Apps that Darwin would have loved

On By Dan KillamIn Biology, UncategorizedLeave a comment

Was Charles Darwin first? Kind of depends – Harvard Gazette

Most people know that Charles Darwin was a cerebral, deep thinking type. He traveled the world, collecting data about those finches and other stuff on field expeditions, synthesizing big ideas over decades to form his magnum opus, On the Origin of Species, where he set out his theories on natural selection and its role in evolution. However, you might not know that on a day-to-day level, Darwin was an all-around nerd’s nerd who just wanted to learn everything he could about the world, motivated by an unending sense of curiosity.

Darwin was a man who pulled plankton nets, filtering seawater just to see what cool stuff would show up when he put the resulting sample of goo under the microscope. He fiddled for earthworms and wrote a book about them over 40 years (including an experiment where he watched their progress burying a bunch of rocks over a 30 year period). He kept a heated greenhouse where he studied orchids and carnivorous plants. I consider Darwin a role model, because it’s hard to find a topic in natural history that he didn’t write about. The dude was just an unfillable sponge of knowledge.

PR-Q-00900-00001-C-00002-000-00025_p423
A view of Darwin’s greenhouse. Source: The Darwin Correspondence Project

I think Darwin would have marveled the online information that we have easy access to today. If Darwin were a researcher today, I could imagine him hosting a forum or listserv where he’d moderate, muse over the natural world and keep correspondence with the other leading scientific minds, much as he was a prolific letter writer with other researchers of his time. He might not be huge on Twitter: a bit too fast paced for his liking I bet; but I think he’d love two apps that I have also fallen in love with over the last few years.

Screenshot_20200424-234506_iNaturalist.jpg
The Explore page on iNaturalist, where you can see what species other people have recently observed in your area!

The first is iNaturalist (Android, iOS), a website and social network where you can upload pictures of any lifeform, attach information about its location, time of day and other info, and the machine learning powering the site will try to identify it for you, with amazingly accurate results. If the AI can’t figure it out, experts are waiting in the wings to provide an identification or confirm yours. Think of it like a Pokedex or Pokemon Go, but for “collecting” real life creatures. And like Pokemon Go, it can be insanely addictive to find out about all the species that are all around us at all times. iNaturalist also has an app called Seek that makes the process even more gamified!

Screenshot_20200424-234523_iNaturalist.jpg
a view of my observations

I am definitely an iNaturalist addict, and have accumulated a healthy collection of observations over the past couple years. My first was a red-shouldered hawk that I saw on campus during my PhD, but then I moved onward to fungi and plants I saw walking from my car to the office, and went back through my past pictures to identify bats I saw in Belize, fish I saw diving, and of course, my beloved banana slugs. I find it’s particularly satisfying to find out how life around you changes through the year, with the seasons. When I felt like pulling my hair out during my PhD, it kept me grounded to be able to know that the first spring flowers were opening, or the fledglings of birds were leaving the nest, or the winter rains were bringing all sorts of new fungus and banana slugs to life among the undergrowth.

I think being in touch with our natural world can help us now. While we’re sheltering in place, we don’t have to be trapped within ourselves. Even in the densest cities, there are so many bugs, flowers, birds and squirrels all around us going about their lives while we are effectively on pause. It brings me relief to know that life continues, and satisfaction to be able to understand them. Knowledge really is power, and if you know the relations between all the types of life both in evolution and ecology, it makes the world make sense in a way that provides a weird zen-like peace.

To that effect, there is a #citynaturechallenge happening starting yesterday, from 4/24-4/27/20. Take pictures of living things around you and upload them to iNaturalist, Twitter and elsewhere with that hashtag! My uploads there have been of interest to researchers studying rare snails of the Negev desert, writing books about tropical bats, and researching invasive beetles. I have been following uploads of giant clams on iNaturalist for quite some time, including the newest described species, Tridacna elongatissima, which users had been observing on the Eastern coast of Africa before it was formally described in a recent paper! I bet Darwin would have been a major, influential user on iNat.

Darwin was also a big nerd regarding rocks and fossils. Evolution is the story of life, and we can only understand that story by turning to the fossil record for information. Environmental changes provide a major motivating factor pushing life to constantly change. Geology in Darwin’s day was a developing field, with the first geological maps appearing only due to the work of William Smith and others, mere decades before Darwin’s work came to be. But his work would not have happened without the growing understanding of the massive passages of time needed to deposit the rocks all around us today. Evolution typically needs time, and fossils provide proof of how life has changed during those almost incomprehensibly long intervals.

https://upload.wikimedia.org/wikipedia/commons/3/38/A_new_Geological_map_of_England_and_Wales_by_William_Smith_%281820%29.jpg
One of William Smith’s geologic maps

To find a fossil of an age we are interested in, we must know the rocks present in the area. And the second app I’ll mention today is RockD (Android, iOS), which we can use to figure out the type of rocks right under our feet, how they were made, how old they are and even what kind of fossils have previously been found within. The data in RockD is pulled from two sources that scientists have lovingly curated. Macrostrat is a database of stratigraphic (rock layer) data that scientists have aggregated into one of the most detailed and comprehensive geologic maps ever made. And the Paleobiology Database collects observations that scientists have made over the decades of almost every fossil that has ever been found and recorded.

Screenshot_20200424-234619_Rockd~2.jpg
Of local geology when you first open RockD (my detailed coordinates obscured ;))

Rather than relying on only printed maps for his work, Darwin would have loved the ability to pull out his phone in the field and instantly know the combined work of dozens of previous researchers to understand the rock he was looking at. You can even “check in” and upload your own pictures of rocks to help researchers improve their databases, and go back in time to look at where the continent you live on was during the time of the dinosaurs!

Screenshot_20200424-234815_Rockd.jpg
Geologic map of my area. Darwin would have seriously nerded out checking out the locations of faults, formations and other features

These are only two of many apps and websites that I think would have blown Darwin’s mind. We are living in a golden age of digital science, with so many new discoveries being precipitated by the availability of easily accessible, free information in the palms of our hands. But more than that, it is fun to go outside and be able to decode the mysteries of the world around you without even being an expert in natural history. In the process, you might find yourself becoming an expert!

Why eating clams sometimes makes us sick (Part 1 of 2)

On By Dan KillamIn clams3 Comments
Image result for oysters
Is eating these a gamble? Science can help improve our odds!

I am often asked if I eat clams. The answer is yes: while I love to observe live clams and appreciate their abilities, I will eat a good clam chowder or plate of grilled scallops if presented with the chance. While I’m generally not a fan of super fishy-tasting foods, I eat bivalves with a clear conscience because farmed mollusks represent a super sustainable way to get protein! However, as many of us have learned the hard way, shellfish can sometimes produce unwanted results later after the meal, if the animals are contaminated with food poison. Eating such “bad” clams can produce a spectrum of food poisoning symptoms ranging from vomiting and diarrhea to memory loss to even paralysis and death.

Humans have known the hazards of eating shellfish for a very long time. It has been suggested that the ban on shellfish present in kosher and halal dietary rules arose as a preventative measure to protect from food poisoning (though eating fish, land animals and even vegetables can poison people in numerous ways as well). Studies of oysters have determined that ancient peoples of modern day Georgia from 5000 years before present selected their season of harvest based partially on knowledge of the seasons when such poisoning was most prevalent in their area.

How and why does this happen, and what can we do to prevent it? It’s a billion-dollar question, because when flare-ups of shellfish food poisoning happen, they are hugely costly to fishermen and the food industry, costing millions of dollars a year in lost business when fisheries are forced to shut down and products are recalled. Such events are increasing in frequency and severity. Which makes it all the more strange that these shellfish poisoning events are not the fault of the bivalves per se, but rather what they’re eating.

oyster.png
Note: people generally get annoyed when you start to point out the body parts of the oyster they’re about to swallow whole. Source

Almost all bivalves are filter-feeders, using their gills to gather small passing food particles, which they then either ingest or discard based on the quality of the food item. Clams are cows crossed with Brita filters, and for many species of clams which we eat, the reason they do all this filtration is to find phytoplankton food. Phytoplankton are microscopic algae suspended by ocean currents that make their living from photosynthesis. They are a hugely plentiful and high-quality food item, making up a huge amount of the biomass available in the ocean. Like plant-life on land, phytoplankton are highly seasonal in their appearance, rising and falling in abundance in periodic “bloom” events.

an image of red tide in Florida
Aerial view of a red tide off the Texas coast. Source: NOAA

But as Spongebob Squarepants taught us, plankton are not always peaceful. Many types of algae produce toxic compounds which may be integrated into the body parts of bivalves that eat them. Scientists call the blooms of algae which produce toxins “Harmful Algal Blooms” (HABs), and such events are growing in frequency and cause huge harm to marine life and sicken thousands of people per year. There are many algae species which cause HABs all around the world, sometimes visible as “red tides,” but not always. When HABs occur, they can lead to mass deaths of higher animals in the food chain that feed on clams such as marine mammals and seabirds. In fact, HABs are at their most dangerous to humans when they catch us by surprise.

source.gif
Who me? I’d never!
https://cdn.coastalscience.noaa.gov/csmedia/2014/02/K-mikimotoi.jpg
Microscope view of the toxic dinoflagellate Karenia. Source: NOAA

When humans eat bivalves which have been dosed with such marine toxins, many types of poisoning can occur. Brevetoxin is produced by a type of dinoflagellate phytoplankton Karenia as well as other species, and when humans are exposed, we can suffer from Neurotoxic Shellfish Poisoning, which causes vomiting, diarrhea and even neurological effects like slurred speech. Saxitoxin is produced by a variety of plankton species including dinoflagellates and freshwater cyanobacteria. When ingested in clams (such as the butter clam Saxidomus which gave it its name), fish or other animals, it can cause Paralytic Shellfish Poisoning, a sometimes fatal syndrome which shuts down nerve signaling, leading to temporary paralysis.

So we know it’s bad for humans to ingest these toxins. What is it doing to the clams? Oddly enough, some types of toxins like saxitoxin are not that harmful to the clams or other plankton eating animals, allowing them to accumulate huge amounts in their bodies with little ill effect. Its presence does not seem to influence their feeding behavior much, or their growth after exposure. Its status as a neurotoxin in mammals might be a total chemical and evolutionary coincidence, as researchers suggest that it may actually serve as a signal in some part of the algae’s mating cycle. This also may be the case for brevetoxin, which appears to be produced when Karenia is under environmental stress. But there is not much agreement in the HAB and aquaculture research fields, because there are many types of algae, which may produce their toxins for many reasons, and it is very hard for us to zoom in to the scale of the microbe and out to the scale of the ecosystem at the same time, to find any kind of universal evolutionary role of these toxins. Some researchers insist that some bivalves are influenced negatively by brevetoxin, but only at the juvenile stage during major bloom events. The effects of the toxin may only influence certain species, or only become significant if the toxin reaches the digestive tract of the bivalve. Overall, research into impact of HABs on clams is still a topic of active research, and the idea that the microbes produce these toxins to defend against bivalve predators is definitely not a slam-dunk, easily proven hypothesis. While some clams are negatively affected by the toxins, it is not consistently observed across species in a open-and-shut way, and it can be a subtle effect to observe and quantify scientifically.

giphy
Karenia to mammals: Oops!

The more I read about this stuff, the more shocked I am at the incredible complexity of marine algae and their toxins. I only started reading about them trying how to to understand how they influence bivalves. I was hoping to find some evidence of their effects on bivalve growth that I could apply back in time in fossil shells to understand the historical occurrence of HAB events. It’s important to understand HABs because they hurt people, cost our society a lot of money and if we understand how to avoid them, we can help minimize such impacts in the future as HABs continue to become more common. In my next post, I’ll talk about some of the ways that researchers have come up with to measure and monitor HABs, so that we can eat clams as safely as possible.

A Make-Up Presentation!

On By Dan KillamIn clams

Hi colleagues! Several weeks ago, I was supposed to present a talk at GSA’s annual meeting in Phoenix at the session “Advances in Ocean and Climate Reconstructions from Environmental Proxies”, but I shattered my wrist in a scooter accident the night before and was in emergency surgery during my talk time. So instead I’ve uploaded my talk with voice-over to Youtube! The whole video is about 15 minutes. You can view it above. Feel free to comment on this post or email me if you have questions!

This work is currently in the last stretch of drafting before submission, but I also discuss some ongoing research and am always open if you have your own ideas for collaborations!

Correction: we are working with geophysicists to understand the shell transport mechanism.

These are the references mentioned at the end:

Crnčević, Marija, Melita Peharda, Daria Ezgeta-Balić, and Marijana Pećarević. “Reproductive cycle of Glycymeris nummaria (Linnaeus, 1758)(Mollusca: Bivalvia) from Mali Ston Bay, Adriatic Sea, Croatia.” Scientia Marina 77, no. 2 (2013): 293.

“Glycymeris nummaria (Linnaeus, 1758).” 2019. World Register of Marine Species. 2019. http://www.marinespecies.org/aphia.php?p=taxdetails&id=504509#distributions.

Grossman, Ethan L., and Teh-Lung Ku. 1986. “Oxygen and Carbon Isotope Fractionation in Biogenic Aragonite: Temperature Effects.” Chemical Geology: Isotope Geoscience Section 59: 59–74.

Gutierrez-Mas, J. M. 2011. “Glycymeris Shell Accumulations as Indicators of Recent Sea-Level Changes and High-Energy Events in Cadiz Bay (SW Spain).” Estuarine, Coastal and Shelf Science 92 (4): 546–54.

Jones, Douglas S., and Irvy R. Quitmyer. 1996. “Marking Time with Bivalve Shells: Oxygen Isotopes and Season of Annual Increment Formation.” PALAIOS 11 (4): 340–46.

Mienis, Henk, R. Zaslow, and D.E. Mayer. 2006. “Glycymeris in the Levant Sea. 1. Finds of Recent Glycymeris insubrica in the South East Corner of the Mediterranean.” Triton 13 (March): 5–9.

Najdek, Mirjana, Daria Ezgeta-Balić, Maria Blažina, Marija Crnčević, and Melita Peharda. 2016. “Potential Food Sources of Glycymeris nummaria (Mollusca: Bivalvia) during the Annual Cycle Indicated by Fatty Acid Analysis.” Scientia Marina 80 (1): 123–29.

Peharda, Melita, Marija Crnčević, Ivana Bušelić, Chris A. Richardson, and Daria Ezgeta-Balić. 2012. “Growth and Longevity of Glycymeris nummaria (Linnaeus, 1758) from the Eastern Adriatic, Croatia.” Journal of Shellfish Research 31 (4): 947–51.

Reinhardt, Eduard G, Beverly N Goodman, Joe I Boyce, Gloria Lopez, Peter van Hengstum, W Jack Rink, Yossi Mart, and Avner Raban. 2006. “The Tsunami of 13 December AD 115 and the Destruction of Herod the Great’s Harbor at Caesarea Maritima, Israel.” Geology 34 (12): 1061–64.

Royer, Clémence, Julien Thébault, Laurent Chauvaud, and Frédéric Olivier. 2013. “Structural Analysis and Paleoenvironmental Potential of Dog Cockle Shells (Glycymeris glycymeris) in Brittany, Northwest France.” Palaeogeography, Palaeoclimatology, Palaeoecology 373: 123–32.

Sivan, D., M. Potasman, A. Almogi-Labin, D. E. Bar-Yosef Mayer, E. Spanier, and E. Boaretto. 2006. “The Glycymeris Query along the Coast and Shallow Shelf of Israel, Southeast Mediterranean.” Palaeogeography, Palaeoclimatology, Palaeoecology 233 (1): 134–48.

So you want to be a postdoc overseas!

On By Dan KillamIn UncategorizedLeave a comment

Here are three issues I wish I had thought of entering my postdoctoral fellowship. These are not intended to scare anyone away from what I have found to be a very rewarding experience working abroad, learning about a new place and taking on some very fun and exciting research, but I found there are very few resources describing these practical concerns. I learned most of this stuff the hard way. For each heading, I will describe the problem and the solution that worked best for me, which may or may not apply to you.

Acclimation is difficult

Problem: The first few weeks of your postdoc will likely be sapped by concerns related to adulting. Adulting is hard enough in the country of our birth, and those difficulties are amplified in a place where the language and cultural practices are different. I’m talking about stuff like finding an apartment, making a bank account to get checks to pay for the apartment, getting a sim card for your phone, setting up utilities and furnishing your place. These will all take an insane amount of time.

Solution: You are likely a self reliant person if you are considering a postdoc overseas. I’m not telling you to give that up, because it’s a good quality, but try to swallow your pride as much as possible. Ask your supervisor, labmates and colleagues for advice, translation and help. Find someone who can be your ally and fixer. I have been so impressed in Israel by the capacity of people to take time to help me with basic stuff, but people usually won’t volunteer. They usually need to be asked.

Also, while it may seem distasteful, consider living on campus, where logistical difficulties like utilities will be prepackaged and therefore won’t be left for you to try to arrange in a place where you don’t speak the language and don’t know how things are done.

10214399122870315
Hermit crabs are actually highly social animals. Postdocs are no different.

You may feel like a hermit

Problem: Loneliness is a universal and growing problem in modern life. Postdocs typically move to a new place where they don’t know anyone and have few connections. Take those issues and multiply them several times over when you move to a new country. You will feel far from your loved ones (even in our internet connected times). You won’t be acquainted with fun stuff in the area. Your mobility may be impacted by not having a car, depending on quality of public transit.

You might feel what I call “culture lag,” a general feeling of unease resulting from seemingly unimportant cultural differences of your host country. Do grocery stores shut down every week on certain days? Is the work week different? Do they have your favorite comfort food at the store? All of these small inconveniences add up and make it easy to decide to retreat and hide in your cave.

Solution: You need to make friends and say yes when they invite you to stuff. Your labmates will be a great group to start. They will be there to invite you to their holiday activities (holidays are by far the most isolating times for foreigners). They will tell you about fun coffee shops you can work at, and which local destinations are fun and which are tourist traps. They can tell you what they do when the grocery stores are closed two days every week.

Reach out to other postdocs or international students at your school, who may also be working abroad and have a lot in common with you. When you’re abroad in a country where you don’t speak the language, being able to talk in person to someone from your own culture every once in a while can feel like coming up for air after many weeks holding your breath. Do not be ashamed to seek out these reminders of home. They’ll recharge you for the times when you feel like a stranger in a strange land.

Being an overseas postdoc is expensive

Problem: As a postdoc, you will most likely be considered a contractor with few of the benefits of formal employment. Being overseas, this makes you vulnerable. You may not be entitled to the same quality of health coverage as citizens of your host countries. For me, I bought into the best available option which was is still bare-bones and only covers care in Israel. Consider for fieldwork and conference travel that you may have literally no worker’s compensation whatsoever. Look up if the medications you need are even offered in your host country, and whether your insurance will cover them.

While you may have a travel budget, it will likely not go as far as you’d like because you won’t be paying just for airfare. Relocation is expensive, visas are expensive, conference registrations are expensive. You may also still have financial obligations back home requiring you to transfer money, which usually costs around $30-45 per bank transfer. All of these expenses add up and will eat out of your stipend.

Individual_taxation_systems
The countries in pink may try to tax citizens abroad! Source: Wikipedia

The United States is part of a very small club of countries which tax foreign income. You will need to know if your host country is going to tax you as well, you will need to tell Uncle Sam about your foreign bank account if it is above a certain balance, and you need to know if your income is above the taxable threshold and whether the length of your residency entitles you to to claim the Foreign Earned Income Exclusion.

Solution: Budget for travel insurance for literally every trip, including going home to visit family. Make a plan for your money transfers, to spread them out as much as you can. Ensure your banks in both countries have given you all the permissions you need to easily transfer money quickly and remotely. Tax software can walk you through some of the foreigner specific tax forms, but consider also seeking advice from a preparer specializing in expat taxes. For me, all of this money and healthcare stuff makes me feel like isotope geochemistry is pretty simple in comparison. The key is to not let it sneak up on you. Ask other postdocs in your country what they did when confronted with these issues

Conclusion

Please don’t let these issues make you give up on your overseas postdoc opportunity. All of these problems have solutions. But the more preparation you do ahead of time, the more time and energy you will have for your research, and even (dare I say it) to have fun in a new country. Please reach out to me on my contact page if you have any questions!

What good is a clam?

On By Dan KillamIn Biology, clamsLeave a comment

Picture1

When I mention to people that I study bivalves, I can sometimes sense from their facial expressions that they are secretly asking “why?” While clams are perfectly content to keep doing what they’re doing without being thanked, I think it’s important to enumerate all of the ways they make our world more livable and functional.

vaughn.PNG
Various roles that freshwater mussels can play in their local food webs (Source: Vaughn and Hoellein, 2018)

Bivalves are ecosystem engineers. While they may seem rather stationary and not up to much at any particular time, they are actually always working to actively maintain their habitat. The majority of clams are filter-feeders, meaning that they use their gills to gather particles from the water column for food. Some of these particles are ingested as food and later pooped out. Some inedible particles are discarded immediately by the clam as “pseudofeces”. Both mechanisms serve as a bridge between the water column and the benthos (the sediment at the bottom). In this way, clams are engines that take carbon fixed by algae floating in the water and transfer that material to be stored in the sediment. Their bodies also act as nutrition to feed all sorts of animals higher on the food chain like sea stars, lobsters, seabirds, sea otters and humans that depend on bivalves as food. They are literally sucking up the primary productivity (algae) to be used by the rest of the food chain.

03-20ae43y.jpg
The filtration rate of oysters. Graphic from The Nature Conservancy

Different clam species vary in their precise filtration rate (how fast they can inhale and exhale water, filtering the particles within), but it is prodigious. Some freshwater mussels, for example, can pick-through 1-2 liters of water per hour for every gram of their own flesh. Since these individual bivalves can weigh over 100 g, they are capable of picking the food out of an immense quantity of water. In doing so, bivalves help improve the clarity of the water column, allowing more sunlight to reach deeper into the water body (the photic zone), providing more energy for additional photosynthesis to occur. While there are examples where invasive bivalves such as zebra or quagga mussels take this phenomenon too far, in well-functioning ecosystems, the filtration activity of clams helps improve the productivity of the community.

Oystershells.jpg
An oyster reef. Source: The Nature Conservancy

Bivalves help make sediment through their filtration of material from the water column, and they also engineer and manipulate the sediment directly. Some bivalves, like oysters, are able to make huge mounds of dirt that serve as habitat for all sorts of life, increasing the diversity of the community. They do so both by excreting sediment, and also by passively trapping it between the shells of neighboring oysters (“baffling”). By doing so, they reduce rates of coastal erosion and increase the biodiversity of wetlands. For this reason, New York and other communities plan to seed oyster reefs to help fight sea level rise and reduce the threat of storm surges like the one that occurred during Superstorm Sandy.

bioturb.PNG
Comparison of sediments without bioturbation by digging animals, and with. Notice how the non-bioturbated sediment is layered and darkened due to activity by anaerobic bacteria, while the well-oxygenated, mixed sediment is light all the way through. From Norkko and Shumway, 2011

Other “infaunal” bivalves (burrowers) help to aerate the sediment through their tunneling, bringing oxygen deep under the surface of the dirt. This mixing of the sediment (also called bioturbation) ensures that nutrition from deep under the sediment surface is again made available for other organisms. Some bivalves can bore into coral reefs or solid rock, creating burrows which serve as habitat for other animals and can free up minerals for use by the surrounding ecosystem. Helpful shipworms assist in eating wood, assisting in returning nutrients stored in that tissue to the ecosystem as well.

https://media.springernature.com/original/springer-static/image/art%3A10.1007%2Fs00338-005-0494-2/MediaObjects/338_2005_494_Fig1_HTML.jpg
Enormous grouping of giant clams in a lagoon in French Polynesia. From Gilbert et al., 2005

Bivalves of course are also famous for their shells, and this activity also provides habitat to sponges, snails, barnacles and many other encrusting organisms specially adapted to live on bivalve shells and found nowhere else. Giant clams are the most legendary “hypercalcifiers,” and in some regions like New Caledonia can rival reef-building corals in terms of biomass. In areas where soft-bottoms dominate, bivalves like hammer oysters, adapted to “rafting” on the quicksand-like surface of the soft sediment, can assist by providing a platform for other animals to take refuge. In the deep sea, bathymodiolid mussels and other chemosymbiotic bivalves can feed directly on the methane and sulfur emitted from hot vents or cold seeps with the help of symbiotic bacteria, creating dense reefs which provide food and habitat for all sorts of life. Even once the clams die, their shells can continue to serve as homes for other creatures.

redcrab-600.jpg
Crabs feeding on Bathymodiolus in the deep sea (NOAA)

The shells of clams provide great scientific value in understanding our world. Much like tree rings serve as a record of environment thousands of years into the past, growth rings in clam shells serve as a diary of the animal’s life. These rings can be yearly, lunar, tidal or even daily in rhythm, with each ring serving as a page in the diary. The chemistry of those “pages” can be analyzed to figure out the temperature the clam experienced, what it ate, whether it suffered from pollution, and even the frequency of storms! The study of rings in the hard parts of animals is called sclerochronology, and it’s what first drew me to study bivalves. I was so fascinated by the idea that our beaches are covered with high-resolution records of the ocean environment, waiting to be cut open and read.

komagoe.png
This giant clam shell recorded an interruption in the animal’s daily growth caused by a typhoon! From Komagoe et al., 2018

While they don’t owe us anything, clams provide a lot of value to humans as well, serving as a sustainable and productive source of food. Humans have been farming bivalves for thousands of years, as evidenced by “oyster gardens” and shell middens which can be found all over the world. Particularly in seasons when food is scarce on land, native peoples could survive by taking advantage of the wealth of the sea, and bivalves are one of the most plentiful and accessible marine food sources available. But they aren’t just the past of our food; they may be part of the future. Bivalves are one of the most sustainable sources of meat known, requiring very little additional food to farm and actively cleaning the environment in the process. Mussels grown out on a rope farm are an easy investment, growing quickly and with very little required energy expenditure. Someday, giant clams may provide the first carbon-neutral meat source, as they gain their food from symbiotic algae within their flesh. I have never eaten one, but I’ve heard they’re delicious.

Conchero_al_sur_de_Puerto_Deseado.jpg
A shell midden in Argentina. Photo from Mikel Zubimendi, Wikipedia
Image result for mussel farm
Mussels being farmed on ropes

Clams are heroes we didn’t know we needed and maybe don’t deserve. They ask for nothing from us, but provide vast services which we take for granted. So the next time you see an inconspicuous airhole in the sand, thank the clam that could be deep below for aerating the sediment. The shell of that long-dead mussel at your feet may have fed a sea star, and now is a home for barnacles and many other creatures. While that mussel was alive, it sucked in algae to improve water quality on our beaches. And the sand itself may contain countless fragments of even more ancient shells. Clams silently serve as an important cog in the vast machine that makes our oceans, rivers and lakes such amazing places to be. Thank you clams!

 

Poster!

On By Dan KillamIn Uncategorized1 Comment

I was happy as a clam to be able to present about my work on giant clams in two settings, as a poster at the International Sclerochronology Conference in Split, Croatia and at the North American Paleontological Convention in Riverside, CA. You can view my poster here. In the poster, I was able to discuss my newest work regarding changes in giant clam texture!Capture.PNG

Thoughts of a clam

On By Dan KillamIn Biology, clams, Uncategorized13 Comments

To us active, dynamic mammals, the humble clam can appear positively…inanimate. Their nervous system is decentralized relative to ours, lacking any sort of brain, and to the untrained eye, it can appear that their only discernible reaction to the outside world is opening or closing. Open = happy, closed = not happy; end of story, right? Some vegans even argue that the clams are so nonsentient that it is okay to eat them and think of them as having no more agency than a vegetable!

You might already have predicted I intend to tell you about just how animate and sentient clams can be. But let’s start out by describing the nuts and bolts of their nervous system. As with many invertebrates, their nervous system is distributed throughout their body as a system of ganglia. Ganglia are clumps of nerve cells which may have local specialization, and transmit messages within neurons using electrical potentials. At the connection between cells (called a synapse), neurotransmitters are used to pass signals to the next cell. Researchers have found that bivalves use “histamine‐, octopamine‐, gamma‐aminobutyric acid‐ (GABA)…like immunoreactivity” in their central and peripheral nervous systems, much like us vertebrates do, and other studies have even found that the response to serotonin and dopamine is localized in nervous tissue linked to different organ systems.

veligernerve.PNG
Nerve cells (bright green) highlighted in a larval oyster with fluorescent dye (from Yurchenko et al 2018)

These systems of chemical nerve transmission are truly ancient, likely dating back to the formation of complex animal body plans in the earliest Cambrian. Researchers have great interest in studying these nervous and hormonal signaling systems in mollusks because they can shed light on the relative flexibility and limitations of these systems throughout the animal tree of life. Characterizing these systems can also allow us to understand the mechanisms that bivalves and other animals use to react to environmental stimuli.

poly-gill-detailsem
Electron microscope view of gill cilia, zoomed in 1000x (from Dan Hornbach)

Like humans, bivalves spend a lot of time and effort eating. Most bivalves eat by filtering food from passing water with tiny cilia on their gills. These cilia work to capture food particles and also act as a miniature rowing team moving water along the gill surface. The bivalve needs a way to control this ciliar activity, and researchers found they could directly control the speed at which oysters move their cilia by dosing them with serotonin and dopamine, which respectively increased and decreased activity.

Bivalves also work very hard to make babies. Most bivalves reproduce by releasing sperm and eggs to fertilize externally in the water column. To maximize their chances to find a mate, they typically save up their reproductive cells in gonads for multiple months and release them in a coordinated mass spawning event. It appears that this process is controlled by hormonal releases of dopamine and serotonin. Researchers have determined that serotonin concentrations vary through the year, with mussels in New England using it to regulate a seasonal cycle of feeding in summer, followed storing of that energy for winter. During the winter when food is less available, they use that stored energy to bulk up their gonads in time for reproductive release in spring months, when their larvae have plentiful access to food and oxygen, ensuring them the best chance of survival. In recent decades, aquaculturists have learned to use serotonin injections to induce spawning in cultured clams, to ensure they will have a harvest ready at a certain time of year.

So bivalves are very sensitive to the seasons. How about shorter term sources of excitement? You might have observed this yourself through the clam’s most iconic activity: opening and closing its shell. Clams close their shells with powerful adductor muscles which pull the two valves together. A springy ligament at the hinge pulls the shell open when the muscles relax. Just like us, the clam needs to use nerve cells to signal the muscle to do its thing. In addition, two different sets of ganglia act to control the foot that some bivalves can extend to dig into sand, with one ganglion acting to extend the foot and the other causing it to contract. While clams don’t have a centralized brain with specialized regions for different uses like we have, this represents a sort of specialization of neural systems with a similar result.

Clam licking salt - Imgur
This iconic gif is often shared along with the claim it shows a clam “licking” salt. It is actually using its foot to search for a place to dig. The salt was not needed.

When a certain neuron is used repeatedly, it can form a cellular memory allowing the organism to acclamate (ugh sorry) and moderate its response to a particular stimulus over time. Giant clams, for example, close their shells when their simple eyes detect a shadow overhead. This behavior can protect them from predation. When I conducted some of my PhD research, sampling body fluid of aquarium and wild giant clams with a syringe, I noticed that captive clams didn’t close up in response to my shadow overhead, while wild clams required me to sneak up and wedge their shells open with a wooden block to do my work. I suspected that after exposure to frequent feedings and water changes by aquarists, the clam had “learned” that there was no reason to expend energy closing its shell. Meanwhile, in the process of proving that our sampling technique was not harmful to the animal, I discovered that clams which detected my shadow would quickly reopen within seconds when I hid from them, while those that were stuck by a syringe would stay closed for minutes before opening and beginning to feed again. Makes sense!

Other researchers noticed this phenomenon as well. One group found that giant clams repeatedly exposed to shadows of different sizes, shell tapping and even directly touching its soft tissue began to habituate (become accustomed) to the stress, opening more quickly and staying open longer each time the stimulus occurred. Even more interestingly, they did not transfer that habituation between stress types; for example, the clams that saw a shadow again and again would still react strongly to a different stress like tapping its shell. This suggests the animal can distinguish between different threats along a spectrum of seriousness, with touching of tissue (similar to a fish pecking at its flesh) being the most serious threat with the most dramatic response.

Another study determined that larger giant clams stayed closed longer than smaller ones in response to the same threat. They proposed this was related to the greater risk large clams face as they have more tissue area vulnerable to attack. While the clams might not have made a “conscious” decision in the way we do as thinking creatures, they were able to place their individual risk in context and vary their response. This ability to tailor a response to different risk levels is a sign of surprisingly complex neurology at work.

Inside the Scallop
Close up of the eyes of a scallop. Each is a tiny crystalline parabolic mirror (photo by Matthew Krummins on Wikipedia)

Scallops show some of the most complex bivalve behaviors. This relates back to their unique adaptations, including simple eyes that can resolve shapes and the ability to swim away from danger. Scallops have been found to discern between predator types by sight alone, to the extent that they did not initially recognize an invasive new predatory seastar as a threat. When swimming, they are capable of using this vision to navigate to places where they can hide, such as seagrass beds. It would be very interesting to compare the behavior of scallops in marine protected areas to those that can be freely harvested. Do they vary their behavior in response?

I hope I’ve made clear that while clams are not exactly intellectual powerhouses, their behavior is much more complicated than simply sucking up water and opening or closing their shells. Like us, they inhabit a complex environment that requires a multitude of responses. Their nervous systems have evolved to allow them to survive and adopt nuanced behaviors which they can vary on the fly, and which us “higher” animals are only just beginning to comprehend.

How does a scallop swim?

On By Dan KillamIn clams5 Comments
uelx7yhbixf01
Scallops spooked by divers’ lights and fleeing en masse to filter somewhere else

The ocean is a place of constant dynamic movement. Fish use their fins to push water away from themselves, and because every action has an equal and opposite reaction, they therefore move forward. Some cephalopods use jet propulsion, constricting their mantle cavity to push water out through siphons, allowing them to jet forward like a deflating balloon. And other life forms sail the seas on constantly moving currents , indirectly harnessing the power of the sun and earth.

Bivalves are a fairly sedentary bunch by comparison. While most bivalves have a planktonic larval form, when they settle they are constrained to a fairly small area within which they can burrow or scramble around with their muscular feet.

graybountifulgopher-size_restricted

But some bivalves have evolved to move at a quicker rate. The most famous swimming bivalves are the scallops, which have evolved to use jet propulsion, similar to their very distantly related cephalopod relatives. But unlike the cephalopods, scallops evolved to use their hinged shells to aid this process!

wyjgzzw
Notice the expelled water disturbing the sediment below the scallop as it “claps” its way forward!

Many filter-feeding bivalves use their shell valves as a biological bellows to pull in water for the purposes of sucking in food, or even to aid in digging, but scallops have developed another use for this activity, to enable propulsion. Scallops draw in water by opening their valves to create a vacuum which draws in water to their sealed mantle cavity. They then rapidly close their valves using their strong adductor muscles to pull them together, which pushes the water back through vents in the rear hinge area, propelling the scallop forward.

esn6uyb
Don’t panic if a scallop swims toward you. They can see, but not super well. This one is just confused.

Using this strategy, scallops can evade predators and distribute themselves to new feeding sites. It’s a surprisingly effective swimming technique, with the queen scallop able to move 37 cm/second, or over five body lengths per second! Michael Phelps would have to swim at nearly 35 km/h to match that relative speed (his actual highest speed is around 1/3 of that). I’m sure sustaining that speed would be tiring for Mr. Phelps, though, and it’s the same for scallops, only using their swimming for short-distance swims.

(video from Supplemental Materials of Robertson et al. 2019)

A recent paper from a team in Switzerland just came out describing an effort to engineer a robot which imitates the scallop’s elegant and simple swimming method. The resulting totally adorable “RoboScallop” closely imitates the design of a scallop, using a pair of hinged valves with rear openings to allow the movement of water backward. The internal cavity is sealed by a rubber membrane draped across the front so that all water is forced through these rear vents when the Roboscallop snaps shut.

roboscallop.PNG
Diagram from the Roboscallop paper (from Robertson et al. 2019)

As seen in the diagram above, the rhythm and relative velocity of opening vs closing is important to make sure the RoboScallop actually moves forward. If the scallop opened as quickly as it closed, it would just rock back in forth. It instead opens slowly so that it does not draw itself backward at the same rate that it can push itself forward. The researchers had to do quite a bit of calibration to get these rates right (equating to about 1.4 “claps” per second), but once they did, they ended up with a RoboScallop that can generate about the same force of forward movement (1 Newton) as a real scallop (1.15 Newtons), and similar rates of speed.

This paper really fascinated me because it is merely the latest in a long line of successful engineering projects imitating the ingenuity of evolution. Other marine robots have been made which emulate the locomotion of fish, manta rays, sea snakes and other forms of swimming. And now we have a clam! Let me know when I can buy one to play with in my pool.

Israel: Field Report!

On By Dan KillamIn travel, UncategorizedLeave a comment

So I’ve been living in Israel since the start of November after a whirlwind of defending my PhD, moving out of Santa Cruz forever and suddenly moving to another continent for a postdoc. I’ve been working on clams, taking samples, using an SEM and planning a new manuscript, but I have also been learning a lot about living in a country that is at once strangely familiar and completely foreign. I’m coming back to California tomorrow for a Holiday break, so I took an hour to reflect on what I’ve learned about this country so far. Here are some random things I’ve learned about Israel during my time here.

Israel is small

Capture.PNG

Israel is a tiny country by my Californian standards. You can take a bus along the entire length of it in less than seven hours. I am in Haifa on the farthest northern part of the Mediterranean coast, but in 2016, I lived down in Eilat for two months. Despite its small size, Israel has a variable climate depending on where you are. Up in Haifa, they have have a classic Mediterranean climate which reminds me of California in a lot of ways (think chaparral and coastal dunes, though a little more humid than I’m used to and with more thunderstorms). The Negev desert is in the South, which is intensely dry, hot and sometimes completely devoid of vegetation.

Happy naturalists!

Hooded crow in Haifa
House crow in Eilat

For birders, I’ve noticed the North is dominated by hooded crows from Europe while the South is dominated by house crows, an Asian species. In general, because they’re at the nexus between Europe, Asia and Africa and the gradient between those ecoregions, Israel and the Middle East overall are very biodiverse. As a result, there is a vibrant culture of naturalists in this country who want to know about every aspect of every species. When I post something to my iNaturalist, within a few hours someone who is an expert on that taxon confirms or corrects me, without fail.

Delicious food+drink

This slideshow requires JavaScript.

Living here, I have been subsisting of a diet based largely on hummus, falafel, shawerma, tahini (try the dark kind!) and pita, with plenty of veggies thrown in. In fact, there are restaurants where they just serve you a bowl of hummus with pita and you have at it. Be prepared for the food coma. For beers, I guess Danish beer companies got a big foothold here early on because the defaults are Carlsberg, Tuborg, Heineken etc. The biggest native Israeli brewery is Gold Star, and they’re not bad! And there are a growing number of Israeli craft breweries. Overall I approve, though they sometimes experiment a bit too much and taste odd, and a lot of them don’t really seem to know what an IPA is.

Cultural diversity

Israel, as you may or may not have heard, is indeed a very complicated place. There is no doubt that the tensions are high between Israelis and Palestinians and Hezbollah and Iran, which is often in the news. But day to day on the ground, Israel is a very safe place and safer than what I’m used to in the States. The crime rate is much lower than almost everywhere in the US, and I can walk around Haifa at night without ever feeling at risk. That is more than I can say for Santa Cruz and many parts of LA.

Haifa is a special place. It is a uniquely diverse city with a significant Arab population. The student body at the University of Haifa is over 30% Arab in descent and I can walk through hearing four languages in one hallway. The main temple of the Baha’i faith is here in Haifa.

There are Israeli Jews of all sorts of backgrounds, including Ashkenazi, Sephardic, Yemeni, Ethiopian and more. There are secular Jews, Conservative Jews, Orthodox Jews and the Haredim (Ultra-Orthodox), along with myriad others I haven’t learned about yet. There also is a huge population throughout Israel of Russian Jews who came here following the collapse of the Soviet Union. Russian is spoken heavily here and is on the street signs. Like America, Israel is a hugely diverse place and I believe could be a great strength for their future growth and prosperity.

Language and cultural challenges

As a secular American, there were some parts of Israel that have proved challenging to adapt to. The biggest challenge for me by far is that Israel’s national language is Hebrew, which is a very challenging language to learn. I now know the numbers, some letters and some words, but there’s no way I’m going to be able to pick up conversational Hebrew during my time here. And as all foreigners know, not being able to read and write makes literally everything about “adulting” more difficult. I have had to learn never to assume that English is understood here. I speak slowly and use hand gestures. I do everything in person, never over the phone. Trying to do something logistical over the phone has not once worked. Seriously, don’t even entertain the notion of trying to do stuff in English over the phone here.

Instead, I recommend going to the place you need to go, ask the person for help with a dumb blank smile on your face, and people will try to help you do what you need to do, whether that is opening a bank account, getting your bus card, or signing a lease for your apartment. People here are generally very direct and no-nonsense in everyday business dealings, but they also have proven very generous and willing to help me, which is not something I can say about service in America. However, on the rare occasions when I’ve found someone who speaks English, is available, and is exactly the person who can help me with the task at hand, I feel as though I should drop to my knees and thank the God of Abraham for his mercy. Day to day life here is tough for a non-Hebrew speaker.

If there was one aspect of life in Israel which I will openly complain about, it is Shabbat (from sundown Friday to sundown Saturday). In most of the Western world, we take for granted that Saturday and Sunday are the days of rest. But here in Israel, it is Friday and Saturday, and Israel is very hardcore about their days of rest. On Shabbat, any eating establishment that wants to be Kosher has to be closed. Almost all public transport is shut down.

There are a small number of more secular, diverse cities, luckily including Haifa, where a couple buses stay running Friday night and Saturday. But on Saturday, if I realize I need groceries, my choice is to splurge on a cab or walk 25 minutes down to the nearest 24/7 market (basically a convenience store). There is a reason Shabbat is a big deal in Israel and I get it. There is no other country on Earth where Jews of all creeds and colors can know that they will get to observe Shabbat in the way it was practiced by their ancestors. But for me as a secular person without a car, it presents a lot of logistical challenges.

Miscellaneous

Here is a list of other things I found notable and unexpected about life in Israel

  • They really like malls. There are new malls opening everywhere and they are always full of people. As an American, I think of malls as very last century, but they’re still the main social place here for many people.
  • They don’t really use mops. Instead, they use giant squeegees to clean their floors. I still don’t get how to use one.
  • When you sign a lease, many landlords want twelve pre-signed checks. I thought this was very strange (where do they keep them?!) and then noticed an option in the ATM to save checks for “safe-keeping.” Weird.
  • Israel is a cell phone paradise. I can get an unlocked SIM card with 30 gb of data, unlimited voice and text for $21.50. This is absolutely insane. How is this possible?
  • In Israel, they charge tenants a bimonthly property tax. That is annoying!
  • People say Israel is super expensive and yes, prices on food and basics are somewhat high by standards of some US States. But coming from California, I have been so relieved. I now can afford to live in my own apartment and pay <25% of my income on rent rather than 50%. I can once again stay under $10-15 a day on food which wasn’t possible for me in California for the last couple years. So I have more discretionary income for fun stuff which has been refreshing.
  • As I’ve noticed in Europe as well, it’s fun paying with coins! They have 10, 5, 2, and 1 shekel coins and I find myself actually using them, unlike the useless pocket change in the states that I just save to trade in later. There are around 3.7 shekels to the dollar.
  • They have an excellent bus system (except Friday or Saturday 😉 ). Buses come by frequently in all parts of Haifa, are clean, and cost about $1.50 per ride (1/3 less than that if you set up your student access card). The bus card allows you to connect for free within a certain time period as well.
  • Most locks in Israel use keys on the inside and outside. I’m not sure if this is an Israel-specific thing, or just something the rest of the world has that the US doesn’t, but it was surprising to see that I’d have to use my key to lock my front door from inside.
  • They have smarter crosswalks in Haifa that generally bridge over a median, with two separate pedestrian lights. You may have to stop in the middle but it means less risk of someone doing a turn and hitting you, and that is good urban planning in my book. Eilat has done away with streetlights altogether, completely converting to roundabouts. I frickin love roundabouts.
  • Israel has a semi private system of healthcare, but with generally very high quality care and low cost.
  • In Israel, life is completely transformed by their mandatory military service. While I have been out of college for a few years, many Israelis are only just starting college as they enter their late 20s after being discharged. So the student body trends older at Israeli universities.
  • I thought I’d stick out as an American goy being here, but apparently I don’t. People keep asking me for directions in Hebrew and Russian and I just say “sorry, English only”, and they look at me with disappointment. I guess I can say I look Jewish!

In conclusion, I have enjoyed my time in Israel so far, and I have found myself just watching life going on around me with great curiosity, because it is a very interesting place full of constant unexpected moments. Let me know if any of you visit anytime soon 🙂

Mystery of the “spurting” mussels

On By Dan KillamIn Biology, clams2 Comments

If you’ve read any of my posts, you should realize by now that clams are pretty weird. Some catch live prey. Some have algae in their bodies that they “farm” for food. Some can bore into hard rock. Some sail the seas on rafts of kelp. Clams live in a competitive world and have had hundreds of millions of years of time to evolve to try out all sorts of weird, unlikely ways of life.

unio_crassus3_a_mrkvicka
U. crassus in a Slovenian river (Alexander Mrkvicka)

The thick shelled river mussel (Unio crassus) is known from many rivers and streams of Central Europe. As this is a very well-studied region of the world, many generations of academics have noted an unusual, seemingly inexplicable behavior undertaken by these mussels at certain times of year.

20_u-crassus_2
U. crassus propped up on its foot (UCforLife)

Using its muscular foot, U. crassus pulls itself to the edges of the streams and rivers it lives in until it is partially exposed to air. It orients itself at a right angle with the surface of the stream with its siphons (two little snorkels coming out of the shell) facing out towards the water. Like all bivalves, U. crassus can act as a bellows by opening and closing its shell to pull in and push out water through those siphons. It has one siphon above the water and one below, and it proceeds to suck in water and spray it into the center of the stream using the power of its suction. The water can travel over a meter away and they continue this spurting about once a minute, sometimes for hours.

squirt
Squirting water into the stream! (Vicentini 2005)

Needless to say, this is a very strange and unlikely behavior to observe in a mussel. It is exposing itself to potential dessication or suffocation from exposure to air. It is vulnerable to predation from terrestrial mammals and birds. There has to be a very powerful benefit from this behavior to outweigh those risks. And why squirt water into the air?

Some researchers proposed that the mussels were traveling to shore to harvest from the more plentiful food particles deposited there. But why would they face their siphons away from the shore then? Other workers suggested that it was a way to reduce heat stress through evaporation, though that also seems unlikely, considering the water is warmest in the shallows. The question persisted for decades in the minds of curious malacologists.

squirttop
Top-down view of spurting behavior (Vicentini 2005)

In 2005, Heinrich Vicentini of the Swiss Bureau for Inland Fisheries and Freshwater Ecology decided to try settle the question of why these mussels spurt. He observed several dozen of the mussels crawl to the edge of the water and diligently begin squirting into the streams. In the name of science, he put himself in the path of these squirts, caught the water and used a hand lens to observe that the squirted water was full of mussel larvae (glochidia).

Lifecyle of U. crassus (Rita Larje via UCforLife)

U. crassus falls in the order Unionida, a group of freshwater mussels distinguished by a very unusual method of reproduction. They are parasites! Because they can’t swim well enough to colonize upstream against the current, they need to rely on fish to hitch a ride. Some have evolved elaborate lures to convince fish to take a bite, then allowing them to release their larvae, which attach to the fish’s gills like binder clips and ride all the way upstream. Once they have reached their destination, they detach and grow up into more conventional burrowing mussels. It’s a weird, creepy and wonderfully brilliant strategy that enabled the mussels to invade the inland rivers which would otherwise be inaccessible to them.

5_anodonta-glochidia-on-roach
Loach (type of freshwater fish) gills with unionid larvae attached (UCforLife)

The mussels appear to be spurting out not only water, but their babies. They gain a couple of advantages from this. For one, their larvae can distribute further than would be possible from the bottom of the creek. Instead, they are released at the center of the surface of the stream, where they can be carried for a much longer distance by the current before they settle at the bottom. In addition, the splash of water on the surface may mimic the behavior of insects and other fish food falling in the water. A curious minnow might venture to investigate the source of the splash, where it would promptly breathe in a cloud of larvae that get stuck on its gills. A pretty rude surprise, but a brilliant trick to give the baby mussels the best chance of surviving.

So again, clams prove themselves to be far more clever and interesting than they might initially seem. U. crassus and other members of the Unionida are an ancient and globally distributed lineage which have evolved all sorts of weird and wonderful ways to maintain their river lifestyle. Unfortunately, rivers are some of the most widely damaged environments in the world. A majority of freshwater mussel species worldwide including U. crassus are endangered by habitat loss, overharvesting and pollution. But more research into their unusual biology can help us understand ways we can enhance their conservation, with the hope of providing more habitat for them to recover populations in the future. New projects in Sweden and other countries aim to recover habitat for their larvae to settle along 300 km of rivers, and research the fish species which their larvae prefer to hitch a ride on. With more work, we can hopefully ensure that the streams of Europe will harbor little mini super-soakers for millennia to come.