A Schooner of Science

Vampire squid on Occupy Wall Street, biology of Vampyroteuthis infernalis

// December 14th, 2011 // No Comments » // The Realm of Bizzare

Occupy Wall Street protesters took up arms – eight of them – in their march on Monday. Carrying craftastic models of vampire squid high above their heads, in homage to Matt Taibbi’s description of the bank as “a great vampire squid wrapped around the face of humanity, relentlessly jamming its blood funnel into anything that smells like money” in Rolling Stones, 2008.

Harsh words, right? I mean, vampire squids are totally awesome!

The vampire squid inhabits the cold, high-pressure environment of the deep sea. Light is absorbed by the water, making it perpetually twilight. A vampire in twilight, that’s not horrifying, that’s dreamy, amiright? Don’t hit your head if you swoon.

We don’t know much about these little dudes because they dwell in that most mysterious of spots, the deep sea. Vampyroteuthis infernalis means vampire squid from hell, but it’s not even technically a squid. Or an octopus. It’s got an order all of it’s own.

They have a consistency similar to a jellyfish, quite gelatinous. Like many jellyfish, it swims by shooting out a jet of water behind it to propel it forward, but it has a couple of fins for manouvering. It has eight arms and two extra arms which hide in its ‘pockets’ and can extend the length of its body when needed.

This National Geographic vid is pure pirate gold for high quality images of the creature.

They hold the title for the largest eyes relative to their body. An individual about six inches long has an eye an inch across, about the same as a full-grown dog. All the better to see you with, my dear. They also have a receptacle behind their eye for spermatangia, the tough sac of sperm ejaculated from the specialised arms of a lover. Just imagine date night

The most brilliant behaviour is their bioluminescence. These guys glow!

When startled, squid may shoot out ink to confuse predators. That’s not much good when you live in twilight, so instead the vampire squid shoots out glowing balls that dazzle and confuse. Over a thousand discrete bright particles within a matrix of mucous. Picture that, you’re out looking for a snack late at night, feeling pretty hungry, you think you smell something good and suddenly there’s some wacko waving glowsticks and snot in your face!

Another defensive ploy is to go into pineapple pose. Turning their bell-shaped tentacles over them, they completely change their shape (going kind of inside out). They light up some spots on their head which animals may take for eyes, which glow and then shrink as if the animal has swum away. Even if you didn’t buy that the animal was gone, looking at the videos, you wouldn’t want to eat that.

Stephen Fry gave respect to these sweet deep sea entities in this clip from QI. Hat tip to Dr M at Deep Sea News.

Oh… and about that quote Occupy Wall Street are marching for. The vampire squid’s diet seems to consist of molluscs, fish and crustaceans. As far as we know, it’s not a blood sucker, and Tree of Life. describes the funnel as absent. That must make it hard to stick said metaphorical blood funnel into anything, whether it smells like money or not.

Recommended links

In the QI link, they say the bioluminescence explosion is like John Barrowman! You might know Barrowman as the immortal Captain Jack Harkness from Dr Who and Torchwood, but blow me down, that captain can dance!

Still got time for more videos? Here’s David Attenborough talking about the deep ocean.

The majority of this info was from Tree of Life.

Future floating laboratory, prospectus of the HMS Beagle Project

// December 2nd, 2011 // 1 Comment » // Science Communication

Yesterday afternoon I went to a prospectus to the HMS Beagle Project while founder David Lort Phillips is in Adelaide.

It’s a CRAZY exciting project which plans to build a modern version of Darwin and FitzRoy’s tall ship the HMS Beagle, kitted out as a floating laboratory.

Marine biologists could benefit from getting much-needed ship time. As it’s a tall ship, it can get closer to land than large cruise vessels, giving it an extra bonus to people studying tidal areas. Groups into DNA barcoding might find it useful too, as it can be tricky to get high quality samples for DNA testing – most are set in formalin which ruins the info. More on DNA barcoding soon.

Climate research can be done from the boat, the connection between biodiversity and climate change could be exploited in the project. There’s a collaboration of the HMS Beagle with NASA, combining observations from space with water samples in the ocean.

In 2009 the Brazilian tall ship Tocorime with the International Space Station, and they ran live hook-ups between scientists on the boat, an astronaut above, and school children in Paraty. Looks like Keven Zelnio from Deep Sea News was there! The students had questions written in English on paper which they screwed into a sweaty ball with excitement, according to Karen James, involved with the HMS Beagle Project.

Most interesting for me is the prospect of science communication on the high seas. We can take high-tech science to ports around the world, including remote areas that often miss out on science engagement events.

I’d like to see the online aspect of the beagle able to webcast and tweet from the deck, setting up chat sessions with classrooms and the public. Maybe people could watch the Beagle’s progress through the ocean, and be updated with the science we on the way. Oh, I gots ideas!

At the moment they have blueprints and some collaborations sorted out, but are still looking for funding to get it built and in the water. The first five years it would retrace the first voyage of the Beagle, including along the South American coast.

Chile are planning to build their own ship in connection to the project, possibly named after the Beagle support ship, the Adventure.

Darwin was 22 when he signed on with the Beagle, an amateur with an interest in science – mainly geology. What he saw from the ship and at port, particularly in the Galapagos Islands, lead him to a world-changing hypothesis.

Maybe the new Beagle will have the same effect on some young scientists. Good heavens, I just really hope they build this tall ship, and when they do, that I’m on it helping to share their discoveries online, in ports, worldwide.

Exploring the blurry line between colony and individual

// August 3rd, 2011 // 1 Comment » // The Realm of Bizzare

I found this great post on the Portuguese man-o-war, known as the bluebottle in Australia, over at Deep Sea News the other day. It’s eating a fish!

The post also said:

Remember this species is colonial and made of four different polyps or zooids, working in unison and dividing labor. The bladder is a single polyp called a pneumatophore. The long tentacles are dactylzooids used for fishing. The dactylzooids bring the fish up to another set of zooids, gastrozooids, responsible for digestion. Last, there is set of zooids, gonozooids, in charge of reproduction.

So it looks like a jellyfish, but it ain’t. It’s a colony of four specialists working together, each with their own nervous system but incapable of living by themselves.

As I was doing a bit of research about bluebottles and how they sting even when dead and dried up, I came across an interesting question. How do they reproduce? If the gonozooids are responsible for getting jiggy with it, don’t they just make more gonozooids? Where do the rest of the polyps come from?

Well, no one really is a hundred percent sure. I guess that’s fair enough, studying a swarm (a navy) of man-o-wars during mating season doesn’t sound too good. But here’s what they think.

A gonozooid from one man-o-war will make sperm which combines with an egg from another man-o-war gonozooid. Hey presto, you’ve got fertilisation and one embryo – which will become the bladder polyp at the top. That embryo divides several times, then reproduces asexually to make more zooids, which bud out of it. The budding polyps will become either tentacle, digestion or reproduction individuals.

That’s where I got confused. Does this mean that each of the zooids actually come from a single polyp? Are they just differentiated forms of the original polyp, specialised for their particular role? How is this different to a human embryo producing heart cells?

One explanation uses phylogenetics – comparing organisms to see how similar and different they are. Each zooid is similar to solitary Cnidaria (the phylum that includes jellyfish, coral and bluebottles), so can be considered an individual in its own right and a bluebottle as a colony.

But if we define an individual as something with similarity to other individuals, then all the cells of a multicellular organism would be individuals. Are individual humans really colonies of individual human cells? Really, the microbes on and in you outnumber your human cells 10 to one, so you’re more like a walking microbial factory anyway.

I think we have a very human-centric model for defining individuals, which is not surprising really. But most species on the planet don’t reproduce like we do, the boundaries between individual and colony are much less clear.

Take aspen trees, which can grow by seeds (sexually) or by underground runners which sprout a tree-clone (asexually.) Over time the runners can decay separating the trees. How can we tell if the trees are individuals or clones, and if we can’t, how do we study adaptation and natural selection?

Tasmania has these Huon pines that are the oldest genetically identical stand of trees which has lasted 10,000 years. Each tree lives about 2,000 years, but the original tree renews itself through genetic clones. Tassie also has the oldest genetically identical plants, clones of King’s lomatia estimated to be at least 43,000 years old.

Strawberries do it too, as do fungus. A single specimen of Armillaria solidepes was found in Oregon the size of 1,220 football pitches and estimated at 2,400 years old. It’s one of the largest organisms in the world.

Where does the individual end and a colony begin? Looking at all the bizarre stuff out there, I can’t help but wonder if we’re the weird ones.

Clarke, E. (2010). The Problem of Biological Individuality Biological Theory, 5 (4), 312-325 DOI: 10.1162/BIOT_a_00068

Read it at the homepage of Ellen Clarke

The red queen, sex and nematode worms

// July 28th, 2011 // 1 Comment » // Recent Research, Sex and Reproduction

In Lewis Carroll’s Through the looking-glass- a whacky book if I ever read one – the laws of physics don’t really apply. Hills can become valleys, straight can become curvy, and forward is really backward.

In one scene, Alice chases after the Red Queen, both running as fast as they can, but when they stop Alice realises they are still right where they started. “Now, here, you see, it takes all the running you can do to keep in the same place” says the Red Queen.

And it might be the same with the evolution of predator and prey, host and parasite. Running doesn’t get you anywhere. So says the Red Queen Hypothesis.

As the host adapts to fight the parasite, the parasite evolves to infect the host. It’s an endless race, and extinction faces the first organism to stop running.

So what’s this got to do with sex? Sex is evolution on turbo. Mixing and matching genes increases genetic diversity, giving a species more opportunities to outlast in the ultimate game of survivor.

Field data supports the Red Queen Hypothesis as describing an adaptive advantage of sex. Models and maths support the idea that coevolving species could select for rare genes and unusual combination randomly created by sex. Direct experimentation of coevolution and nookie is tricky business.

New research, published in Science, grew several populations of nematode worms (C. elegans, roundworms) which are usually asexually, but reproduce sexually 20% of the time.

The populations were differently exposed to bacterial parasites (Serratia marcescens) as shown.

One population was given the parasites and left to their own devices. They and their bacteria could evolve together. These nematode worms increased their rate of sexual reproduction to 80-90% over time, and maintained a high level of sexy-times.

The other nematodes were given frozen stocks of bacteria every generation, so the parasites weren’t evolving as the worms did. At first, sexual reproduction increased in the worms, but then it dropped back down to 20% – the same level as nematodes which hadn’t been exposed to the bacteria at all.

Parasites on their own don’t increase sex – coevolution does.

A second experiment supported their conclusion. Nematodes mutated to be unable to reproduce sexually (asexual obligates) became extinct after 20 generations when exposed to the parasites. But mutants that always required sex to reproduce (sexual obligates) never became extinct.

When it comes to coevolution, it’s fall behind and be left behind.

Never stop running.

Morran, L. et al (2011). Running with the Red Queen: Host-Parasite Coevolution Selects for Biparental Sex Science, 333 (6039), 216-218 DOI: 10.1126/science.1206360
Brockhurst, M. (2011). Sex, Death, and the Red Queen Science, 333 (6039), 166-167 DOI: 10.1126/science.1209420

The electric, flashy development of tadpoles

// July 22nd, 2011 // No Comments » // Recent Research

Tufts researcher Dany Adams was filming the development of tadpole embryos, when she decided to leave the camera hooked up to a microscope going overnight. She was hoping to get some good time-lapse footage. What she got was bioelectric patterns which flashed across the developing tadpole face, outlining the future positions of eyes, nose and mouth.

“I was completely blown away.” said Dany, Ph.D, according to the Tufts press release. “I think I thought something like, ‘OK, I know what I’ll be studying for the next 20 years.” It had never been seen before, and was published in the August issue of Developmental Dynamics. Watch the video below.

“When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo,” said Dany. “We believe this is the first time such patterning has been reported for an entire structure, not just for a single organ. I would never have predicted anything like it. It’s a jaw dropper.”

Bioelectric signals cause cells to form patterns marked by differences in pH levels and membrane voltage, according to the researchers. The tadpoles were stained with a reporter dye that caused negatively charged areas to shine brightly while other areas look dark.

There were three bioelectric waves they saw in the footage.

First, a wave of negative ions flashed across the whole embryo at about the same time as cilia formed, tiny hairs which allow the embryo to move.

The second flash was a patterning that matched shape changes that were soon to occur in the face region. Bright areas, negative ions, show places where the surface will fold in.

Thirdly, localised regions of bright, negative areas formed, grew and disappeared without disturbing the existing pattern. At this point, the embryo began to elongate.

If bioelectric signalling is important to embryo development, you would expect development to be altered by screwing around with the signal process – and that’s exactly what happened. The researchers disrupted signalling by inhibiting a protein involved called ductin, which transports hydrogen ions. Some embryos grew two brains, others had unusual nasal or jaw development, and so on.

Interesting, I guess, but a bit sad for the baby tadpoles imho. Plus, I feel like it doesn’t take much to disrupt embryo development. Take away any protein that’s switched on at that sensitive time and development takes a detour…

All the same, bioelectricity may play a crucial role in embryo growth. Laura Vandenberg, another author on the paper, said “developmental biologists are used to thinking of sequences in which a gene produces a protein product that in turn ultimately leads to development of an eye or a mouth. But our work suggests that something else – a bioelectrical signal – is required before that can happen.”

Vandenberg, L., Morrie, R., & Adams, D. (2011). V-ATPase-dependent ectodermal voltage and ph regionalization are required for craniofacial morphogenesis Developmental Dynamics, 240 (8), 1889-1904 DOI: 10.1002/dvdy.22685

Alcoholic art, crystals of liquor

// July 12th, 2011 // 2 Comments » // Just for Fun, Science Art

So it’s appropriate that I’m a little bit tipsy while writing this.

Alcohol under a microscope! That’s today’s post. BevShots take photographs of alcohol crystallized on a slide, shot under a polarized light microscope. It can take up to four weeks for the alcohol to dry completely on the slide. It’s art, distilled. And quite magnificent.

Mmm margarita. And do you like pina colada?

What pretty rum. I think the citric acid helps. Anyone for a pint?

Bevshots sell the pics (there’s heaps) as metallic prints, on canvas or as merchandise – like hip flasks, for example. Look, I’m not big on promoting items, but these would make a sweet gift for a 21st birthday. They’re stunning, and only $28. It’s a nice personal touch if you know their favourite drink.

Oh, and vodka shot glasses! So cool…

There’s even an iPhone app, so you can pick your poison and see the bevshots version. I imagine this will increase your popularity and attractiveness with every drink. Kind of like beer glasses.

Isn’t this just the best mix of science, alcohol and art? They should be paying me for this kinda publicity (feel free to send me a gift, guys!)

A Gingerbread Laboratory

// January 19th, 2011 // No Comments » // Just for Fun, Science at Home

Thought I’d share some pictures of this awesome gingerbread laboratory my dad made me for Christmas.

It’s a science and research lab. Unfortunately some of the roof caved in during transit.

The lab comes complete with helipad. You can see some of the decorations inside through the “sky light.”

Royal icing, smarties, jelly beans, mint leaves, marshmallows and licorice allsorts decorate the interior while icing sinks ensure proper hygiene. Here’s the view from the front door.

OpenLab10 – best of the blogs for 2010

// December 16th, 2010 // No Comments » // Science Communication

Quick note and heads up to check out OpenLab10, which has published a list of some of the best blogging efforts from 2010. A good bunch in anyone’s book!

From this epic list they will narrow down to a mere 53, which will be published in an anthology on actual REAL paper, like the kind you see on TV.

Me own blog is listed for two posts. Firstly, How aqua regia saved Nobel Prize medals from the Nazis, a fiction based on a true science story and lively tale of chemistry trickery (chemitrickery) and bravery. Secondly may favourite monotreme, the weird, the wonderful, the Platypus. A poisonous, egg laying mammal with ten sex chromosomes.

I would invite you (nay, beg you) to vote for me, but it’s not that kind of thing so you’re off the hook.

But if you want to read some truly amazing examples of scientific writing, check out the submissions for OpenLab10! (Bookmark me first so you can come back later. You have me on RSS, right? Just checking.)

Happy reading!

New MolBio Carnival is up!

// December 7th, 2010 // No Comments » // Jibber Jabber, Science Communication

Ahoy there,

A quick note to send you over to me good mate Lab Rat, who blogs regularly about the amazing world of microorganisms and provides insights into life as a lab rat. She’s the host for the latest MolBio Carnival, a collection of the best blogs on molecular biology about.

I’m honoured to have been included on the list, although I blogged about something a little bit bigger (the marsupial joeys of the last post.)

Check it out here, and enjoy the picture at the bottom!

Platypus. Poisonous, egg laying mammal with ten sex chromosomes

// October 13th, 2010 // 7 Comments » // Recent Research, Science Communication, Sex and Reproduction, The Realm of Bizzare

Ah, the elusive platypus. The water dwelling animal with fur, webbed feet and a beak. It may just be the strangest animal on the planet. Not only does it look weird, it’s poisonous, can sense electricity, lays eggs and secrete milk through their skin, and have an excessive number of sex chromosomes.

It’s poisonous.
It is SERIOUSLY poisonous. The males have poison barbs under their front feet which they mainly use during the spring breeding season. One scratch from these babies and you will be in terrible agony.

My friend studied platypuses (yes, that’s the plural I checked) in honours and her colleague injected himself with platypus venom in the name of science. For months he had excruciating pain for months which did not respond to any painkillers, including morphine. Because of this quality, platypus venom could help scientists develop drugs which work differently to our current repertoire.

Research into platypus venom is lacking because it is hard to come across samples. But just last month researchers identified 83 possible venom genes using DNA extracted from an active venom gland. Some of the genes are similar to those in snakes, pufferfish and starfish. Now the platypus hardly evolved from a starfish. Instead, it’s an example of convergent evolution, traits that arise separately in different species and give a selective advantage. Illustrious journal Nature says platypus venom confirms the convergent evolution theory for venom. (Research paper Whittington CM, & et al (2010). Novel venom gene discovery in the platypus. Genome biology, 11 (9) PMID: 20920228)

Electroreceptor bill
Sharks use electroreception to find prey by sensing the electricity animals have in their body. Monotromes (mammals that lay eggs) including platypuses and echidnas, are the only mammals with the same ability, and the platypus is the strongest. Closing its eyes and nose when it dives, the platypus relies almost entirely on electrolocation and touch to find the tasty crustaceans it snacks on. Sharks and platypuses are hardly related, making this another yet another example of convergent evolution.

Electroreceptors are located in rows on the bill, which might help it find prey by noticing which receptors pick up the electricity first. We do the same thing with our ears, hearing noises at slightly different times tells us which direction the sound is coming from. When the platypus hunts, it moves its bill side to side, which might reveal how far away the prey is. It’s similar to how pigeons bob their head for depth perception.

Laying eggs
A female platypus has two ovaries, but only the left one is functional. Why? We don’t know.

Eggs spend 28 days developing inside their mother’s body and 10 days outside. The babies (often called puggles) are born with teeth, which drop out as they mature.

The mother produces milk, but she doesn’t have teats or nipples. Instead puggles lick or nibble on her skin to drink, gaining nutrients and probably an immune system. Living in mud, platypuses are born with no immune system, making them worse off than human babies which have immature immune systems at birth and rely on colostrum to boost their protection.

Sex chromosomes
Since the platypus genome was sequenced in 2008, we know a bit about these strange sex chromosomes. We know that they are more similar to birds than mammals, suggesting that our own mammal-like reptile ancestors might have had sex chromosomes like the birds of today. But there’s one big difference that makes the platypus unique.

They have ten sex chromosomes. Males have five X and five Y. Females have ten X. Humans, in fact, almost all mammals have only two. During platypus sperm production, the sex chromosomes pair up as X1Y1, X2Y2, X3Y3, X4,Y4, X5,Y5, so they can split evenly to make sperm that have 5X or 5Y. Phew. After all that, I’m surprised the males have any energy left for mating.