*

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.

For The New York  Times, I did this story about libraries.

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.”

ARTE theme evenings –

Themenabende/Soirées thématiques

For the public television network ARTE, which is run jointly by French and German public television, I curated and produced theme evenings.

These are multi-hour evenings on one theme. They are made up of different genres: feature films, short films, documentaries, animation and experimental genres, too.

I enjoyed producing these, taking them from idea about an evening-long narrative arc, through development to broadcast.

Some films we bought, others we produced or co-produced. Plus we produced graphical vignettes in between the pieces which could have any length. We told smaller stories within the arc of a larger story.

Im Testfieber

For Süddeutsche Zeitung, I wrote a story about studying for the GRE.

Counting proteins

Here is a story in Nature Methods 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.

It’s not a faraway dream to tally proteins in single cells. Credit: Stéphane Larochelle, Erin Dewalt Springer Nature

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.

When microbiologists plunge into the ocean

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 in my Nature Methods story 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)

For Science, I did a story called Beautiful Bioimages for the Eyes of Many Beholders.

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 in Nature Methods. 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.

Steam Power takes to the Road again. 

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.

To cut or not to cut

For New Scientist, with Graham Lawton I wrote about male circumcision. It’s a decision parents of baby boys face and it’s not an easy one.

For Die Zeit, I did a story about zebrafish research, friendship and rivalry in science.

Von Fischen und Frauen

Sugars–cells use them in all sorts of ways

Here is another podcast. It’s 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.