Thursday, March 29, 2012

It's currently complicated

A few weeks ago I wrote about the problem of plastic in the ocean. In that post I used a simple graphic showing the location and direction of rotation of the five oceanic gyres. On seeing that diagram you may have guessed that things were actually a little more complicated. Well, they are. Something that might have tipped you off was the swirls in the photos of plankton blooms I posted, here and here. If you want to get a sense of just how complex the ocean currents are, here is a great visualisation of a NASA ocean current model. This too, is a simplification.

Monday, March 26, 2012

Tweets in the deep

When the intrepid adventurers in the Lord of the Rings reached Moria they heard drums in the deep. Now James Cameron has reached the oceans deepest point, the Challenger Deep in the Marianna Trench off Guam. I'm not sure if he heard drums, I suspect he didn't, but he's sent a tweet:

Just arrived at the ocean's deepest pt. Hitting bottom never felt so good. Can't wait to share what I'm seeing w/ you.
I'll bet he can't wait because he's going to charge you money to "share" what he's seeing with you. He has plans to release two documentaries with the footage he collects.

It's the first time since 1960 that anyone has been to the Challenger Deep. At 10, 898 meters below the surface, it's an impressive feat. Nice work James. And nice work Australian engineering team who built the submersible he piloted. Now how about lending me the keys?...

Saturday, March 24, 2012

Flight is the new black

There are several kinds of animals that leave the water by jumping. A few have adaptations that allow them to increase the distance that they travel in a jump. For instance, flying fish and flying squid use their fins (and tentacles in the squid) to help them glide above the surface.

A flying fish in flight. Note the enlarged pectoral and pelvic fins to assist in gliding (photo Danielandmelora).
It's long been thought that jumping and gliding are an adaptations to aid in predator avoidance.  By leaving the water it is harder for predators to track their prey. And, prey that glide can change direction in the air to make it even harder for predators, because it becomes more difficult to determine where the prey will re-enter the water. 

A squid (probably Ommastrephes bartramii) in flight. Note the way the fins and tentacles (with membranes between the arms) are held for gliding (photo Geoff Jones). 
Recently, though, some researchers have suggested that squid might use aerial gliding to reduce the energetic cost of migration. They were able to collect data on the acceleration and velocity of squid in air from analysing photographs of jumping squid taken in rapid sequence. They found that travel in air was five times as fast as any measurements of squid movement in water. I'm a little skeptical of this claim. Mostly because speed is not a good way to measure the energetics of movement. 

Squid have two ways of moving. They can use their fins or they can use a jet propulsion system. The jet propulsion system is the primary form of movement in most squid, but often it's used in concert with the fins. And it's the jet propulsion system that squid use to exit the water. To move this way, the squid takes up water into its mantle cavity and then forces it out a narrow funnel beneath its head.  

The funnel of Illex illecebrosus, which is used in jet propulsion. The arrows in the image point to the lateral adductor muscles that support the attachment of the funnel to the head (photo M. Vecchione).

To help direct the water through the funnel, rather than back out the mantle opening, squid have a specialised apparatus to 'lock' the mantle shut. Cartilaginous pegs (one on each side) on the  inside rim of the of the mantle slot in to clips on the upper margin of the funnel. These lock the mantle closed as it contracts, which forces the water to squirt out through the funnel in a jet.

The funnel-locking apparatus of a flying squid, O. bartramii. The peg on the right is found on the inside rim of the mantle and fits inside the clip on the left, which is found at the top of the funnel. They clip together to lock the mantle opening shut and help to direct water through the funnel. The tissue in the image has been stained blue (photo R. Young).
Squid must achieve quite high speeds when using their jet propulsion system to exit the water. And the squid continue to shoot water out through the funnel to rocket through the air. Travelling at this speed is likely to have a metabolic cost because oxygen demands increase exponentially with increasing swimming speeds1. I suspect that, although jetting through the air is more efficient than putting the same effort into swimming, it’ll be more energetically efficient to travel at speeds that are too slow for flight. The effort required for flight may explain why squid are rarely seen jumping and have never been observed making repeated jumps. 

Jet propelled squid (probably Sthenoteuthis pteropus). Note the trails of water behind the squid, squirted from their funnels (photo Bob Hulse).

Another paper2 that's just come out shows a whole new group of swimmers are able to fly too. The animal part of the plankton, or zooplankton, is made up in large part by tiny crustaceans called copepods. Copepods swim by beating elongated antennae like oars, which moves them through the water in a typically jerky fashion. With just a single swimming stroke some copepods are able to exit the water and travel up to 17 centimetres through the air. Not bad for an animal that's only a couple of millimetres long. 

Copepod crustaceans make up a large part of the zooplankton. They swim by beating their elongated antennae producing a typically jerky swimming motion.

Just like flying squid and flying fish, copepods can travel further through the air for the same effort than they can travel through the water. But, the swimming speeds required to exit the water are extremely high. Indeed, the study reports that before they leave the water the velocity of the copepods was higher than the previously documented maximum swimming speeds of similar sized copepods.

The really neat thing about this paper is that the authors were able to document why the copepods were jumping. And it was not because it’s a more efficient way of travelling. It’s a way of avoiding predators. The authors observed the jumping copepods in the wild and found that they jumped in response to approaching predatory fish. And it seems to be a pretty successful escape mechanism too. Of the 89 escape jumps they observed only one individual was eaten.

You can read more about the jumping copepods and see a video of them jumping on the ScienceNow website.

1. Webber, D. M. & D'Or, R. K. (1986) Monitoring the metabolic rate and activity of free-swimming squid with telemetered jet pressure. Journal of Experimental Biology 126, 205 - 224

2. Gemmell, B. J., Jiang, H., Strickler, R. J., & Buskey, E. J. (2012) Plankton reach new heights in effort to avoid predators. Proceedings of the Royal Society B: Biological Sciences doi:10.1098/rspb.2012.0163

Saturday, March 17, 2012

The gorilla genome

Recently the gorilla genome was published. It showed that 30% of the genome was closer to  humans or chimpanzees that chimps and humans were to each other. The creationists were delighted, for they though they thought that the 'evolutionists' had just provided them with evidence against common descent. They were wrong...

Nobody was surprised that they were wrong; it's a habit of their's. Similarly, nobody with a good understanding of evolutionary genetics was surprised that humans had some genes in common with gorillas that they didn't share with chimps. It was, indeed, expected. But, it provides an interesting lesson for some common misunderstandings of evolution.

There is a pervasive idea that humans are the pinnacle of evolution and that chimpanzees and gorillas are 'primitive'. But, in reality, chimps and gorillas have an equally long evolutionary history and have changed just as much as humans since our lineages split from one another. And one study has shown that more genes in the chimpanzee lineage have been under selection than genes in the human lineage since the split.

Another misunderstanding is that the genetic differences observed now, must have appeared at the time the lineage split. But, the divergence of two species is not instantaneous; the genetic divisions become deeper over time. Moreover, some genetic differences may have appeared long before the split and were lost, by chance, in the populations that gave rise to one lineage, but not the other. The tree diagram for individual genes may, therefore, look very different from the phylogenetic tree. This phenomenon is know as incomplete lineage sorting (ILS). 

The important thing for evolution is that on average the human genome is more similar to the chimpanzee genome than either are to the gorilla genome. And this is the case. I suspect that many of the creationists shouting about this latest paper disproving evolution know that this is the case. But, I also think they know that it is a technical and often misunderstood part of our evolutionary knowledge and are using it to spread doubt about evolution through misinformation.

To understand ILS, you have to think not just about genes, but about the populations and species that genes occur in. When there is more than one version of a gene, each version is known as an allele. In apes (and most animals) any given individual will have two copies of a gene, which may be different alleles. But, in a population there are likely to be alleles that aren't present in every individual. Similarly, in a species all possible alleles may not be present in every population.

As populations diverge to form species, some of the alleles present in the ancestor will be lost because they won't be present in both populations. Others, however, will be retained in both descendant species. Fast-forward to another division in one of the species and the same thing can happen. By chance some of the alleles present in the common ancestor to all three species will be present in only one of the recently diverged species and in the more distantly related group. If the creationists had read more than part of one sentence of the gorilla genome paper, they would have seen this process illustrated in the very first figure.

Figure 1 from Scally et al. (2012) showing the phylogenetic tree for humans (H), chimpanzees (C), gorillas (G) and orangutans (O) with an example of incomplete lineage sorting overlaid in grey. In the example, the branching of one gene (grey line) does not map with the average genetic distance between species (percentages at the bottom). If we were to look at the example gene only, we would infer a more recent common ancestor for chimps and gorillas than for humans and chips. And that's why we don't construct phylogenetic trees based on single genes. 

Further reading:
Scally, A., et al. (2012) Insights into hominid evolution from the gorilla genome sequence. Nature 483:169-175 

Bakewell, M. A., Shi, P., and Zhang, J. (2007) More genes underwent positive selection in chimpanzee evolution than in human evolution. Proceedings of the National Academy of Sciences 104 (18) 7489-7494

Friday, March 16, 2012

Sharks are good swimmers

It's hardly surprising that sharks are good swimmers, given their more than 400 million year evolutionary history in the ocean. But, it's the way that they achieve their swimming prowess that is surprising. Two recently published papers show how sharks achieve more thrust than their muscle movements alone would suggest that they should. One involves their tail and the other involves their skin.

Vortices generated by the water jets from a swimming shark's tail (image Brooke E. Flammang)
The main function of a sharks tail is, obviously, to provide thrust and drive the animal forward through the water. As the tail moves to and fro it creates jets of water that travel backwards, propelling the shark forwards. For most fish, just one jet is created at the end of the swing. The sharks in the first study, however, generated two by stiffening and slightly changing the shape of the tail mid-swing. So, the sharks generated thrust at the extent of its tail-stroke and at the midpoint.

The shape of a shark's tail tells you something about how it swims.
The study looked at two species of dogfish, which have similar tail shapes. Many sharks, like the dogfish, have 'heterocercal' tails. That is, the upper lobe of the tail is larger than the lower lobe. An extreme example of this tail shape is the thresher shark. Other sharks, like the great white, have more 'homocercal' tails, where both upper and lower lobes are roughly equal in size. It would be interesting to know whether all sharks use the same 'tail-stiffening' strategy as the dogfish, or whether different tail shapes require different strategies.

The second study looked at the skin of the sharks. Sharks have placoid scales, which are also known as dermal denticles ("skin teeth"). Dermal denticle is often the preferred term because they are structurally similar to vertebrate teeth and likely have the same evolutionary origin. Dermal denticles have a flat plug inside the skin, passes through the skin as a narrow neck, then flattens into a more elaborate crown-like form. In most sharks the points of the crown are directed backwards, so the skin feels smooth running a finger from head to tail, but sandpaper-rough running a finger from tail to head.

Scanning electron microscope image of the dermal denticles of a bonnethead shark, Sphyrna tiburo. The green scale bar indicate 50 um (photo Oeffner & Lauder).
The orientation of the dermal denticles was long thought to decrease the drag on a shark as it swam. But, the authors noted that this hadn't been properly tested. They attached shark skin to a rigid metal plate and moved it through water to simulate a swimming shark. Then they sanded back the dermal denticles and repeated the test. Curiously, the skin performed better without the dermal denticles.

The authors decided that the rigid metal plate did not adequately mimic the body of a shark, which flexes as the shark swims. So, they removed the metal plate and repeated the tests of the skin, with and without denticles. This time the skin with dermal denticles performed better then than sanded skin. Further analysis showed that the reason for this is that as the denticles move on the flexing skin they create a leading-edge vortex that sucks the shark forward. The denticles, therefore, not only reduce drag, but increase thrust.

The articles:
Flammang, B. E., Lauder, G. V., Troolin D. R.,  and Strand, T. (2011) Volumetric imaging of shark tail hydrodynamics reveals a three-dimensional dual-ring vortex wake structure. Proceedings of the Royal Society B: Biological Sciences 278 (1725), 3670-3678

Oeffner, J. and Lauder, G. V. (2012) The hydrodynamic function of shark skin and two biomimetic applications. The Journal of Experimental Biology 215 (5), 785-795.

Thursday, March 15, 2012

Phytoplankton from space, redux

An image taken by the Modis instrument on the NASA Terra satellite of a massive phytoplankton bloom in the East Antarctic (image NASA & Jan  Lieser).

A while ago I wrote about plankton blooms that were visible from space. Now a satellite image documents the biggest ever recorded plankton bloom in the Southern Ocean. The image above was taken 15 days after it was first detected (in mid-February), when it measured 200 km by 100 km. It's unclear what has caused the bloom, but it's suspected that strong offshore winds have carried nutrient filled snow from the Amery Ice Shelf out to sea. The Aurora Australis, the Australian Antarctic Division's research and resupply vessel, has visited the area near the bloom to collect water and algal samples. 

Wednesday, March 14, 2012

Diving gannets

Many years ago I stayed on an island off Wilsons Promontory in Victoria. Nesting on the island were a huge number of mutton birds. Every evening they would all come back from feeding and crisscross the island looking for their nests. It was amazing that so many birds could fly in so many directions at such high speed without colliding. Just as I was pointing this out to the people I was with, two birds clipped wings. We hadn't even stopped laughing before another two birds had a far more serious head-on collision. Both birds must have survived because we couldn't find them on the ground, but they could have been seriously injured.

It turns out that it's not uncommon for other seabirds to have collisions, some of them fatal. Gannets are an interesting seabird that plunge into the water at high speed order to catch fish from close to the surface (although I've heard of divers seeing them 40 meters down!). Gannets can form large flocks above schools of fish. At high densities collisions become more likely as one or more gannets target the same fish. Although collisions are not uncommon, deaths seem to be.

Now there is some cool underwater footage of gannets feeding with sharks and dolphins in Hauraki Gulf, New Zealand. It was taken by Gabriel Capuska, a PhD student at Massey University. It shows a collision between gannets and some interesting other behaviours. For more detail, go to the Massey University story.

Tuesday, March 13, 2012


Many Australian science lovers had their fingers crossed that the enormous Square Kilometer Array project would be built in Western Australia. Now Nature is reporting that South Africa has won in the bid.

Friday, March 9, 2012


Many people were rightly disappointed when Melbourne University cut its Viking Studies course. The Massachusetts Institute of Technology is turning the tide against the loss of subjects that teach the art of pillaging on the high seas. They're now offering pirate certificates. Learn sailing, fencing, pistol shooting and archery and you too can be an MIT pirate.