Flat foram

Windy ride
By  Nicole Webster

I had a thin section made of one of my shells, and it came back with a serendipitous hitchhiker. A foraminiferan, you know, those single celled protists that make a gorgeous test (shell) usually out of calcium carbonate? Well it was at just the right place to be beautifully sectioned itself. The section is 30um thick of a 5cm shell, and the foram itself is only 0.5mm wide.

Foram thin section in plane polarized light. Credit N. Webster

Foram thin section in plane polarized light.  The darker spots inside the test are probably dried up tissue, and the little balls underneath the test are probably the glue used to attach the foram to the shell. Credit N. Webster

Foram thin section in cross polarized light. Credit N. Webster

Foram thin section in cross polarized light. Credit N. Webster

Thin sections are typically used in geology to identify different crystals, and thus the rocks that they are made up of. I recommend a quick Google image search, some are really quite pretty. Here I was using it to see how many layers and in what orientation the crystals are layed down in my snails.
A chunk of rock (or shell) is ground down as smoothly as possible to 30um (0.03mm) so that it is transparent. Once under the microscope, a polarizing filter is used to see crystal features better. A cross polarizing filter is used to see interference colours, allowing greater characterization of the mineral. That is why the second image looks a little like something from the 60s. Although the CaCO3 is relatively clear, the glass of the slide refracts the light quite a bit, making a psychodelic pick rainbow. This is a very simplistic view of thin sectioning, please correct me if I’ve misunderstood something.

PS I learned a new word making this post. Arenaceous. It means sandy, or likes sand (for plants), and specifies a geologic grain size ranging from 2 to 0.625mm. In this context it means those foraminifera that don’t grow their own shell, but rather glue bits (read:sediments particles) together to make a shell.

1. Rock-Forming Minerals in Thin Section. Steve Dutch, Natural and Applied Sciences, University of Wisconsin. https://www.uwgb.edu/dutchs/Petrology/thinsect.htm
2. Corliss, B. H. 1985. Microhabitats of benthic foraminifera within deep-sea sediments. Nature 314:435-438.

Jack O’ Lanterns Made with R

Figure 1.

Figure 1. Jack O’ Lanterns carved with the statistics application R, by students in the Bamfield Marine Sciences Centre Fall Program.

Maybe you already know that the computer programming language R can be used for statistics, and data visualization. You can also use it to draw pictures. The easiest way to do this is by using the ‘locator’ and ‘polygon’ functions. You can make your own Jack O’ Lantern with R using the script provided in the previous post “Pumpkin Carving with R”.

And now for something completely different

By Nicole Webster

Perhaps we are a little focused on invertebrates here, or perhaps this gorgeous weather has gone to my head, but I have a ‘treat’ for you for an Image Fest Friday.

Fish bones dried on the docks. Not that interesting. Can anyone ID the parts?

Fish bones dried on the docks. Not that interesting. Can anyone ID the parts?

Yeah, sorry, its poop. but whose?

Yeah, sorry, its poop. but whose?

That is clearly no bird poop. From the diameter I was thinking cat-sized.

That is clearly no bird poop. From the diameter I was thinking cat-sized.


It was all over the docks, to the dismay of Janice who washed it all off. She also solved my mini mystery. Its river otter poop! It is regularly appearing on the docks, and I saw a couple playing there earlier in the year, so there may be some living nearby.

Some Intertidal non-crustacean arthropods

By Nicole Webster

The intertidal is a transitional zone, from the water to the air, but also from salt to fresh water. A lot has been said about the ecological consequences of this transition, perhaps idealized by salmon’s migration and how they transfer nutrients from the marine to terrestrial/freshwater ecosystems (Cross-boundary subsidy). I’m not going to say anything in depth about this, and if you are interested, I recommend speaking to Caroline Fox (uvic website), who is in and out of Bamfield semi-regularly and is completing her PhD on this topic.

This post is nothing so ecological or philosophical. This summer I came across a couple arthropods (non-crustacean) that are not commonly mentioned and wanted to expand your view of the intertidal.

This is Diaulota densissma (I believe).


This is a rove beetle (Diaulota densissma) in a petri dish, with possibly a larva. They are not easy to photograph. I could have sedated one for better ID and imaging, but didn’t. Credit: N Webster

I encountered these beetles on the barnacle rocks that I heave to the lab to feed my greedy snails. Quite a few of them I found regularly swimming desperately on the water in my seatable and crawling around on the dry rocks. At first I thought they were unfortunates brought in from a true terrestrial habitat, but there were too many, and too consistent. It was suggested to me to check out Kozloff’s Seashore life of the Northern Pacific coast. It is not a field guide, nor is it like his Key to Marine Invertebrates. It is really a nice introductory book about the seashore, looking from high to low intertidal, from sandy to rocky shores, and describing the types of organisms found there.


This is the beetle on a barnacle rock. Credit: N Webster

Indeed my rove beetle is in the book. It is a small intertidal predator that eats mainly amphipods and other tasty arthropods at low tide. According to Ahn (1996) these beetles live even in the low intertidal, and can spend most of their day submerged. They don’t have gills, they just find an air pocket (barnacle test, under a rock) and wait. Watching them swim, they obviously have a highly hydrophobic coating, probably with lots of hairs to trap air bubbles.


This is Neomolgus littoralis. It is an intertidal mite, known as the red velvet mite.

Red velvet mite on some Ulva, in the high intertidal on Edward King. They are ~3mm in length. Credit: N Webster

Red velvet mite on some Ulva, in the high intertidal on Edward King. They are ~3mm in length. Credit: N Webster

These mites are found in the high intertidal and eat kelp flies (another intertidal insect). They are very easy to spot, as they are shockingly red.



  • Kozloff, E.N. 1993. Seashore life of the Pacific Northwest: an illustrated guide to northern California, Oregon, Washington, and British Columbia. 370 p.
  • Kozloff, E.N. 1974. Keys to the marine invertebrates of Puget Sound, the San Juan Archipelago, and adjacent regions. Seattle, Washington, University of Washington Press, 226 p.
  • Kee-Jeong Ahn. 1996. A Review of Diaulota Casey (Coleoptera: Staphylinidae: Aleocharinae), with Description of a New Species and Known Larvae.The Coleopterists Bulletin Vol. 50:3, pp. 270-290


“Why Bamfield, BC is unique awesome and you should go there” – Bridgette Clarkson

A friend of mine has a wonderful blog. It is insightful, delightful and full of photos. Bridgette just completed a stint working as a public educator for BMSC, and described herself as a biologist and science education consultant.

Crashing Bull kelp (c) Bridgette Clarkson

In honour of World Oceans day (yesterday), she posted the 2nd part of her 3 part series about her time in Bamfield this year.

I strongly encourage you to check them out, if only for the breathtaking imagery.

Do check out some of her other posts like how to check marine forecasts, or her flickr stream.

Hand-fed Gooseneck barnacle

By Nicole Webster

I have below what we believe to be the first footage of someone hand feeding a Pollicipes polymerusThese gooseneck barnacles are found only in high flow areas, and feed differently than your average acorn barnacles. Rather than swat the water for prey with their legs, they let the water to the work for them, holding out their legs, and let the tide wash in their food. They eat larger pieces (as you can see below), and here appear to actually grab it.

These videos were taken by my lab mate Tomonari Kaji, a postdoc who’s looking at the development and plasticity of barnacle leg segments, and how they change leg length in different environments.

Moving Barnacles

Windy ride

By  Nicole Webster

I want to share this obscure paper with you:

J. E. Moriarty, J. A. Sachs and K. Jones. 2008. Directional Locomotion in a Turtle barnacle, Chelonibia testudinaria, on Green Turtles, Chelonia mydas. Marine Turtle Newsletter 119.

I’m going to give you the punchline first: They found evidence of barnacles moving!

Now that I’ve got your attention, lets start with some basic introduction. Chelonibia testudinaria is a species of barnacle that lives specifically on the backs of sea turtles. It is part of an entire superfamily of barnacles (Coronuloidea) that are obligate epibionts, meaning they only live on other living organisms. Members of this group live on everything from whales, manatees, crabs, molluscs, and turtles. This is how these barnacles get to travel the world!

Chelonibia patula on a Blue crab Credit: Cirriphilia (Wikipedia)

Chelonibia patula on a Blue crab Credit: Cirriphilia (Wikipedia)

To date, no one has shown any significant harm these barnacles do to their hosts (nor benefit), and this is considered a commensal, not parasitic relationship. In contrast, there is evidence that they may preferentially settle in wounds (ouch!). I imagine this might relate to chemosensory settlement cues that would be strongest at an open wound. It is thought the main advantages to the barnacles are dispersal, and predator evasion (what sea star or snail will climb on the turtle just to eat them?)


Moving sessile organisms

In general, sessile organisms (like barnacles), are considered sessile for a reason. They don’t move as adults. The larvae settle out of the plankton based on certain cues (many are poorly understood at best) on what they hope is a good spot, and then metamorphose, binding themselves to a location for their entire life. This extends to coral, barnacles, sponges, mussels, tunicates, tube worms, bryozoans, and anemones.

This isn’t 100%. Life is full of exceptions. A big one is anemones. Some of the swim (Stomphia), but even less spectacular anemones have the ability to crawl slowly.

This would be of great advantage to a sessile organism. I was with a tour group last week, and someone asked why all the anemones were in pits and crevasses. At first I thought it might just be differential survival, but no, I’m pretty sure those anemones would move to the more sheltered locations all by themselves.

I have not heard of coral, sponges, tunicates, or tube worms moving once settled, but mussels (at least when they are small) can move about as well. They use byssal threads to attach to the substrate, and can move by progressively moving where their byssal threads attach. This is separate from their ability to crawl using their foot.

Barnacles is new, and very exciting (to me at least) as an addition to the list of sessile organisms that are not so sessile!

So what about this paper then?

It is known that filter feeding organisms do best in areas of high flow: more units of water pass by, carrying more food. On a turtle, this would be the front edge or dorsal ridge on the shell. It was previously known that barnacles are more common on these regions of a turtle carapace, but this was thought to be due to cyprid (the barnacle larva stage that settles and metamorphoses) movement and differential survival.

This paper was a casual case of observation. The authors were studying Green Turtles, Chelonia mydas in florida, and noticed that the barnacles were in different locations on the same individual. It doesn’t say so in the paper, but I imagine the reaction was more along the lines of: “What? That can’t be right, check again!”, in the paper this is stated as: “Casual inspection of the photographs indicated that the barnacles were moving on the carapace of these turtles over a period of months. To investigate this, we assembled a series of photographs for each of the three turtles.”

All in all they had 8 barnacles on  turtles that moved. Most moved anteriorly and medially (towards the middle and front), as you would expect based on where the highest flow is.

Green turtle bearing the gray locomotion trail of a relocated Chelonibia testudinaria. Moriarty et al 2008.

Green turtle bearing the gray locomotion trail of a relocated Chelonibia testudinaria. Moriarty et al. 2008.

How fast? Average rates varied from 1.4 mm – 0.27 mm/day! Seems kinda slow, I know, but definetly faster than 0. They even leave a trail on the shell, so you could see part of their track.

The authors raise an interesting point: the ideal settling location is in high flow, and its difficult to settle there for the same reason. If you are capable of moving after you have settled, that gets the best of both worlds. A low flow settling location to get properly attached, followed by a migration to an ideal feeding spot.

Unlike many barnacles, C. testudinaria does not have a base plate, making moving a bit easier. The authors suggest they move by creating tension in the leading edge of the shell, causing it to move forward with growth increments of the shell.

To be fair, some barnacles are capable of rotating in place, or getting pushed by growing neighbours, and the settling cyprid larvae can migrate, but this is the first evidence of large scale adult barnacle motion.

Also, there are only three turtles, and less than a dozen barnacles in this study, so some caution is warranted, but I believe the pictures speak for themselves. This paper is available free online here, so take a look for yourself.

Extra bonus paper

I love phylogenies, I admit it. So there’s a cool side note to this story. Zardus et al. 2014 just threw a big wrench into our understanding of these turtle barnacles. Previously there were 5 species of Chelonibia, each with a specific range of hosts (different sea turtle species, as well as some crustaceans and manatees), and associated morphologies. I won’t go into the nitty gritty of this paper, but the conclusion is that there are only two species of Chelonibia, and all that host specific morphology is simply phenotypic plasticity! One is Chelonibia caretta which is specific to a few types of sea turtle, but all the others are being grouped together as morpho-types of C. testudinaria.  (Why can’t I hear you whooping in excitement?).

Putting these papers together, does this mean the barnacles on manatees can move too? What about whale barnacles? The soft tissue embedding seems to me unlikely to allow migration, but who knows? I’m pretty sure there’d be no reason barnacles on crabs couldn’t wander about…

There are so many cool things out there just waiting for you to notice them! Take your time, and don’t brush off anomalies.


J. E. Moriarty, J. A. Sachs and K. Jones. 2008. Directional Locomotion in a Turtle barnacle, Chelonibia testudinaria, on Green Turtles, Chelonia mydasMarine Turtle Newsletter 119:1-4

J. D. Zardus, D. T. Lake, M. G. Frick and P. D. Rawson. 2014. Deconstructing an assemblage of “turtle” barnacles: species assignments and fickle fidelity in Chelonibia. Marine Biology 161:45-59

Slow life- Coral, sponges, and echinoderm time lapse

I just came across this mind-blowingly beautiful time lapse work of some slow organisms. Take a look (on a big screen at full size and resolution):

This was done by Daniel Stoupin. You can learn about how he made this video, or check out his other amazing work on his blog or website.

Fractals with R, Part 5: Sierpinski Carpet with ggplot2

Figure 1. Sierpinski Carpet

Figure 1. Sierpinski Carpet.

By Allan Roberts

This post uses the graphics package ggplot2 (Wickham, 2009) to illustrate a new method of making an image of the Sierpiński Carpet, which was featured in a previous post (Fractals with R, Part 2: the Sierpiński Carpet). The method used to make the matrix representing the fractal is the same; again, the algorithm is essential the same as the described in described in Weisstein (2012), but implemented in R. In this post, I have used the graphics package ggplot2 to display the image. The ggplot2 layer “geom_tile” produces output much like the function “image” in the base graphics package. View ports made with the “grid” package are used to make the four panels of the plot shown in figure 1; one of the advantages of ggplot2 is that it makes it relatively easy to work with the grid package in this way. Because the function “ggplot” takes a data frame as an argument,  some extra work was required to turn the matrix representing an iteration of the fractal into a data frame with X and Y columns for the positions of cells, and an indicator column I to represent the colour of the cell. Running the script provided below requires that you have the “ggplot2” package installed; if you have an internet connection, this can be done by entering install.packages(“ggplot2”) on the R command line. (The grid library should come already installed with the basic installation of R.)


H. Wickham. ggplot2: elegant graphics for data analysis. Springer New York, 2009.

Weisstein, Eric W. “Sierpiński Carpet.” From MathWorld– A Wolfram Wed Resource Accessed Oct. 22, 2012: http://mathworld.wolfram.com/SierpinskiCarpet.html

R Script

#Written by Allan Roberts, Feb 2014
SierpinskiCarpet <- function(k){
Iterate <- function(M){
A <- cbind(M,M,M);
B <- cbind(M,0*M,M);
M <- as.matrix(1)
for (i in 1:k) M <- Iterate(M);
n <- dim(M)[1]
X <- numeric(n)
Y <- numeric(n)
I <- numeric(n)
for (i in 1:n) for (j in 1:n){
X[i + (j-1)*n] <- i;
Y[i + (j-1)*n] <- j;
I[i + (j-1)*n] <- M[i,j];
DATA <- data.frame(X,Y,I)
p <- ggplot(DATA,aes(x=X,y=Y,fill=I))
p <- p + geom_tile() + theme_bw() + scale_fill_gradient(high=rgb(0,0,0),low=rgb(1,1,1))
p <-p+ theme(legend.position=0) + theme(panel.grid = element_blank())
p <- p+ theme(axis.text = element_blank()) + theme(axis.ticks = element_blank())
p <- p+ theme(axis.title = element_blank()) + theme(panel.border = element_blank());
A <- viewport(0.25,0.75,0.45,0.45)
B <- viewport(0.75,0.75,0.45,0.45)
C <- viewport(0.25,0.25,0.45,0.45)
D <- viewport(0.75,0.25,0.45,0.45)

Death on the point

Windy ride
By  Nicole Webster

The 'tidal flat' on the point beside first beach. Does this have a geographical name? Credit: N. Webster

The ‘tidal flat’ on the point beside first beach. Does this have a geographical name? Credit: N. Webster

On the same hike with the escaping amphipods, I also saw a tidal flat (is that the right word?) covered in dead things. I’m unsure what the cause of the death was. We were just at the end of a neap tide cycle (with smaller tide fluctuations), and the weather had been really nice (~20C, http://climate.weather.gc.ca/). Perhaps it was just too hot, and this spot was fairly high up on the shore. Perhaps a combination of no really high tides with many hot days was too much. This is unsurprising, and certainly happens all the time. There are many occaisions where you can see swathes of dead barnacles and sea weed after a scorching summer day with a mid-day low tide. This was the first time I saw a diversity of organisms. Beyond fish and chitons (pictured) There were many empty limpet shells and crabs.

A unknown fish, already well stripped, with some Littorina sniffing around. Credit: N. Webster

A unknown fish, already well stripped, with some Littorina sniffing around. Credit: N. Webster

A poor dead chiton, being gleefully devoured by a small hermit crab. Credit: N Webster

A poor dead chiton, being gleefully devoured by a small hermit crab. Credit: N Webster