I was a Knight Science Journalism Fellow at MIT and I am a graduate of the Columbia University Graduate School of Journalism where I was a Robert Wood Johnson Foundation Fellow.
I’ve been a Neal Award Finalist and a Woods Hole Marine Biological Laboratory Science Writing fellow.
For a while, I was a commissioning editor and senior producer with ARTE and ZDF. ARTE airs across Europe and is a joint venture between French and German public TV. I have also worked on projects for these networks: ZDF, WDR, BR, HR, WGBH.
In a research article I thought about some factors shaping journalism. It’s titled ‘One potato, two potato, couch potato, mouse potato: How the mouse and the remote control are shaping journalism.
It’s published in Convergence: The International Journal of Research into New Media Technologies.
In mind and heart and sometimes also in body, I roam the globe for stories, also to produce podcasts and sometimes videos.
I enjoy being a multicultural person with a jumbled heritage. I grew up in the US and Europe. I speak English, French and German and have worked in those languages.
Will my Python skills progress beyond my the baby Pythonista-level? Maybe. Will my repertoire of French idioms grow? I hope so.
Visual idioms: onions from Vivien M on Vimeo.
When you learn a language, idioms are fun but hard to remember. Am starting a series to help with that.
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.
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.
Chemistry and imagination
Sometimes the podcast is a conversation with one scientist. Here is Carol Robinson, professor of chemistry at the University of Oxford, Dame Commander of the Order of the British Empire talking about science and imagination.
“…One thing I think is important in science is imagination. I think we all get a bit kind of constrained. And somebody once said to me, oh, you know, if you hadn’t had a career break, you would never have tried those experiments because we’d all worked out what the limits would be. And I just thought, well actually I’m glad I didn’t know that, because if you knew limits, then you kind of work to that, whereas if you don’t know anything and you just kind of use your imagination, you can go beyond what people think are the limits. I think it’s not to be too constrained, really?…”
Neuroscience, equity and communication
Here is a podcast with a sneak-peek of the annual meeting of the Society for Neuroscience (SfN), also about what conferences mean to neuroscientists and about the importance of collaborating and communicating. And there’s a word-game. I co-hosted it with Jean Zarate from Nature Neuroscience. The guests are: Gina Turrigiano, Brandeis University researcher and current President of the Society for Neuroscience, Robbie Greene of the University of Texas Southwestern Medical Center, current chair of SfN’s Public Education and Communication Committee and Dr. Damian Fair from the University of Minnesota, incoming chair of SfN’s Public Education and Communication Committee.
We talked about the meeting and also about conferences more generally and how to bridge the different scales in neuroscience. Gina Turrigiano:
“…these issues of equity, and also climate change, and all of these things, people being worried about COVID, but also just people in, you know, in a lab with not enough money, maybe to send all their trainees or in a country where they can’t get a visa, all of these things are really issues that we’ve been thinking a lot about in terms of, you know, we are an international organization, and we want to make sure that everybody has access.”…
Among other questions Jean asked …”What do you think we need to do to now bridge across all of these scales of neuroscience?…I wonder whether or not terminology is a thing is a crucial factor here, the culture might have changed. But at some point, there’s a lot of jargon that happens at each of the scales.” Damien Fair :
…”it’s a very salient point, because I talk about this a lot, because we do a lot of public outreach and working with the community and I’m realizing how bad of communicators we are, as scientists often, you know. It’s not our fault.
Of course, no one teaches us you know, anything about it, it’s not part of our training or anything. And potentially, you know, my guess is that, you know, it’s part of the acceleration process of doing exactly what you’re describing, will require the field to kind of shift, you know, their value systems a little bit to understand those types of barriers and actually put some energy into doing better, creating common standards and language across the different layers of neuroscience.”
Here is an episode with Paola Oliveri, developmental biologist at University College, London.
“So how can we generate novelty? How can we be different in many different ways? So echinoderms have done an enormous amount of novelties. And so to understand, including, you know, completely reshape their body, the body pattern from bilaterial to pentaradial, which is absolutely dramatic.”
Some are with several 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.
Invisible Adversity is with and about Uri Manor, a researcher at the Salk Institute who studies the dynamics of cells and Aly Putnam, who is a PhD student at University of Massachusetts in Amherst. They are researchers in different career stages. They share the fact that they are people with disabilities. They take on their disabilities, and the world, head-on with strength, creativity and humor. Uri Manor:
…”as a hearing impaired person, I was very socially isolated….I did not care about school, I did not give a sh*t. And so I wasn’t a very good student, and I’m not sure anyone would have predicted that I would actually be successful in academia. Right? It’s it’s quite a contrast. …But the thing that saved me was guitar, I started wanting to learn how to play guitar, and I loved music, music, unlike people, I can turn up the volume.”
There’s a series about protein structure prediction such by using a platform called AlphaFold developed by DeepMind Technologies, a company that Google bought in 2014. Protein structure prediction is hard, but AlphaFold, ‘an AI,’ tackles this hard problem, which might not be NP-hard.
In this episode, Janet Thornton from the European Bioinformatics Institute and David Jones of University College London chat abouty the impact of AlphaFold on their science and the scientific community more generally. David Jones did his PhD with Janet Thornton, so there is much banter. We talked about blobs, about models, about being compute-constrained and about what can happen when you are not compute-constrained.
In this episode of Ukraine and science, I chatted with Dmytro Gospodaryov, a researcher in the department of biochemistry and biotechnology at Vasyl Stefanyk Precarpathian National University in Ivano-Frankivsk, West Ukraine about how the war has affected him and his family, his lab, friends and colleagues.
You can listen to any of these podcasts on Apple podcasts, Google Podcasts, Spotify, Stitcher, Breaker, on transistor.fm.
The CRISPR Children.
How are the ‘CRISPR babies’? The children were born in China and to an uproar. It was 2018 when, as far as is known, the first children with genomes edited before their birth, were born. They are now toddlers. How might their edited genomes affect the lives of Lulu and Nana and a third child I name Amy. She was not mentioned in the talk by He Jiankui who had been invited to present at the Second International Summit on Human Gene Editing. He decided last minute to talk about the children–that had not been planned previously.
The reporting this story took me into science, commerce, culture and history. And secrecy. The investigative story about them in Nature Biotechnology was three years in the making. It’s accessible here or here.
To go along with the story, I did some blog posts and podcasts. More podcasts on this subject are underway. The scientist responsible for for this is now out of jail and, it seems, starting a biotech company. To me the issue is about these children as well as the ethics of it all. And how this event is shaping the present and future of medicine.
Here are some resources. This podcast 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: The CRISPR Generation: The Story of the World’s First Gene-Edited Babies
And here is episode 2, 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.”…
Here is episode 3 with anthropologist Eben Kirksey from Deakin University. He is also author of the book:The Mutant Project
“Dr. He definitely had some very powerful backers within the Chinese Communist Party. And he worked with them. He gave them foreknowledge in the same way that he gave the Associated Press foreknowledge of the birth and planned a release very much with blessings from important political factions in Beijing. As a speaker at the summit, I watched kind of the public takedowns emerge in real time.”
Here is episode 4 with Alison van Eenennaam from the University of California, Davis.
“That’s when we started: what if we fertilize only for six hours. Well our fertility goes down but we get reduced rates of mosaicism. So for us that’s more important. If instead of getting 40 blastocysts we get 10 blastocysts but they’re all non-mosaic, that’s a better bet for us then getting 40 mosaic blastocysts. Those are the types of things in a long-lived species like cattle where you have three years to get to maturity and have their own offspring, you don’t really want a mosaic because you need to breed that out of them. And that’s a decade.”
The brain is a crucial organ we have on board that’s networked with our identities. Some of how it manages its feats is known but most remains a mystery. For example how we and others learn to vocalize and why we do. Here’s a story I did on that subject. and here’s an excerpt:
Stella and Disco are feathered, talking YouTube stars. “What do you think?” asks Stella, a starling, speaking directly into the camera. “I’m Disco and I know it,” says Disco, a parakeet, in a separate video. Some songbirds have a knack for mimicry. Lyrebirds can imitate the songs of many bird species, the sound of car alarms, camera shutters and chainsaws. Disco sings his species-typical song as well as TV theme songs, and he can beatbox. “They’ll pick up anything,” says UCSD neuroscientist Timothy Gentner about songbirds.
Labs study brain anatomy; here’s a story I did in Nature about how anatomy can help with understanding networks. Researchers clear brain samples, to remove and transform the tissue so it becomes transparent and they can study the neuronal networks as they are in the brain. Here’s my story on some of that work. The researchers might combine approaches such as electrophysiology and genomic sequencing. Here’s a story I did in Nature Methods about Patch-seq.
Neuroscientists explore how neurons send and receive signals to and from other neurons. From my Nature story: A deep look at synaptic dynamics:
“Kiss-and-run sounds like a schoolyard prank, but it is also the informal name for one of four vigorously debated hypotheses about what happens in neurons in the brain before and after they transmit signals to one another at the cell-to-cell junctions called synapses.”
They try to untangle the puzzling and difficult aspects of disorders such as schizophrenia. From my story Convergence in neuropsychiatric research
Cross-disciplinary consortia promise to brook divides, but too many researchers tell a colleague only “what they think you need to know, which creates silos and loses much of the benefits of cross-disciplinary collaboration, and reduces the opportunities to learn from each other,” says a scientist who wished to not be named. Over time, such behavior will retreat. “The cool thing, I guess, is that we actually are now getting a suite of technologies that are up to the task that we need,” says Sullivan, the principal investigator of the Psychiatric Genomics Consortium (PGC), which includes more than 800 scientists from over 40 countries. He’s also part of PsychENCODE2 , a consortium focused on regulatory elements in neuropsychiatric disorders.
They assess social behavior in animals such as in marmosets, here’s my story on some of that work. And also a blog post about observations of wild marmosets. Here’s an excerpt:
…”Atsushi Iriki, who directs the laboratory for symbolic cognitive development at Riken Brain Science Institute and who is also part of Brain/MINDS has also spent time in Brazil observing marmosets in the wild and he noted how different they are from wild Japanese macaques that are more familiar to him. What struck him was how cooperative marmosets are in their group as they spend all day together, as they move around or forage for food. They are always keeping track of one another in the dense bush by calling out to one another and they are always helping one another. They might, for example, share food with one another or help the younger ones jump from one branch to another.”…
For this story I asked neuroscientists and stem cell biologists how far a model of depression in a lab dish takes them. An excerpt:
In the human brain, serotonin neurons have diverse roles including effects on mood, cognition, sleep and appetite, and they have been implicated in conditions such as depression, autism spectrum disorders and anxiety. With access to large numbers of serotonin neurons, researchers could explore the cell biology of these neurons and probe poorly understood questions such as how the release of the neurotransmitter serotonin is regulated, says Patricia Gaspar, a neurobiologist at the Institut du Fer à Moulin, which is part of INSERM, the French Institute of Health and Medical Research. The neurons could be used to study the effect of drugs that target them or to screen for potential new drugs. Labs might assess whether grafting these neurons can treat brain disorders linked to serotonin deficiency.
Another approach to model the brain is to grow stem cells into organoids. I wrote about organoids in neuroscience here. An exceprt:
Organoids lack the anatomy of the real human brain, says Giorgia Quadrato from University of Southern California’s Keck School of Medicine. But, she says, they are models that let us characterize human brain development and disease in ways that have eluded the neuroscience community for decades.
Here is a podcast about organoids with Eve Marder, a neuroscientist at Brandeis University. Here’s an excerpt:
I have a perverse side in me, which is why I still study lobsters and crabs and things like that. But that perverse side of me, which I’m very proud of, finds organoids extremely intriguing.
And then the conservative neuroscience reductionist in me still believes that they’re made up, so that there are things you’re going to see in organoids that may be not terribly useful in terms of understanding how things work in the real brain. And there are other things that are going to be revealed in organoids that could open up whole new lines of investigation because you see something you never would have otherwise imagined in that way.
And I’m perfectly capable of maintaining two belief systems, which seem to be mutually system. At the same time, I learned that from my mother, who was very able to always do that. But I think both are true in the sense that organoids tell you a lot about the potential of biological materials themselves, but they are not going to tell you how the actual brain did it they’re going to tell you potentially could give you insight into many of the fundamental mechanism. But the way those fundamental mechanism are called into play during normal brain development might be different in important ways and possibly unpredictably important ways.
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.
And I also had this piece in The Daily Beast:
James Cameron and Investors Seek to Lasso and Mine an Asteroid
It’s 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.
ARTE theme evenings –
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.
For Nature, I did a story–The big challenges of big data— on uncorking data bottlenecks.
“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.”
For Nature Biotechnology I wrote this story about data-sharing.
Oversharing is embarrassing in social media but sharing is always a virtue for scientists. Although many scientists embrace the idea of sharing data in research, few manage it in practice.
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 about theoretical physicist Ettore Majorana from the University of Naples. He disappeared “mysteriously” in 1938. He had studied at the University of Rome with Enrico Fermi who reportedly called Majorana a man of “deep brilliance.”
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.
Two stories, available here and here, are about what it takes to build and maintain computational pipelines so they don’t go ‘clank.’ 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.
Here are some videos I shot, edited and produced. Here is a video about ants and insect social societies. It’ a nano-documentary.
And here is one about The Vertebrate Genomes Project. Scientists are working to sequence and assemble the genomes of 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. Information about the project’s progress can be found here.)
Here is the animation:
And here is a mini-documentary about The Vertebrate Genomes Project.
And here is a video I did on the Berlin Institute for Medical Systems Biology.
For The New York Times, I did this story about libraries and open-access publishing.
Technology: In DSpace, Ideas Are Forever
An excerpt: “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.”…
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 did a podcast on long COVID-19 and the brain. 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.
“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?” says Avi Nath.
Another long-COVID related podcast is about genetic diversity and it’s with Nadia Rosenthal, scientific director of The Jackson Laboratory. The podcast and transcript are on this page.
“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.
Primer detectives is an investigative piece about what went haywire with the test for SARS-Cov-2, the virus that causes COVID-19. In the US, the PCR assay from the CDC was giving inconclusive results, right at the start of the pandemic when the test needed to be rolled out in a massive way.
In Lessons from the Global South on COVID-19 I traveled virtually to some countries of the Global South including Cambodia, Cameroon, Kenya, Nigeria and Uganda to hear how researchers jumped to the frontlines in the battle against this public health emergency. The podcasts from this reporting are on this page. I am calling the series Creative Grit because that is what researchers are deploying to get this work done.
Two billion people, a quarter of humanity, play a special role with COVID-19 infections. Perhaps they have special vulnerabilities. Thomas Egwang, director general of Med Biotech Laboratories, a research lab in Kampala, Uganda spoke with me about why they matter for the development of treatments and vaccines. The podcast with him is here.
Coronavirus jolts labs to warp speed is a piece about the many ways labs accelerated 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 about assays under development–smaller, faster more simple ones. These attributes 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 junior structural biologist from Singapore who was training in Germany when COVID-19 led to a detour in his life. His experience is one example of many around the world of people whose education and training were interrupted by COVID-19.
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.
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….
A friend’s young daughter has cancer. “I would gladly take his daughter’s disease from her and place it on top of my own a thousand times,” says Ken. His plan is to beat his cancer and to better his research for the benefit of others. “Cancer shot itself in the foot when it screwed with me. Period,” he says….
Ken passed away with his wife Laurel by his side. This text is based on Ken’s blog and on conversations with him. He saw a version of this article before his death. His wife saw it, too and I am grateful she let me into her and Ken’s life.
You can read the piece on Medium here.
For Die Zeit, I did a story about zebrafish research, friendship and rivalry in science. The piece is with Nobel Laureate Christiane Nüsslein-Volhard and MIT researcher Nancy Hopkins. Von Fischen und Frauen
For The Lancet, I wrote NIH global health fellowship reinvents itself.
It’s about a US National Institutes of Health (NIH) program to train global health researchers widening its medical focus. I had the chance to speak with former fellows of the NIH Fogarty Global Health Program for Fellows and Scholars, such as pediatrician Eric McCollum from Johns Hopkins University who went to Lilongwe, Malawi and at the time was heading back there soon. He seeks better ways to treat respiratory illness and malnutrition in children with HIV/AIDS and other conditions he sees in under-resourced hospital wards.
And there was Ana-Claire Meyer, a UCSF neurologist who studies the effects of infectious disease on the nervous system. She mainly lives in Kisumu, Kenya and explains how she has expanded her medical scope given that her Kenyan colleagues ask about treating epilepsy, stroke, and dementia.
Also for The Lancet, I did a piece called FDA Reform Plan Edges closer to Realisation on a Congressional bill that modifies the US Food and Drug Administration regulation of drugs and devices. For example, it involves $6.4 billion in ‘user fees’ for FDA from drug makers over five years, the necessity for drug companies to inform FDA of looming drug shortages and the increase of jail terms related to drug counterfeiting.
For New Scientist, I wrote Steam Power takes to the road again. It’s 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 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.
Also for New Scientist, with Graham Lawton, I wrote To cut or not to cut about male circumcision. It’s a decision parents of baby boys face and it’s not an easy one.
IMAGINE a quick and simple surgical procedure that trials have shown could give your newborn child lifelong protection against HIV and may ward off sexually transmitted diseases and cancer too. It involves a little pain and bleeding, and occasionally goes wrong, but the risk of serious adverse effects is tiny. Would you have it done? Chances are you would. But what if you found out that other trials have called the procedure’s benefits into question, and that it involves cutting off part of your child’s penis. Now how do you feel about it?
In another piece for New Scientist called Everything must go I wrote about the science of advertising.
JUST before kick-off at a recent American football league game at the Ford Stadium in Detroit, fans watched in amazement as three trucks burst through a doorway and raced across the pristine playing field dragging giant billboards. The game started moments later – the trucks hadn’t disturbed a single blade of grass. In fact, no one in the stadium had seen a thing. Only viewers watching at home had seen them. The trucks are the latest of a new breed of TV advert that hits the “target”, as advertisers affectionately call us, with eye-catching virtual images.
For Science, I did a story called Beautiful Bioimages for the Eyes of Many Beholders.
“A handful of image-sharing databases and software systems is becoming available, and these images might change the way biologists look at their own and other researchers’ data–if several obstacles can be overcome. Aside from the technical difficulties of creating user-friendly databases and interconnected networks of images in the scientific literature, there are pesky legal and ethical questions, such as ownership and credit.”
For my Nature story Stop the microbial chatter I asked researchers about the many ways microbes signal to one another.
Bacterial communication was first studied in the 1960s, and not long afterwards, researchers found that a marine bacterium known as Vibrio fischeri would start to shine brightly once its population reached a certain density1. The finding that bacteria will turn their light on synchronously under certain conditions suddenly rendered bacterial behaviour visible and measurable, says Princeton University researcher Bonnie Bassler. But because most scientists believed that bacteria were incapable of “fancy things” such as signalling, she says, the collective behaviour was generally dismissed as a “goofy phenomenon of bacteria living in the ocean”.
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)
In this story I write about how scientists decipher which microbes are in their sample, all the way way down to the strain-level. To explain the task of strain-level identification, Christopher Quince of University of Warwick Medical School helped with a tale about a monk. It starts like this:
What the monk saw: a metagenomic tale
Dramatis personae: libraries: microbial samples; book: a microbial species; book versions: strains; words and letters: genomic data; reconstructions: continguous genomic segments (contigs); shared colors: metagenomic binning, which uses shared frequencies across samples in order to assign contigs to species or strains.
A bibliophile medieval king wants to survey Europe’s libraries by copying all the books. Some libraries hold many copies of one title, such as the Bible or Aesop’s Fables. The king seeks out a monk who is a renowned, fast copyist, albeit a little unfocused.
The monk travels far and wide to monastery libraries. He randomly pulls out a book and copies 50 words onto a parchment snippet. He repeats this task a million times, sometimes with the same, sometimes with a different book. He puts the snippets in a sack and travels onward. Over time, he enlists other copyists to help with the copying tasks….
In reporting different microbio story, here, I heard from scientists who work on ways to engineer microbiomes.
Microbiomes are bustling, evolving, complex microbial communities, as spatially and temporally variable as they are heterogeneous1. To take on this complexity, says Harris Wang, a researcher at Columbia University’s Irving Medical Center, his lab’s philosophy is: “Embrace some of the messiness of natural environments,” since it will help with engineering technologies resilient to such variability.
Biology and medicine
For this Nature story, The genome jigsaw I spoke with researchers about genome assembly.
“To understand why high-throughput gene-sequencing technology often produces frustrating results, says Titus Brown, imagine that 1,000 copies of Charles Dickens’ novel A Tale of Two Cities have been shredded in a woodchipper. “Your job is to put them back together into a single book,” he says.
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 tally how many proteins there are in a cell.
Having this tally is another big step toward understanding cells. And understanding the differences between healthy cells and those afflicted with disease.
For this story Erin Dewalt again did a fabulous illustration.
This idea for this illustration arose as I interviewed people and heard how powerful dream this concept of single-cell proteomics was to them.
This method is about labs find out and capture which genes are expressed where in a tissue or cell. It’s called spatially resolved transcriptomics. Here is my story in Nature Methods, 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….
And here are two podcasts on this theme. Here is one with Patrik Ståhl and Fredrik Salmén. Here is one with Bosiljka Tasic and Hongkui Zeng.
Much work in life science labs is about single cells, which is work that builds relationships. One of my stories on single cells is here. A number of them are about genomics. My Nature piece The DNA of a Nation is about the plan to sequence 100,000 genomes from the general population. And it’s about how the companies are selected to take part in this project.
Some of my articles are about gene-editing. Here is one on base-editing ands here is one on guide RNAs.
I have written a few pieces on plants. Here for example is a piece about ways scientists focus on plant cells to study larger aspects about plants that remain a puzzle. Excerpt:
The Trembling Giant is a forest of 50,000 slender aspens that gets its name from the sound of its trees’ leaves rustling in the wind. These 80,000-year-old trees in Utah’s Fishlake National Forest are a single plant clone. All of the trees are genetically identical because they have grown asexually, through a process called suckering, from one parental root. Plant biologist David Galbraith of the University of Arizona wonders how a clonal plant with identical somatic cells could have survived predation and global climate change for so long, and which cellular mechanisms mattered in its survival. There’s no answer to this question yet, he says. Another question that intrigues him is whether individual somatic cells of plants are identical or differ genetically, epigenetically or in some other way.
Such questions call for cell-based assays, which might not seem to be as prominent in plant-based labs as in labs focused on animal or human cells. But Philip Benfey, a plant biologist at Duke University who began his career working with animal cells, says, “I don’t think that there’s a sense that we just can’t do certain things that are being done in the animal field, because we don’t have a technique.” Plant biologists have assay options with which to study cells in their normal or near-normal context.
And I just wanted to include this lovely image from the story. Plant biologist Jen Sheen from Massachusetts General Hospital is also a painter.
(Jen Sheen, MGH)
And here is one, Exploring the diverse, intimate lives of plants. Exceprt:
“I’ve invented a new algorithm to predict phenotype from genotype,” says the presenter in a cartoon about a lab meeting. “Brilliant!” “Superb!” exclaim the attendees. Says another meeting attendee, “Someone did it in plants in 1978.” In next cartoon panel, that last commenter is tossed out a window. Scientific findings in animals are sometimes “hailed as breakthroughs” when in fact they were predated by discoveries in plants, as in the case of RNA interference and immune receptors, notes1 Nick Talbot, who directs the Sainsbury Laboratory in Norwich, UK, where he also runs a lab. Plant blindness, as the underappreciation of plants is sometimes called, is an eye-roll-inducing evergreen. A number of plant labs develop and use new approaches to assess how plants, fungi and microbes interact. There’s more than give and take between plants and microbes; dramatic, intimate strategies are at work2,3,4,5,6. Given that climate change demands attention, a deep understanding of these interactions offers new ways to address how to sustain ecosystems and biodiversity. “We are in a new era that puts networks in the center of our understanding of biodiversity,” says Toby Kiers, an evolutionary biologist at Vrije Universiteit Amsterdam.
In my reporting, I interview people and often I get to profile them. Sometimes these stories are about the interaction between two people, as in my story for Die Zeit about Christiane Nüsslein-Volhard an Nancy Hopkins. In other instances, it’s been about individuals such as Michael West, former CEO of Advanced Cell Technology and now CEO of AgeX Therapeutics. He had a fascinating way of dealing with people protesting in front of his ACT lab. He used to be an evangelical Christian and he understands where the protestors are coming from. He invited the protestors into the lab for a discussion. They declined.
For Nature Methods, I have profiled many scientists for a column called The Author File. They are all listed in my Google Scholar profile here.
I developed a column for the journal called Lab & Life and it’s also about people and their research. I often do podcasts and blog posts related to these columns. Here is one such blog post called The joy of transcending disciplines.
It’s with Aviv Regev who is executive vice president and global head of research and development at Genentech/Roche, Hattie Chung, a postdoctoral fellow at the Broad Institute of Harvard and MIT whom Aviv Regev advised when before she left The Broad for Genentech, Yang Bai from the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences (CAS) in Beijing, Kay-Hooi Khoo who explores how glycans and proteins interact at Academia Sinica in Taiwan and Hari Shroff who is at Janelia Research Campus. Excerpt:
Aviv Regev says she has had privilege of spending her entire career thus far in a borderless, boundary-crossing world, so in a sense, this is the only way she knows and “this has brought richness and joy to my work and life.” …
“When I inevitably feel frustrated by the limitations of a given field — for example, a biological problem appearing too big and complicated to address with traditional lab techniques — I tend to also see alternative possibilities: how could another, perhaps seemingly distinct, discipline help me address this limitation or answer this question?”