Why I like scicomm on Mastodon!

A geoduck clam (also called "elephant clams") next to the elephant-like Mastodon mascot. The clam has along trunk-like siphon.
A geoduck clam (also called “elephant clams”) next to the elephant-like Mastodon mascot

Over the last couple weeks, I’ve seen hundreds of academics, nerds and everyday people I know open new accounts on Mastodon, in a phenomenon that has been called the great #TwitterMigration. Mastodon is an open-source microblogging platform similar in format to Twitter, but running on thousands of servers interconnected with each other in an open network called the “Fediverse” (referring to the fact that these services are “federated” to each other). Many researchers are disillusioned with the current state of Twitter, which was purchased recently by an erratic, bigoted oligarch, and are registering their disapproval by seeking out other places to share their science.

Personally, I am not “migrating” per se, as I have been using Mastodon for over 4 years now. I don’t intend to close my Twitter account, because I think the site will survive the current damage being done to it, though I’ve stopped posting for the time being, while they work through the process of learning the hard way that hate speech can never be allowed on the platform. I wanted to write about my experience using Mastodon to communicate science and why I think it has a lot of advantages over Twitter for certain use cases, precisely through the ways it does not seek to be a direct Twitter replacement.

Posting how I want

First of all, Mastodon gives me way more freedom to post the way I want. It is a true “micro-blog” in the way Twitter can’t be, since I get enough characters (500 at scicomm.xyz, and more on some servers!) to allow me to post a real paragraph. I have never found Twitter’s 180 characters to be enough space to really tell a satisfying story. Some people get around this by posting threads, but I also have never enjoyed writing threads! Other than that time I went on a giant clam fact rant. Mastodon also supports threads if you’re into that, and also allows you to set the visibility on your subsequent posts, so that your replies to yourself don’t spam everyone’s feed.

In my four years writing #clamfacts on Mastodon, I’ve written short facts. Long facts. Silly facts. Meaningful facts. I just have a lot more freedom with the format. Mastodon was also much faster to enable accessibility features like image descriptions than Twitter was. So the facts I shared are more accessible to disabled folks. While Twitter now includes alt-text, it still feels like Mastodon’s alt-text is a more mature feature. As with subtitles and other accessibility solutions, these features end up improving usability for everyone. In the case of alt-text, it gives me tons of space to describe scientific diagrams for anyone who might need additional context.

Mastodon recently added the ability to edit posts, which has been very advantageous for me, as a typo-prone individual. For Twitter, that feature is still locked behind a subscription. But even before editing was available on Mastodon, there was an option to “Delete and redraft”, which I used frequently to re-post when I had forgotten an image description, or to fix a typo. Mastodon has long provided far more options to control who can see a post and how, which is why I felt more incentive to be creative there than on Twitter.

A small pond by design: Engagement and sustained connection over reach

Twitter sometimes feels like an RSS feed with comments. Particularly for the more popular accounts or viral posts, while you can reply, there is such a torrent of feedback on the other end that it is difficult for them to respond to everyone. For my niche specialized clamposting, I am not interested in going viral. I just want to engage with people and learn from them as much as I share knowledge with them.

Mastodon is very well designed for this. Your posts get shared across the federated network, but only as much as other people “boost” it (analogous to retweeting) or reply to it. There are favorites (similar to the like button), but those are mostly just a direct message that someone liked a post, and have no impact on whether it spreads larger over the network. So the main people seeing my posts are my direct followers. And because Mastodon is a reverse chronological feed, with no opaque algorithm determining whether or not to show someone something, I am more confident that a bot moderator isn’t going to misidentify my clam content as NSFW and hide it by default from people’s feeds.

Culturally, Mastodon is driven by following people, and making your feed for yourself, rather than having posts from people you don’t follow pushed to you by a computer. If you follow someone back, you’re more likely to make a lasting connection through time, rather than trusting some algorithm to figure out who you enjoy to see. This leads to more lasting, meaningful connections in my experience. Truly powerful scicomm never happens in one direction; it relies on exchange.

I think that Mastodon will stay like this in the future, even as it continues to grow by leaps and bounds. Rather than one giant, sometimes dangerous ocean like Twitter, it’s more of a collection of small ponds. My reach is restricted to my followers and their followers, and sometimes their followers’ followers. That produces much more meaningful, sustained connections.

Hosted and moderated by scientists, for scientists

My home since the start has been Scicomm.xyz, a server run by a scientist in the UK going by the username Quokka. Recently he recruited another scientist and me to be moderators on the server, and we’re looking to add more. But since the start even before I was moderating myself, I’ve felt more secure sharing science when it’s hosted and moderated by another scientist. Even before Twitter laid off moderation staff en masse, and before the site announced scientific misinformation is now fair game, Twitter was not a place run by scientists, for scientists. If someone replied to me with misinformation about the coronavirus or climate change, my recourse against them was limited, since the moderation staff there are not exactly experienced peer reviewers. On Mastodon, there have always been data-conscious nerds running things. And now, there are a constellation of sciencespecific servers to choose from!

Science, including scicomm, is always more at home in an open-source environment

The last point I’ll bring up is that science always works better in an open-source environment. Mastodon is available free and open-source on Github for anyone to download, alter and run themselves. I prefer to use such open-source solutions in my own scientific work, from including Rstudio, QGIS, ImageJ, Raspberry Pi, Arduino, Ubuntu, Inkscape, Firefox/Thunderbird and more. So hosting my science communication on an open platform feels like preaching what I practice, as opposed to allowing a for-profit company to own my scientific content.

For all the reasons above, I have been extremely pleased to see the wave of scientists, technologists and other interested people join Mastodon over the last few weeks. I feel Twitter will still have a place in my science communication once it has worked through its current drama. But in the meantime, I look forward to sharing my clam facts with all the people I can, in my little pond on Mastodon.

Research Explainer: How I learned to stop worrying and trust the clams

Two giant clams off the coast of Israel. Left: Tridacna maxima, the small giant clam. Right: Tridacna squamosina

Another year, another new paper is out, another clamsplainer to write! The fourth chapter from my PhD thesis was just published in Proceedings of the Royal Society B. This study represents five years of work, so it feels great to finally have it leave the nest. In this study, we investigated the comparative growth of fossil and modern giant clams in the Gulf of Aqaba, Northern Red Sea. Back in 2016 during my PhD, I knew I wanted to study giant clams because they are unique “hypercalcifying” bivalves that grow to huge sizes with the help of symbiotic algae living in their bodies. The clams are essentially solar-powered, and use the same type of algae that reef-building corals depend on! Unlike corals, which are the subject of a ton of research related to how they are threatened by climate change, habitat destruction and pollution, comparatively little is known of how giant clams will fare in the face of these environmental changes. Are they more resistant than corals, or more vulnerable?

T. squamosa on the reef off the coast of Eilat.

I had strong reason to suspect that the clams are struggling in the face of human changes to the environment. They can bleach like corals do when exposed to warm water, and have been observed to be harmed when waters are less clear since they are so reliant on bright sunlight to make their food. But I need a way to prove whether that was the case for the Red Sea. I needed to travel to a place where fossil and modern giant clams could be found side by side, so their growth could be compared using sclerochronology. We would count growth lines in their shells to figure out how fast the grandaddy clams grew before humans were around, and compare that ancient baseline to the growth rate of the clams in the present. Giant clams make growth lines every day in their shells, giving us the page numbers in their diary so we can figure out exactly how fast they grew! We can also measure the chemistry of their shells to figure out the temperatures they experienced from the oxygen isotopes, and even what they were eating from the nitrogen isotopes.

A map of the Gulf of Aqaba, where our study took place. My talented marine scientist partner Dana Shultz made this map!

It just so happened that UCSC’s Dr. Adina Paytan was leading an NSF-funded expedition to the Red Sea in summer 2016, which represented a perfect place to do this work. There are many age dated fossil reefs uplifted onto land around the Gulf of Aqaba on the coasts of Israel and Jordan, and there are three species of giant clam living in the Red Sea today: Tridacna maxima (the small giant clam), Tridacna squamosa (the fluted giant clam), and Tridacna squamosina. Tridacna squamosina is particularly special because it is only found in the Red Sea, making it an endemic species. It is extremely rare in the modern day, with likely only dozens of individuals left, making it potentially endangered.

So I set off with Adina and two other students to live for two months in in the blazing hot desert resort town of Eilat, Israel, working at the famous Interuniversity Institute. Getting a permit from the Israeli National Parks Authority, I collected dozens of empty giant clam shells (no clams were harmed in the course of this study!) from the surf zone and from ancient reefs ranging from a few thousand years to almost 180,000 years old. I also spent a week over the border in Aqaba, Jordan where I worked with Dr. Tariq Al-Najjar, my coauthor and director of the University of Jordan Marine Science Station. Tariq is a specialist in algal productivity in the Gulf and was an excellent resource in trying to understand how water quality has changed in the area through time. He pointed out that over the years, the Gulf of Aqaba has had an increased nutrient supply far above what it received in historic times. For nearly 20 years the Gulf was subjected to excess nutrients from Israeli fish farms, which caused tremendous damage to the reefs of the area with their releases of fish waste. The farms were finally forced to close after a long lobbying campaign from Israeli and Jordanian scientists and environmentalists. But even after the farm pollution stopped, there was still increased nutrient supply from runoff and even carried into the Red Sea by dust in the form of nitrate aerosols. These aerosols are produced when our cars and power plants release nitrogen oxide gases, which react in the atmosphere to form nitrate and fall during periodic dust storms that hit the Red Sea a few times per year.

All of these sources of nitrogen are fertilizer for plankton, causing what scientists call “eutrophication.” When plankton blooms, it literally causes the water to be less transparent, which could reduce the clams’ ability to gather light and lead to them growing more slowly. At least that was my hypothesis, but I had to prove if it was true or not. So during that summer and over the next few months, I cut dozens of clam shells into cross-sections, used a special blue dye called Mutvei solution to make their growth lines visible, and took pictures of those lines with a microscope. Then I counted those lines to figure out how many micrometers the clam was growing per day.

A picture showing some of the fine daily lines visible in a blue-stained shell

Here I hit my first challenge: it turned out some clams were putting down one line per day as expected, but some were putting down twice as many! But the way I was using to discern between the two was to measure the oxygen isotopes of the clams’ shells, which forms a record of temperature. By counting how many lines appear between each annual peak of temperature, we confirmed some were daily and some were twice daily. But the oxygen isotope approach is expensive would not be scalable across the dozens of shells I had collected.

Annual growth lines in the shell of a Tridacna maxima clam

Then I remembered that I could measure the lines in the inner part of the clams’ shells, which are formed annually. By counting those lines and then measuring the length of the clam, I could get an approximate measure of how much it grew per year on average. This would allow me to calibrate my band-counting and discern which records represented daily lines and which were twice daily! What a relief.

So I went through all of the shells, counting lines and gathering growth info for as many shells as I could muster. It meant many hours staring at a microscope, taking pictures and stitching the pictures together, then squinting at my computer screen highlighting and measuring the distance between each growth line. I had hoped to come up with an automated way to measure it, but the lines turned out to be faint and difficult for the computer to distinguish in a numerical way. So instead I just powered through manually. When I had the raw growth data, I then transformed them to a pair of growth constants commonly used in the fisheries literature to compare growth across populations. When I put the data together across all 55 shells, I was surprised to discover that my hypothesis was totally incorrect. The clams were growing faster!

Growth constants for all three species, comparing fossils and modern shells. We used two growth constants (phi prime and k) to help control for the fact that our clams were at different sizes from each other. You wouldn’t compare the growth rate of babies and teenagers and try to make any broader assumptions of their relative nutrition without some additional attempts to normalize the data!

Science rarely goes according to plan. The natural world is too complex for us to follow our hunches in understanding it, which is the main reason the scientific method came about! But at a human level, it can still be shocking to realize your data says you were totally wrong. So after a few days sitting and ruminating on these results and what they meant, I remembered what Tariq and other scientists had said about nitrates. The clams are essentially part plant. They use photosynthetic symbionts to gain most of their energy. And much as nitrate pollution can fertilize plankton algae growth, maybe it could do the same for the algae within the clams! It had previously been observed that captive giant clams grew faster when “fertilized” with nitrates or ammonia. But such an effect had never before been observed in the wild. We needed a way to demonstrate whether the Red Sea clams were experiencing this.

Fortunately, the clams also keep a chemical record of what they’re eating within the organic content of their shells. Shells are a biological mineral, made of crystals of a mineral called calcium carbonate. But within and between those crystals, there’s a network of proteins the clam uses like a scaffold to build its shell. Those proteins are made of amino acids that contain nitrogen. That nitrogen comes in different “flavors” called isotopes that can tell us a lot about what an animal eats and how it lives. The ratio of heavier nitrogen-13 and lighter nitrogen-12 increases as you go up the food chain. Plants and other autotrophs have the lowest nitrogen isotope values because they use nitrate directly from the environment. For every level of the animal food chain, nitrogen isotope values increase. Herbivores are lower than carnivores. If you live on only steak, your nitrogen isotope values will be higher than a vegetarian. The same will be true for clams. If the clams were taking in more nitrogen from sources like sewage or fish farms, they would show higher nitrogen isotope values in the modern day.

We found that nitrogen isotope values were lower in the modern day!

Taking bits of powder from several dozen of the shells, we worked with technician Colin Carney at the UCSC Stable Isotope Lab to measure the nitrogen isotopes of the shell material. A machine called an Elemental Analyzer literally burns the shell material to release it in a gas form. A carbon dioxide scrubber absorbs the CO2 and carbon monoxide gas, leaving only the nitrogen gas behind. That gas is measured by a mass spectrometer, which essentially separates out the different isotopes of nitrogen and tells us what fraction is nitrogen-13 or nitrogen-12. Plotting all the shell data together, I discovered that my hypothesis was…totally wrong. The nitrogen isotope values of the modern shells were lower than the fossils. The clams had moved down in the food chain, but how?

A dust storm rolling over the Israeli Negev Desert. Source

After ruling out a bunch of other explanations including the preservation of the shells, we propose that this represents a human-related change in the environment that the clams are recording. As I mentioned before, the Red Sea these days is regularly hit by huge dust storms which are conduits for nitrate aerosols. Our cars emit nitrogen-containing gases which, through a complex web of chemical reactions in the atmosphere, end up in the form of nitrate particles called aerosols. These nitrate aerosols bind to the dust delivered by strong windstorms called haboobs, which carry the dust long distances, with some of it being deposited several times of year. This deposition of nitrate has been found to form up to a third of the nitrate supply hitting the Red Sea, and was a source of nitrogen that wasn’t available to the clams in historic times. These nitrate aerosols are extremely low in nitrogen isotope value, and would be very likely to explain the lower nitrogen isotope value in our clams! If the clams ate the nitrate, their symbionts would grow more quickly, providing them with more sugars through photosynthesis and accelerating clam growth!

Some additional factors probably also have influenced giant clam growth in the region. The Red Sea historically had regular monsoon rains which likely slowed growth in fossil clams, as storms are known to do for giant clams in other areas, but such monsoons no longer reach the area. The Red Sea also had much higher seasonal range of temperatures in the past, with colder winters and warmer summers. Both factors (storms and extremes of temperature) have been previously shown to depress giant clam growth, and so the modern Red Sea may be a goldilocks environment for the clams: a consistent year-round not too cold or hot temperature.

However, as we discuss in the paper, these factors don’t necessarily mean that the clams are healthier. Faster giant clam growth has been found in other research to lead to more disordered microstructure in their shells, which would have uncertain effects on their survival against predators like fish, lobsters and humans. Additionally, a higher nutrient supply to reefs often causes the corals that build the reefs to lose out to competition from algae that block sunlight and crowd out coral colonies. If the reefs are harmed by the climatic changes that have potentially helped the clams, the clams will still lose. Giant clams are adapted to live only where coral reefs are found, and nowhere else. So more research will be needed in the Red Sea to determine if the health of clams and corals is hurt or harmed by these nitrate aerosols, and what that will mean for their long-term survival in the area.

Over the course of working on this research, the giant clams taught me a lot about life. They taught me that my hypotheses are often wrong, but that’s alright, because my hypotheses can still be wrong in a way that is interesting. I learned to go with the flow and trust the clams to tell me their story through the diaries they keep in their shells. I have followed their lessons wherever they led. Now I am doing follow-up work growing giant clams in a giant coral reef tank at Biosphere 2 in Arizona, to directly observe how the clams’ symbiosis develops and create new forms of chemical records of their symbiosis! The work described in my paper here has led to a suite of different ongoing projects. The clams have many more lessons to teach me. Thank you clams!

Recent Science Communication!

At Biosphere 2, our science is essentially done in public. Every time I’m in the water checking on our clams and the sensors around them, I’m in view of the public and essentially an attraction for the public to watch. This is a really unique way to do science unlike any of my past experience, when I’ve been out in the field with a collaborator, or in the lab with a laboratory technician. I was initially intimidated by the idea of doing my science with an audience, but I’ve decided to lean into it as a huge opportunity. It is rare that the public gets to see all the steps going into our science; they usually only see the end of the story and not the whole journey leading up to that point. So recently I participated in two new ways of sharing my work while it’s in progress with the public.

The first was a collaboration with Mari Clevin, a videographer with the University of Arizona who made a really nice profile of my crazy clam journey. It was a lot of fun showing her around B2, trying to capture what it’s like to work here. It was fascinating seeing how all her footage and interviews came together into a video, and how she captured the key points of our conversation into a narrative!

The other scicomm event I participated in was a “Research Show and Tell” event run by the PAGES Early Career Network. Early Career Researchers include PhD students, postdoctoral researchers like me, and early career faculty. The ECN is intended to help us band together to share opportunities and plan events relevant to our interests. Among the North American regional representatives for the ECN, we saw a real need for more informal ways to share our research to an advanced audience of our peers. We’re all burned out from Zoom webinars, and on the other side Zoom coffee hours don’t typically provide much opportunity to share scientific content, so there’s a real need for events in the middle. So I was excited to share my research with a group of my peers, touring them around the Biosphere, showing them my clams via pre-recorded video and then having a Q and A to describe the work. It was a lot of fun and you can watch the whole hour-long event below!