The world’s deepest zoo harbors clues to extraterrestrial life – my first piece for kids

Roundworms on a biofilm deep underground in a South African gold mine. Credit: Gaetan Borgonie

I’m excited about the publication of my first piece for kids, about the World’s Deepest Zoo, written for Science News for Students.

It covers the same topic as my Smithsonian piece from last year, i.e. life living deep beneath the Earth and the scientists who venture into underground mines in order to study them.

Of course, I had to re-report and re-write this feature for a much younger audience (about middle school level), which was quite challenging but a lot of fun. I certainly hope to write more stories for kids, I really enjoyed the process.

And perhaps it’s fitting that my first piece for kids came out after I had a kid of my own. She’ll need to be a bit older to appreciate it, but perhaps someday she’ll enjoy reading it 🙂

Ants, impostorism and a few more updates

It’s been a while since my last update, although this time I have a better reason than usual for being so busy-my wife and I were blessed with a lovely baby girl a few months ago! Between frantically trying to finish up assignments before she was born, and then being busy/sleep-deprived taking care of a newborn, I haven’t had much of a chance to post any updates (and I’m not sure how regularly I’ll be able to update in the near future, so I’ve changed my website’s front page to a static About Me page).

That said, I did finish some nice articles before/shortly after the baby arrived, here’s a quick roundup:

    The Secret Lives of Ants: This was a really fun article about a researcher trying to create the first model ant system in order to understand ant communication and behavior. It turns out there’s currently no way to do genetics on ants, and the article describes all the effort put into trying to change that, with lots of fun little details.
    Feeling like a Fraud: The Impostor Syndrome in Science Writing: As someone who’s struggled with impostor syndrome at various points in my career, it was great to dig into the research that’s been done on this topic, and how it applies specifically to science writing/journalism. I’m not sure what surprised me most about this piece–all the high-profile, highly successful science journalists who said they felt like impostors, or all the others who had never experienced it and weren’t even sure it was a real thing…Either way, I think this article should serve as a useful resource for anyone who wants to learn more about impostor syndrome and how to deal with it.
    Discovering Novel Antibiotics: Another article for The Scientist magazine, this time for their Lab Tools section on techniques used to discover novel antibiotics. Given the rise in antibiotic resistance, there’s a lot of research being done to find new antibiotics. Interestingly, scientists have identified lots of hidden gene clusters in the genomes of antibiotic-producing bacteria. These clusters could serve as potential new sources of antibiotics, but first we have to figure out how to express them. This article highlights some of the promising new techniques being used to do this.
    I also wrote a couple more Inner Workings articles for the PNAS Front Matter:

    Tiny organisms could reveal how animals evolved: I’ve been fascinated by choanoflagellates ever since I found out about them while writing this previous article. These tiny eukaryotes are the closest living relatives to animals, and scientists have been studying them to figure out how multicellularity evolved. This article summarizes recent advances in our understanding of choanoflagellates and what we’ve learned from them about the evolution of multicellularity.

    Bacteria work together to survive Earth’s depths: This one’s a more in-depth look at some of the things I briefly mentioned in my Smithsonian feature on deep life from early last year–specifically, how exactly do bacteria get food deep under the Earth where there’s no sunlight and little air. It turns out different types of bacteria cooperate with each other to survive these harsh environments. It’s an interesting finding that wouldn’t have been possible even a few years earlier, before the advent of single-cell sequencing and protocols to extract and preserve high-quality RNA and DNA from tiny samples. And of course, it wouldn’t be possible without researchers spending countless hours in deep underground gold mines painstakingly collecting enough samples for their analysis.

So that’s a quick summary of some of my work from the end of last year/early this year. I finished a few more articles that have yet to publish, will post those whenever they’re up. It might be a little while before any other major updates, I’m currently taking things a bit slow, particularly when it comes to challenging features–turns out babies can be quite time-consuming (and a lot of fun :).

How the tiny parasite Toxoplasma alters its host’s behavior

Scanning electron micrograph of a Toxoplasma gondii tissue cyst in the brain of an infected mouse. Credit: David Ferguson / EurekaAlert.org

Scanning electron micrograph of a Toxoplasma gondii tissue cyst in the brain of an infected mouse. Credit: David Ferguson / EurekaAlert.org

It’s been a while since I received my PhD, but I finally got around to writing an article about the parasite I spent so many years studying in graduate school. That would be Toxoplasma gondii, a tiny intracellular parasite that infects just about any warm-blooded animal, including humans.

My PhD thesis focused on how Toxo invades human cells and makes itself at home, but this parasite is probably more famous for its ability to make rats and mice lose their instinctive fear of cats. That’s a pretty handy trick, as that could in theory make Toxo-infected rodents easy prey for cats. And cats are the only host where Toxo reproduces sexually, so getting into felines allows the parasite to complete its life cycle.

How exactly does a tiny intracellular parasite influence its host’s behavior? Figuring that out has been a challenge. Every time researchers think they have the answer, Toxo seems to confound their expectations.

What makes this particularly interesting is that Toxo is estimated to infect about a third of all humans, and has been associated with various disorders in humans as well, from schizophrenia and suicide attempts to traffic accidents and cultural differences. To be fair, a lot of the human data isn’t particularly robust or convincing…part of my motivation to finally write about Toxo is the fact that there are a lot of misleading or overly speculative articles about what Toxo does in humans, and the evidence for a lot of those effects is pretty weak.

Still, in theory if we understand what Toxo does in rodents, that might help us figure out how it affects us.

We may finally be getting closer to understanding how exactly Toxo manipulates mammalian behavior, and there are some pretty compelling new theories. You can check out my new feature in Ars Technica for more details.

There were definitely pros and cons to writing about a parasite I know so well, and spent so much time thinking about and working on for so many years. On the one hand, I was excited to finally write about Toxo, and I knew a lot about the parasite before I even started my reporting. On the other hand, I maybe knew too many details… I had to work pretty hard to keep the article interesting for a general audience, rather than delving into minutiae that only Toxo researchers would care about.

I also initially included a lot more details about the research in humans, but as I mentioned, that research is pretty messy and inconclusive, and doesn’t really relate very well to the research in rodents, so I decided it was better left to a future article.

Anyway, check out the feature here for a deep dive into how Toxo manipulates rodent behavior.

How the gut “tastes” parasites, blood vessels “see,” and kidneys “smell” fatty acids and regulate blood pressure in response

Tuft Cells in the gut "taste" parasites

Tuft Cells in the gut “taste” parasites

In my latest feature for The Scientist Magazine, I wrote about how sensory receptors — the light, taste, and odor receptors that are primarily present in our eyes, tongues, and nose — are present all over the body, and have all kinds of functions. 

It turns out taste receptors in the gut and airway influence some of the earliest immune responses to bacteria and parasites, and your ability to taste bitter substances could influence how prone you are to respiratory infections. 

Also, blood vessels relax in response to light, and odor receptors in the kidney regulate blood pressure in response to fatty acids produced by gut bacteria, providing a means by which diet could directly affect blood pressure. Other odor receptors could affect how prone muscles are to injuries, how quickly skin wounds heal, and how sperm find their way to the egg.

Check out the full article here, and here are some illustrations for it.

An online feature about deep life for Smithsonian

Nematodes (blue) wiggle inside a stalactite from a South African gold mine in this image taken with an electron microscope. (Credit: Gaetan Borgonie)

Nematodes (blue) wiggle inside a stalactite from a South African gold mine in this image taken with an electron microscope. (Credit: Gaetan Borgonie)

I just got done with a Smithsonian feature on microbes that live in extremely inhospitable environments deep beneath the Earth’s surface, and the researchers who venture 2 kms or more underground in South African gold mines to study them.

It’s hard work, but they’ve found a surprising diversity of life living in these deep environments, and it turns out studying these microbes can give us clues about life on other planets. Check out the story here.

Really enjoyed reporting and writing this one, especially since it’s about microbiology, something that I spent so many years studying both as an undergrad and during my PhD…

How scientists can get credit for peer review: Science Careers article

Thanks to all the time I spent getting my PhD, I’ve maintained an interest in writing about careers in science, especially articles that might be helpful for graduate students and postdocs.

I wrote this article for Science Careers about different platforms (such as Publons, Elsevier’s Reviewer Recognition Platform) that allow scientists to get credit for peer review. It was very interesting to learn about these services, and I hope the article is helpful for early career researchers. You can check it out here.

Keeping busy, writing about molecular biology for BioTechniques

Developing Drosophila Embryo (Credit: Credit: Raghav Chhetri, Fernando Amat, Yinan Wan, Burkhard Höckendorf, William Lemon & Philipp Keller, Janelia Research Campus.)

Developing Drosophila Embryo (Credit: Credit: Raghav Chhetri, Fernando Amat, Yinan Wan, Burkhard Höckendorf, William Lemon & Philipp Keller, Janelia Research Campus.)


I’ve been meaning to update this website for a while, unfortunately I’ve been too busy writing articles to do so.

Among other things, I’ve been writing regular articles for the journal BioTechniques. It’s been a nice way for me to keep in touch with the latest in molecular biology, a field that I haven’t extensively written about for a few years.

I’ve written a bunch of articles for them so far, including short articles on a new way to study membrane receptors and a drug that helps worms stay young longer.

I also wrote some longer articles on the hottest topic in molecular biology right now, CRISPR-Cas9, as well as advances in how researchers photograph developing embryos and in synthetic biology, where researchers engineer cells to perform basic computational tasks.

I have several more articles on a wide variety of topics coming up. It’s just amazing to see the rate at which research techniques in the life sciences are advancing!

You can check out any future BioTechniques articles here

When it rains, it pours: my article about the monsoons and floods in India

Indian floods

Indian floods

This article on flooding in India and Pakistan has been a long time coming. I did the bulk of the reporting last year right after the devastating September 2014 floods in Kashmir, only for the article to get delayed until now.

Floods occur every year in South Asia, causing widespread damage and loss of life. Unfortunately it turns out that floods in both India and Pakistan are likely to get more frequent and more devastating, due to a combination of climate change and poorly-planned development. More will have to be done on both fronts to try to prevent flood disasters in the future. Check out my article for more details.

This was an interesting one to write and report, on what I think is an important topic, I hope to do more such stories. Obviously the long delay necessitated some revisions and compromises, and also resulted in a broader focus, mostly I’m just happy to see the article published at last.