Milly: Polarization Paradise 2

Enjoying myself on my latest research cruise off
the coast of the UK. Photo: Zan Boyle.

Lizard Island, a tiny island on the Great Barrier Reef in Australia, famous for its abundance of bison lizards and known amongst scientists as a prime spot for marine science. The tranquil, aquamarine waters surrounding the island come as a welcome change from the turbid, brown, worm infested Atlantic I spent so long staring at during my last trip. My mud sieving days are over, instead, I'll be collecting animals from the reef and testing their polarization vision. "Do you make them wear sunglasses?". Sometimes I regret talking about science with my friends. No sunglasses, but plenty of polaroid and LCD screens.

Cats love to be breaded. Photo: web.

Sick of your office judging you for spending your lunch break perusing breadedcats.com? All you need to do is tweak your computer screen and you can hide your cat compulsions from the world. If you were to remove the front layer of an LCD screen, it would appear blank, but those loaf wearing cats are still there, all you need is a piece of polaroid to bring them back. LCD screens work by emitting polarized light at different angles. By putting a piece of polaroid in front of this system, changes in polarization angle alters the amount of light the viewer can see. The polaroid works by blocking light polarized at one angle (appearing black) and transmitting it at a perpendicular angle (appearing white). To the people working in my lab, I looked like very stange, sitting at a blank screen with sunglasses on...but little did they know, breadedcats.com.

So, if we want to test the ability of animals to see polarized light, what better than to use an LCD screen that allows us to create any image we want, and show it as a polarization signal. We will be testing cuttlefish, animals with a fascinating visual system, lacking colour vision entirely but possessing an extremely sensitive polarization visual system. Using LCD screens, a member of our lab, Dr Shelby Temple has discovered that cuttlefish can distinguish surprisingly low differences in polarization angle, far better than what we thought possible but how they are able to do this remains a mystery.

A cuttlefish showing off it's polarization pattern visible
here in a false colour image. Photo: Shashar et al., 1996.

You might be wondering what benefit detecting different angles of polarized light gives an animal living on the reef. Cuttlefish, like mantis shrimps, are able to signal by polarizing the light reflecting off their bodies. Scientists think that this could allow them to signal covertly to other members of their species without alerting prey or predators nearby, pretty nifty. To do this, mantis shrimps have an exoskeleton with special optical properties due to its structure. Cuttlefish however have a mechanism that allows them to control the polarization patterns they produce. Specialised pigment cells, iridophores, under control of the neural system are able to undergo ultrastructural changes in seconds, producing a changing polarization signal all over the body. All of this on top of changing colour and iridescence. The cuttlefish is an underwater disco.

So in in a nutshell, one of our projects will involve using LCD screens to display polarized stimuli to marine animals in tanks, and judging their responses to get a further insight into the mysterious world of polarization vision! More later...

Milly: Polarization Paradise

I've not been the most active of writers on this blog of late but, fear not, I'm going to write another series of posts as I blog/blather from the field.

Lizard Island, Australia. Photo: Michael Bok.

In just under a month from now, my lab and I (Ecology of Vision Group) will be flying to Australia, Lizard Island, on a mission to unveil more secrets about the vision of marine animals. You may be wondering why it is necessary to travel across the world to do this. Well, aside from the fact that scientific success increases significantly when in an idyllic location (obviously), we need access to Australia's diverse range of reef dwelling beasties, including the charming octopus and the not so charming mantis shrimp, more likely to rip your hand off than to shake it.

A mantis shrimp (stomatopod).
Photo: web.

Our team have collected all of the gear we will be needing for experiments: LCD screens, perspex tubes, lightbulbs, cameras, 3D glasses and milk. Now, it may sound like we are planning to watch a film, but actually we are going to do some serious and exciting science.

The word that binds our research together is polarization. If my colleagues and I were the mince, polarization would be the egg that binds us together forming the burger (?!) that is our group. Slightly off the beaten (egg) track.

Serious science time:

What is polarization?

Unpolarized light coming from a light source is oscillating at all
possible angles in that plane, however, when it is passed through a
filter (polaroid) it becomes polarized, oscillating only at one angle.

When applied to light, polarization means the direction that the light is oscillating in. If you imagine that you are holding a rope and you shake it up and down, waves form, travelling down its length. You can shake the rope from side to side, or also swirl it round forming a rotating pattern that also travels along the rope. This same idea can be applied to light as it too oscillates as it is travelling along as a wave. Just like the wavelength of light can inform an animal of the colour of something it can see, polarization can also provide additional information as light bounces off different structures or is scattered by particles.

How can an animal detect polarized light? 
We, as humans, know that polarized light exists around us, but unfortunately, without polaroid filters, we cannot see it. Unless of course you are one of the lucky few who have deliberately tried to view strong sources of polarized light such as LCD monitor outputs and are now cursed, forever having a strange yellow bow tie shape appear randomly on the desktop. It's called Haidinger's brush if you fancy having a go yourself. To detect polarized light oscillating at one angle, your photoreceptors must be aligned at that same angle, to absorb the maximum amount of light. If your photoreceptor is, say, 90degrees out compared to the polarized light, then it's not going to absorb very efficiently. This sort of arrangement of photoreceptors where one lies at one angle and a second, connected photoreceptor is lined up perpendicular to it, is very common in invertebrates and is the basis for their polarization vision. Simply put, it allows them to compare the outputs of these two receptors and figure out what angle the light is oscillating at.

Why is polarization vision useful?

Unpolarized light bouncing off the surface of the
water becoming polarized horizontally.
Photo: Wehner (2001).

At first it might sound like polarization vision could be disadvantageous, since you have the potential to lose information every time polarized light hits your receptors at the wrong angle. What it does do, however, is convey valuable information. When light bounces off a shiny surface, such as water, much of the reflected light becomes horizontally polarized (oscillating at the same angle as the water's surface). If the light hits the water at Brewster's Angle, then all of the light is horizontally polarized. Now, imagine that you are a water-seeking insect where the survival of your species depends on you reaching water to mate and lay your eggs. Some strong selection pressures there. If you have receptors aligned horizontally and pointing down towards the ground, you have a perfect water detecting device. This is a common feature of water-seeking insects. Unfortunately, lots of man-made surfaces are shiny so if you have ever wondered why you find dead beetles and mayflies on the highly reflective bonnet of your car...now you know. Polarization vision isn't just useful for this one task, light is also polarized as it travels through scattering media such as water, or the atmosphere. As the light scatters it becomes polarized at an angle depending on the incident light. If this is happening millions of times in the sky as the light travels towards the Earth, a predictable pattern is formed which acts as a map to navigation and orientation in bees, beetles and other insects where the landscape is complex, moving and changing or devoid of any useful visual landmarks on the ground. The same applies underwater.

Invertebrates such as insects, crabs and cuttlefish have polarization
sensitive cells in the eye consisting of perpendicularly oriented
light absorbing microvilli. You can see the two orientations in the
TEM image of dragonfly photoreceptors above.
Photo: Meyer and Labhart (1993)

I still haven't got to the bit where I explain what we are doing in Australia. I think that is quite enough for one post, time for a cup of tea.

Milly: Deep sea flashers

Some brilliant research by Sarah Zylinski that came out of the deep sea research cruise in 2010. Strange to think that even in deep, dark, remote regions, animals still need camouflage...

A link to the paper here.

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"Here you are" said Alan, all blasé, as he passed me something he had picked out of the trawl net. It looked like a dead hand on the end of a stick and smelt like one too; I didn't have a clue what I was looking at. The more learned scientists told me it was a stalked crinoid, a sea lilly, part of the Phylum Echinodermata, so related to starfish, sea cucumbers and sea urchins. As I looked closer I realised that it was much more attractive than a decomposing fist, with many intricate feathery arms that I imagined would actually look quite nice when underwater.

Having a gander at the feeding arms of the crinoid, note the long
stalk in the background, these can be 1 metre long! Image: Zan

Close up of the main body of the crinoid
showing the stem leading to the calyx
and then the feeding arms at the end.
Image: Zan

Another species of deep-sea stalked crinoid called Moulin Rouge
(Proisocrinus ruberrimus) photographed on the sea floor. Pretty sexy, for a crinoid.
Image: National History Museum

These fascinating creatures look like plants (hence the name 'sea lily') but have the features of animals such as a basic gut, a simple nervous system and a fully functional circulatory system that transports nutrients, gases and waste products around the body. The many feathery arms found near the mouth (and also unfortunately the anus) are used to filter out small particles in the water where it is trapped in sticky secreted mucus and pushed into the mouth.

They are sometimes referred to as 'living fossils' as they seem to remain relatively unchanged morphologically since their radiation during the Paleozoic Era (about 550-250 million years ago).

A fossil stalked crinoid,
looks a lot like the modern version.
Image: web

Shallow water crinoids are often free-swimming, and crinoids with long stalks, such as the one from our trawl, are usually found at depth, anchored to the ocean floor (ours was found at about 4500m). I say anchored...but scientists recently observed sea lilies up-rooting and crawling along the sediment, seems there is yet more to be discovered about these strange animals....

Milly: Ugly Fish pt 7

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Always dark on the night shift... Image: web

Prepare to commence trawl two. When you have been on a night shift from 4pm to 4am and a trawl is due to hit the deck at 2am, chances are your body clock is going to be a tad confused. Last time I nearly fell asleep in my fish dissection, started writing backwards and couldn’t retain a two digit number in my head for more than 1millisecond. Not doing that again. New tactic! Since I had allocated rest time before the trawl... I decided to stay awake for 28 hours before the trawl, have a sleep then be all fresh and ready for action once the slimy catch was brought aboard. Problem with that is staying awake for 28 hours with absolutely nothing to do tends to send you a bit West. I became inaudible, talking at extremely low baritone frequencies if you can even call it talking, more like incoherent blatherings. The day shift tolerated me well. The rewards were great however, and this time, we were super fish team extraordinaire (well, we functioned without any breakdowns anyhow).




Much like last time, the trawl net was opened (noticeably more rotund this time, a good sign) and catch was spilled into a large bucket ready for inspection. Unfortunately on the last trawl we managed to scoop up a large amount of clinker (burnt coal from steam ships of the past) which made sorting through the cucumbers and delicately removing gelatinous fish nigh impossible. This time, we had little ocean floor debris so I zealously sunk my arms into the cold, slippery assortment of fish, cucumbers and crustaceans and pulled out a big, heavy object. “Oh wow, an exciting find" I thought to myself. “Doesn’t feel like a cucumber, maybe it is a big leathery fish, woohoo!" It was a shoe, a big, woman’s boot. I then proceeded to dig out two bottles and a rock. Thankfully Alan and Juliette were being slightly more sensible and actually searching for fish shaped objects and so commenced a slithery extraction of rattails, smooth-heads, some unfortunate midwater fish and a huge cusk-eel.

Is it a fish?! Is it a holothuriuan?! No. It's a bloody shoe.

Histiobranchus sp., a deep sea eel. Image: Zan 

Cusk-eel! Image: Zan 

 Lovely cusk-eel (Ophidiid). Image: Nina

We had fewer fish this time round, but they were all in really great condition, great for samples we thought, but then memories of hours in the dark surfaced in my brain and I realised that watching 3 horror films to try and stay awake was, perhaps, a terrible idea. Juliette and I managed to put aside a few minutes whilst our fish eyes were on ice to explore the trawl and the sorting process in the wet lab. It looked how I would imagine a backstreet fishmongers from a sci-fi film to look. All manner of strange beasts being weighed and measured and samples for DNA analysis being taken left right and centre. The fish were amazing. There was one fish, aptly named ‘Jellyface’ by Zan, which had a large rounded nose, a small mouth and two, what looked like sensory pits, next to the eyes. The skin on the head felt very bizarre, much like a stubbly beard. The cusk-eel felt even stranger, as you ran your fingers across its skin you felt a crackling sensation which could be due to tiny bubbles under the skin forming as the fish is brought up from depth, decompressing the air within its cells. 

'Jellyface'. Image: Zan

Juliette having a good rummage around in the cucumbers. Image: Nina

Not the most attractive of creatures.
According to one scientist this cucumber is "cute", "look at it's little hat!" she said. I later discovered this 'little hat' is in fact a parasitic anemone. The deep sea is a very strange place! Image: Nina

I had been challenged by one of my supervisors to kiss a benthic fish. Now, he may well have been joking, but I considered this something I should take very seriously and so I sought out the loveliest of all the fish in the catch, the cusk-eel and planted my lips firmly upon its slimy....mouthparts. Picture taken. Job done.

I think the picture says it all. Image: Nina

So why is all of this necessary? Larking about aside, we are taking samples for serious and important science and all possible information is always gathered from these trawls, to make the most of each catch. Stay tuned for an explanation of the science behind the sampling, most likely in the form of an interview with Juliette McGregor (she doesn't know this yet). Roll on the final trawl. Fingers crossed my supervisor doesn’t up the stakes, kissing a benthic fish is one thing, but kissing a sea cucumber, well that's a whole different level of gross.

Milly: Ugly Fish Pt 5

Alan with his lander 'Dave', about to be deployed
over the back of the ship. Image: Nina

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Things have been relatively quiet over the last few days. No riots here, just high base levels of madness, but then you have to be slightly weird to want to go on a research ship for half of your summer. A few of us have put our heads together and have come up with some ideas for thwarting the violence. We propose the development of a porridge cannon firing hot, sloppy, honey saturated oats. "You would have to counter it with milk and sugar" said one scientist, "they wouldn't expect that". I'm not here to comment on the riots, nor should I make light of the situation but it is very odd reading the updates from sea, it all feels very unreal.

"What exciting thing have you discovered today?!" I imagine my supervisor will be thinking. Well Julian, personally absolutely nothing. I got up, went to the gym then ate a giant plate of shepherds pie and cabbage for breakfast. Proper scientists however have been discovering some really amazing stuff.

Alan Jamieson from Oceanlab, Aberdeen, has sent his lander 'Dave' to the sea floor to photograph the mud (mud again), haha only joking, to photograph the animals! Sorry mud scientists but I've had quite enough of your mud for the time being, especially when there are ugly fish to be photographed!

An Ophidiid, Bassozetus sp., a cusk-eel. Image: Alan Jamieson

An abyssal grenadier (Coryphaenoides armatus) looking rather sad. It must be hard being a deep sea fish.
Image: Alan Jamieson

Nine abyssal grenadiers at the bait. Image: Alan Jamieson

The lander is essentially a large aluminium frame with a number of cameras attached to it, a giant flash and a weight with bait attached to it (more stinking mackerel). It gets sent to the bottom and (hopefully) paparazzis all of the beasties who come to dine at Alan's table. Whilst it may seem relatively easy to chuck a piece of kit over the side to sink to the bottom of the ocean, getting it back is a complicated process. And actually there is no 'chucking' involved, but careful winching and manoeuvring to ensure the lander doesn't get destroyed by the ship's propeller.

To get Dave back (and all of the photos) an acoustic signal is sent from the ship into the water where it travels down to Dave and triggers the release of it's (his?) weights via the movement of mechanical arms. Dave then floats up to the surface powered by the buoyancy of the glass floats attached, where he is collected by the ship! Phew. How on earth this signal manages to travel from the boat all the way to the bottom of the ocean, intact, is beyond me. Mysterious wizardry.

Trawl on Saturday morning, really hope we catch this fella, Bassozetus compressus, the abyssal assfish. Excellent.

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Milly: Ugly Fish Pt 7

I've just realised it's also unlucky to look at a picture
of a pig. This does not bode well...

It appears we nightshifters are cursed. Possibly because we are a team of 6 women and only one man. Bad luck. Maybe it's because I decided to bring green overalls which apparently make me look like I work in a garden centre, not quite the look I was going for. If this was a commercial trawler I'd have been thrown overboard for wearing green, but I would have had to pass myself off as a man first to step foot on that ship. I've been hearing about all sorts of strange superstitions, an alarming number are pig related. The word pig mustn't be used and if you see a pig on your way to the ship, well, you might as well go home. This all seems to be based on the Garadene swine, the unlucky pigs Jesus cast a load of demons into when he exorcised them from a madman. Oh and then the pigs drowned, so that makes loads of sense. Apparently this is why pigs have so many alternative names, grunter, porker etc. Strange.

Whoops, massive tangent. So the nightshifters on two accounts now have been ready to roll, mud slicing equipment at the ready, and twice the megacorer (mud sampling device) has come back with empty tubes. We have had some fun at 2am prancing around in fishing gear however.

Juliette checking out the amphipod catch

Hundreds of tiny amphipods caught in the baited trap

What have been more successful are the amphipod traps and towed camera, WASP. Amphipods are a bit like marine cockroaches, the crustacean scavengers of the deep. Hugely speciose, they come in all shapes, sizes and colours but one thing they have in common is they all scurry around eating dead stuff. Four traps, baited with possibly the worst smelling mackerel on the planet, were deployed to the bottom of PAP, about 4000m. They came up brimming with amphipods, ready to be barcoded by the geneticists.

Scientists having a gander at the WASP footage

The towed camera WASP (wide area seafloor photography) has been taking pictures of the sea floor as the ship has been sailing along. Makes your average biological transect seem pretty lame, in comparison. This equipment gives scientists a glimpse of what the seafloor looks like without (too much) disturbance. It looks to me like the surface of the moon, covered in hundreds of tracks made by holothurians (sea cucumbers) and a hefty amount of cucumber crap. They are bizarre looking creatures with weird abilities like turning their bodies to liquid to squeeze through gaps or turning themselves inside out to evade predation. But, what they seem to be extraordinarily good at is crapping, and crapping in the most delightful way!

Cucumber crap. Isn't it nice!

On that note I better get some sleep, trawl will be coming up soon and I'm definitely not mentally prepared.

Milly: Ugly Fish pt 2

RRS James Cook

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We made it! We are on the James Cook, phew.  Since we have been sailing for a few days you might think I'd have worked out where everything was by now but I still end up on the forecastle (I have no idea what that is) deck when trying to find my cabin. Quite a confusing error to make since the forecastle is at the top and my cabin is in the bowels of the ship. My room has no windows which is quite handy as I'm on the 4pm to the 4am shift. So, apparently there is a sauna here but I'm not sure if this is a crew in-joke whereby I turn up at the 'sauna' in a bikini to find that it's actually the engine room.

Tubes of ocean floor

The weather has been extremely good and the boat has been hardly moving at all. I've stayed away from the sea sickness tablets thus far, however there has been mention of 'dreadful conditions' in the next few days and when an experienced deck officer uses the word 'dreadful', you know you're in trouble.

There is an interesting mix of scientists aboard this cruise, exploring the Porcupine Abyssal Plain (PAP). Many people from the National Oceanography Centre (NOC), at Southampton, seem to be interested in mud. Not just the mud, they say, but the wee beasties that reside in it. One important group of organisms are the Foraminifera, or forams for short, strange protists that can be used as indicators of environmental change, as they give scientists an indication of what's happening to the oceans' currents. To study forams, this group are sending a machine, consisting of a frame and 8 tubes, flying the bottom of the Atlantic. When it hits the ocean floor the tubes stick into the mud triggering a mechanism that closes them, then bingo, all you need to do next is drag the thing back to the surface and you have loads of lovely mud!

An unfortunate little sea urchin, captured by one of the tubes

Yesterday I was learning how to slice mud. Easy? No, not easy. For starters it's all carried out in a cold room at 4 degrees, secondly you have to somehow get the mud out of the tubes in some sort of sensible manner so you know what bit you are sampling and thirdly, the mud isn't sloppy, oh no, it's hard like a big rock sausage. Fun though, and now I have something new to add to my CV 'is able to slice deep sea mud'. Tastes nice too.

Carefully removing mud from the tubes

We are currently steaming to PAP and will arrive in an hour or so. There we will be sending down various bits of kit to image the sea floor. As lovely as mud is, I'm excited to see what else PAP has to offer...

(I should also mention that Juliette is still alive)

Milly: Ugly fish

Stomiid. Image: Camilla Sharkey and Julian Partridge

Milly: Ugly Fish pt 2
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Milly: Ugly Fish Pt 7

When asked about my summer holiday plans recently, I informed my friend that I would be spending a month off the coast of the UK on a months fishing trip. She laughed; I wasn't joking. Come August I'll be up to my ears in gelatinous, benthic fish brought up from thousands of meters and rather alarmingly I've been purchased full body overalls due to the "repulsive stench" of the fish that "never leaves the fabric". I'll be aboard the RSS James Cook for a month, so to stave off insanity I'm planning to blog from the ship to keeping you up to date with the latest discoveries. It seems to be a little known fact that members of the Bristol Biology department study deep sea fish and so I thought it best to bring a little of the research into the lime light.

Dr Nick Roberts, part of a team of Bristol vision scientists, has gathered together a group to investigate colour and light in nature. As part of this, a new post doc, Dr Juliette McGregor, will be looking at the effect of pressure on photoreceptors. The pressure exerted on deep sea fish is enough to alter the protein structure and this includes that of visual pigments so in August, Juliette and I will be collecting deep sea fish retinal tissue which will be used to examine their spectral properties under pressure (whilst trying not to be sick onto the specimens as we dissect stinky fish...on a rolling boat...in the dark).

Another ongoing project has been looking at the eyes of Malacosteus niger (image below) the stoplight loosejaw, a fish with red eyes, gaping mouth and a light organ underneath each eye that emits red light.

Stoplight loosejaw, Malacosteus niger

Most deep sea animals can only detect blue light (a colour common at depth as many animals produce blue bioluminescence) so by producing red light, M.niger can hunt prey or communicate with other individuals without fear of detection! Now what is particularly amazing about these creatures is what's found in their red eyes. In order to detect longwave red light, they use chlorophyll as a photosensitiser. But that's in plants I hear you shriek! Well, even stranger than that, the visual properties of the pigment is very similar to that found in small crustaceans it eats (see paper). So does M.niger use chlorophyll it obtains from its diet to alter the wavelength of light it can see?! We don't have the full story yet so watch this space...

Dolichopteryx longipes photographed from above

Another amazing discovery was made during a past research cruise by Professor Jochen Wagner (University of Tubingen), Prof. Ron Douglas (City University London) and Prof. Julian Patridge from Bristol. Whilst midwater trawling they discovered a live specimen of Dolichopteryx longipes (image right). Previously only one preserved fish was available for studying this unique species, the only vertebrate found to form images using a mirror instead of a lens which reflects light onto a second retina.

These fish appear to have four eyes and although there are just two, each is separated into two parts, one looking upwards and the other down. This allows D.longipes to detect silhouettes of animals above it, but also detect bioluminescence produced by animals below. For more info on this fascinating fish see this news article or paper.

I think that's quite enough biology for now, but I hope I leave you with a better idea of what strange things are going on in the Bristol University biological department and keep your eyes peeled for posts in August from the Porcupine Abyssal Plain, eek!