Tuesday, December 18, 2012

Giant squid in full HD!!

A week ago the Discovery Channel announced that it had footage of a giant squid that it would be releasing in January 2013! It could be the first video footage ever captured of a live giant squid in its natural habitat. Previous footage of a live giant squid has been taken at the surface after the squid was caught. In 2005 and Japanese team lead by Tsunemi Kubodera and Kyoichi Mori took the first still images of a giant squid attacking a baited line. The next year a team lead bu Kubodera caught a small female squid using a similar method and filmed it as it was brought into their boat.

A giant squid attacking a baited line (photo Kubodera & Mori)
I'm guessing that Kubodera is involved again, but other researchers may have used similar methods to get this latest footage. Basically, look for where sperm whales are diving, drop a baited line down a few hundred meters with a camera on it and wait. Easy!...

Monday, December 17, 2012

Shifting baselines in coral cover

ResearchBlogging.orgA great problem for conserving marine ecosystems is that we rarely have a good data on what things were like before human impacts started. In my last post, I wrote about a study that showed that coral cover had declined on the Great Barrier Reef by 50.7% since 1985. At the start of the study coral cover was at 28%, but pristine coral reefs can have over 70% coral cover. This suggests that impacts on the Great Barrier Reef predate the time monitoring started by many years.

A coral outcrop on the Great Barrier Reef (photo Wikipedia)
John Pandolfi at the University of Queensland has been trying to establish the past state of the Great Barrier Reef in numerous ways. One way is to take sediment cores from coral reef and compare the historical diversity and abundance of corals on the reef to the modern community composition. A new study lead by Pandolfi has reconstructed the past coral communities on reefs around Pelorus Island in the Palm Island group. They took cores containing coral remains dating back as far as the mid-third century.

They found that there was a pronounced transition in the coral species on the islands reefs between 1920 and 1955. The transition strongly correlated with a 5 to 10 fold increase in the amount of sediment found in the cores beginning in 1870, but showing several large peaks between the 1920s and 1970s. White settlement and land clearing of the area began in about 1870, the same time that high sediment loads were found in the cores. Prior to that, there was remarkable stability in the coral communities and the amount of sediment reaching the reef.

The new study highlights that reefs in 1985 that were thought to be relatively pristine probably had not been for 50 or 60 years. Therefore attempts to conserve reefs as they were in 1985 is inadequate because these reefs are likely to be already severely impacted by human activities. If we a serious about returning coral reefs to a pristine state, we should be restoring them to what they were like prior to white settlement, not what they were like now after a century of mistreatment.


Roff, G., Clark, T., Reymond, C., Zhao, J., Feng, Y., McCook, L., Done, T., & Pandolfi, J. (2012). Palaeoecological evidence of a historical collapse of corals at Pelorus Island, inshore Great Barrier Reef, following European settlement Proceedings of the Royal Society B: Biological Sciences, 280 (1750), 20122100-20122100 DOI: 10.1098/rspb.2012.2100

Monday, December 3, 2012

Conservation priorities on the Great Barrier Reef

ResearchBlogging.orgA recently published paper on the decline of coral cover on the Great Barrier Reef serves to illustrate an important point; even without climate change we are doing a great deal of damage to some ecosystems. The study by De'ath et al. and published in the Proceedings of the National Academy of Science, finds that coral cover has declined by 50.7% since 1985. They partitioned the losses into 48% tropical cyclones, 42% predation by crown of thorns starfish and 10% to coral bleaching.

The crown of thorns starfish, Acanthaster planci (image Wikipedia)
The declines were not uniform across the reef. Most of the declines were in the southern part of the reef and near to shore, where more people live. Partly this may be due to more frequent storms in the southern part of the reef, but storm frequency has declined in the last 100 years or so. Mostly it's probably because outbreaks of crown of thorns starfish are linked to human activities, such as agriculture and fishing. And these same human activities leave coral less resilient to other impacts and make it more difficult for them to recover from disturbances.

Pollution, sedimentation and overfishing can all change the dynamics of coral reef communities by impairing the ability of corals to recover from other disturbances. Human activities can also increase the mortality of adult coral and reduce the number larvae that survive to become coral. Shifts from coral-dominated communities to seaweed-dominated communities due to these impacts are well documented.

Overfishing, particularly of herbivorous fish, has been strongly linked to shifts in community composition. In direct competition corals lose out to seaweed, which overgrows coral and in some cases uses toxins to kill the coral. Herbivorous fish though, eat the seaweed tipping the balance in favour of the corals. So important are herbivorous fish to corals that some have formed mutualistic relationships with fish, which they signal for help when seaweeds encroach on their space

Overfishing has also been suggested to reduce predation on larvae of the crown of thorns starfish, allowing it to reach plague proportions when fish would normally control their numbers. A second hypothesis is that nutrient inputs from farms and cities provides the crown of thorns larvae with large amounts of food, increasing their survival. Neither hypothesis is well supported, but there is growing evidence that both mechanisms are playing a role in crown of thorns outbreaks. 

For corals, like seagrasses, access to light is critical for their survival. Coral derive as much as 90% of their energy from symbiotic algae growing in their tissues. Nutrient inputs and sedimentation reduce the light available to their algal symbionts, which reduces the energy available to them. This can decrease the resilience of corals to other stressors, such as natural disturbance events. The main sources of sedimentation on the Great Barrier Reef are from human activities, such as agricultural run-off and dredging.  

De'ath et al. conclude that there is an urgent need to control crown of thorns outbreaks, especially through improvements to water quality. In the absence of disturbances, the data showed that reefs were able to increase in cover by nearly 3% per year. This is likely to be higher when the full impact of human activities are taken into account. Moreover, their data only go back to 1985, but human impacts on the reef date back to about 100 years before that. The true decline of coral cover on the Great Barrier Reef is, therefore, likely to be far greater than that measured in their study.

De'ath et al. also highlight the impending effects of climate change and ocean acidification. Many people are focused on human emissions of carbon dioxide as the sole problem we need to fix to save the reef. But, it's clear that even without the threats of climate change and ocean acidification the Great Barrier Reef is in great deal of trouble. In order to conserve the reef we need to address the source of these issues now.

De'ath, G., Fabricius, K., Sweatman, H., & Puotinen, M. (2012). The 27-year decline of coral cover on the Great Barrier Reef and its causes Proceedings of the National Academy of Sciences, 109 (44), 17995-17999 DOI: 10.1073/pnas.1208909109

Friday, November 30, 2012

Everyone loves bacon


Researchers at the VENUS Observatory put a pig carcass in 300 meters of water and watched to see what came to eat it. Mostly amphipod crustaceans, it would seem.


Results vary only slightly when the carcass is not in a cage. The wounds that appear early in the video are caused by sharks, I'm pretty sure.

Wednesday, November 21, 2012

All the better to carry you with

Over at Why Evolution is True, Mathew Cobb makes fun of adaptationist "just-so stories" about a beetle that evolved handles so that it could be more conveniently carried by termites. It's definitely worth a read.

Tuesday, November 13, 2012

More on the iron fertilisation "experiment"

A little while ago I wrote a post on the actions of Russ George, a businessman who has been trying to sell ocean iron fertilisation as a viable method for reducing carbon dioxide in the atmosphere. His arguments about the success of such schemes are way out in front of the science required to support them. He released 100 tons of iron sulfate into the north-eastern Pacific in what he calls an experiment, but what nearly all other pundits have been calling an irresponsible and reckless action.

His supporters have rallied behind him though and have had a presence in nearly every comment thread of prominent science news sites that have covered the issue. So, I thought I would take some time to put my views on the potential dangers of large-scale fertilisation of the ocean with iron.

Phytoplankton is not only reliant on iron to survive. There are several other important nutrients that limit phytoplankton numbers in areas where iron is abundant, such as phosphorous. Large blooms of phytoplankton that are produced by the addition of iron could rapidly deplete other limiting nutrients. Once the bloom has consumed the added iron and collapsed the population may not recover back to what it was prior to the bloom because it is limited by more than iron. 

When the bloom dies and decomposes, it could reduce a molecule that is highly important to a great many marine organisms, oxygen. Areas of the ocean that become so low in oxygen that they are no longer able to support life and know as dead zones. The appearance and expansion of dead zones is often caused in areas where human inputs of important nutrients, such as phosphorus and nitrogen, increases the abundance of phytoplankton. The bacteria that consume the dead phytoplankton also consume the dissolved oxygen, depleting it to levels dangerously low for many other organisms.

The rain of dead phytoplankton could also have serious effects on the seafloor community beneath. Indeed, one of my very first posts on this blog was about how the energy balance in the deep sea was critical to maintaining a high diversity of species in an energy poor, seemingly homogenous environment. A huge input of nutrients from the detritus of a plankton bloom that reaches the seafloor is likely to upset the ecology of the communities found there.

While I think that these are all legitimate concerns, it is important to note that, to my knowledge, none of these effects have been observed in iron fertilisation experiments. Oxygen depletion is a known and well documented effect of phytoplankton blooms. But, iron fertlisation on the scale of Russ George's venture may not be large enough or persist for long enough to have this effect. And natural phytoplankton blooms on the scale of the one observed in the area that George dumped his iron are not unknown.

In fact, some researchers are claiming that the observed phytoplankton bloom was already underway before George released the iron sulfate. Many reports I have read say that that the iron fertilisation occurred in July at the time the plankton bloom was getting started. But, it seems the ship which released the iron sulfate didn't leave port until the 8th of August and probably couldn't have started fertilising until a week later. Natural blooms are known to occur regularly in the area, particularly during summer when offshore currents carry iron-rich water hundreds of kilometers out to sea. Unfortunately, the design of the experiment is so poor that it's hard to tell whether the iron sparked the bloom or how much it contributed to it.



.

Tuesday, November 6, 2012

Rare whale washes up in New Zealand

Ed Yong is a great science writer with a blog on Discover Magazine's website. He has an interesting post on a whale so rare that has never been seen alive. In 2010 two individuals washed up on a beach in the north of New Zealand. They were misidentified as the related Gray's beaked whale, Mesoplodon grayi, until genetic analysis of samples taken from the dead whales showed they were in fact the elusive spade-toothed whale, M. traversii. The subject of Ed's post is a recently published paper the reports on the genetic analysis and provides the first morphological description of a complete animal.

Update
The Science Now site has a story on these whales too. It makes the claim that the beached whales were found alive. I don't know which version is correct. 

Thursday, October 25, 2012

Polar sea ice sets two records

On August 26th this year, Arctic sea ice extent fell to its lowest ever since records began in 1979. Sea ice continued to melt into September reaching a minimum of 3.41 million square kilometers on the 16th of September. Which is 790 thousand square kilometers less than the previous record minimum (2007) and roughly half the average minimum from 1979 to 2000 (7.04 million square kilometers).

At the other end of the planet Antarctic sea ice was setting a new winter maximum of 19.44 million square kilometers on the 26th of September. Which is 740 thousand square kilometers more than the 1979 to 2000 average maximum (18.7 million square kilometers). So the gain in the south is far lower than the loss in the north. And the gain in the Antarctic is no cause for celebration.

Antarctic sea ice extent on the 26th of September when the record maximum was set (image NSIDC)
The gain in sea ice in the Antarctic is likely to be due to two effects. The hole in the ozone layer has a cooling effect on the continent because ozone is a greenhouse gas. Warming in the Southern Ocean, which is well documented, has also lead to an increase in the strength of westerly winds. This has pushed more sea ice away from shore expanding its extent in most places except the Antarctic peninsula where it has decreased.

Wednesday, October 17, 2012

Playing Russian Roulette with Gaia

The addition of iron to the oceans has been suggested as a mechanism to reduce the amount of carbon dioxide in the atmosphere. In several parts of the ocean, plankton abundance in much lower than expected given the availability of nutrients and sunlight. But, these areas are also low in iron, leading many people to suggest that it's the availability of iron that limits plankton numbers. A while ago I wrote about an experiment in the Southern Ocean that investigated this hypothesis. 

Permission to conduct these experiments was hard to get because the UN has agreed to a moratorium on iron fertilisation until more is known about the effects on other marine life. But, in contravention of the moratorium a rogue businessman has conducted an iron fertilisation 'experiment' in the northeastern Pacific, off the coast of Canada. Russ George has been trying to sell his iron fertilisation scheme to the world as part of the lucrative market for carbon credits.

He convinced the Haida Nation to provide one million dollars funding, apparently by telling them that the dumping of iron would increase salmon numbers in the area. With that money he dumped 100 tons of iron sulfate into the ocean 200 nautical miles west of the islands of Haida Gwaii in July this year. The plankton bloom this created reached 10,000 square kilometers in size. In comparison, the experiment in the Southern Ocean dumped just seven tons of iron sulfate and the bloom peaked at 800 square kilometers.

In conducting this 'experiment' Russ George may have broken international and Canadian laws. It violates the UN moratorium on iron fertilisation and he may have committed fraud in obtaining the funds from the Haida Nation. In any case, there is no evidence that plankton blooms will improve salmon number and only limited evidence that iron fertilisation is an effective mechanism for reducing carbon dioxide. And we know next to nothing about the potential negative impacts of such large blooms.

For more information, including Russ George's history in trying to sell iron fertilisation as a carbon credit scheme, try The Guardian and Deepsea News.

Monday, October 15, 2012

It's Yoda, but not as you know him

ResearchBlogging.orgA new species of acorn worm has been named after Jedi Master Yoda, the best character in the Star Wars trilogy*. Acorn worms are not true worms. They are more closely related to echinoderms (starfish, sea urchins, sea cucumbers, etc.) than they are to worms. They were once placed as a subphylum of the chordata (i.e. our own phylum), but are now placed within their own phylum, the hemichordata.

Yoda purpurata, the newly described species of acorn worm
The paper described three new species of deep-sea acorn worms in the family Torquaratoridae. Two of which, Allapasus isidis and Tergivelum cinnabarinum, were from previously known genera. But, Yoda purpurata is a new genus and species. It's named after Yoda because the appendages at the head end of the animal are reminiscent of Yoda's ears. All three species were found at about 2.5 kilometers deep on the mid-Atlantic ridge.

*To count as a true Star Wars film, it can't just carry the name. You also have to be able to sit through it without wanting to punch George Lucas. This caveat leaves just three films that can be considered part of the Star Wars canon. And these three films are the originals, not the remakes. 
Priede, I G, Osborn, K J, Gebruk, A V, Jones, D, Shale, D, Rogacheva, A, & Holland, N D (2012). Observations on torquaratorid acorn worms (Hemichordata, Enteropneusta) from the North Atlantic with descriptions of a new genus and three new species Invertebrate Biology, 131 (3), 244-257 DOI: 10.1111/j.1744-7410.2012.00266.x

Sunday, October 14, 2012

Human-induced evolution

ResearchBlogging.orgHuman activities have influenced that evolution of many species and not just through artificial selection. Our impacts on ecosystems, use of drugs and pesticides and our harvesting of wild populations is all having an effect on the rate and direction of evolution in many organisms. In fact, many of the frequently cited examples of 'evolution in action' are also examples of human-induced evolution, such as mosquito resistance to DDT and drug resistant bacteria.

The detailed studies on the peppered moth, Biston betularia, provide a classic illustration of evolution in action. The peppered moth is nocturnal, resting during the day on light coloured trees, where it is reasonably well camouflaged. However, during the industrial revolution, trees in forests between London and Manchester became covered in soot and dark coloured morphs increased in frequency from 0.01% of the population to 98% due to increased bird predation on the less camouflaged light coloured morph.

The light (top) and dark (bottom) coloured morphs of the peppered moth, Biston betularia (images Wikipedia)
Although we don't often think of ourselves as predators, hunting and fishing are essentially the same thing. Like predation on peppered moths by birds, they can produce evolutionary change in the target populations. For instance, trophy hunting of bighorn sheep, Ovis canadensis, results in sheep with smaller horns and lighter body weight over time. A couple of recent studies show that behavioural traits are selected too.

Bighorn sheep in Montana (image Wikipedia)
Using GPS devices, Ciuti et al. tracked 122 (77 females and 45 males) elk, Cervus elaphas, to monitor their movements over the course of a year. The males that were the most likely to fall victim to hunters were those that moved more often, traveled the furthest and made greater use of open areas. The pattern was similar, but less pronounced, in females. Older females tended to move less and use of open areas less than younger females, suggesting that they may learn to avoid hunters. They could not assess learning with age in males as all the tracked males were of the same age.

A male elk (image Wikipedia)
Ciuti et al. suggest that the bolder behaviour of the elk that were harvested may provide them with protection from other predators, like wolves and bears. Moving long distances and using open areas may make it easier for elk to avoid natural predators, but it favours harvesting by humans with high-powered rifles. It's a neat hypothesis and they say that they intend to test it in future experiments.

A second study in rainbow trout, Oncorhynchus mykiss, looked at growth rate, a trait closely correlated with activity rate. To fuel a fast growth rate, it's thought that fish must spend more time actively searching for food, which is supported in the literature. Biro stocked four fishless lakes in Canada with trout that were slow-growing, intermediately-growing and fast-growing. By stocking the lakes, Biro knew the numbers of fish present in each lake and in each experimental group. He then randomly sampled the four lakes using a sampling method that wasn't size-selective.

Rainbow trout (image US Fisheries and Wildlife Service)
There was substantial variation in the proportion of each of the experimental groups that was caught in each lake. However, faster growing trout were consistently more likely to be caught than intermediate or slow-growing trout. Overall, fast-growing trout were nearly twice as likely to be caught than the two groups with slower growth rates. Importantly, size did not matter; small, slow-growing fish were still less likely to be caught than small, fast-growing fish.

Biro's study has the issue that it did not directly assess behaviour, but relied on growth rate as a proxy measure. However, it is consistent with other studies that show fish personalities influence the probability that they are caught by different collection techniques. Bluegill sunfish, for instance, are more likely to be caught in the wild by angling when they're less active. Intriguingly, there is also an interaction between habitat and capture method as less active bluegill sunfish are also less likely to be caught by angling in the open areas of artificial ponds.  

I'm troubled by the correlation between growth rate and supposed personality traits. It suggests that what is being measured as personality might actually be a by-product of physiology and not a separate trait. But, other studies I looked at showed that in some situations less active fish grow faster than more active fish, which suggests that they are independent traits.

In any case, the Cuiti et al. and Biro studies show quite nicely that humans are probably influencing the direction of evolution in the populations that we harvest by hunting and fishing. Their work adds to a growing body of research that humans are influencing the evolution of many species. Indeed, Stephen Palumbi has argued that humans are currently the World's greatest evolutionary force.

Biro PA (2012). Are most samples of animals systematically biased? Consistent individual trait differences bias samples despite random sampling. Oecologia PMID: 22885993  

Ciuti, S, Muhly, T B, Paton, D G, McDevitt, A D, Musiani, M, & Boyce, M S (2012). Human selection of elk behavioural traits in a landscape of fear Proceedings of the Royal Society: B, 279 (1746), 4407-4416 DOI: 10.1098/rspb.2012.1483  

Palumbi, S R (2001). Humans as the World's greatest evolutionary force Science, 293 (5536), 1786-1790 DOI: 10.1126/science.293.5536.1786  

Wilson, A D M, Binder, T R, McGrath, K P, Cooke, S J, & Godin, J J (2011). Capture technique and fish personality: angling targets timid bluegill sunfish, Lepomis macrochirus Canadian Journal of Fisheries and Aquatic Sciences, 68 (5), 749-757 DOI: 10.1139/f2011-019

Thursday, October 11, 2012

Tuesday, October 2, 2012

Thursday, September 27, 2012

ENCODE continues to fester

Many expert bloggers are still annoyed with the science communication failure that was the ENCODE project's coverage in the popular science press. Larry Moran has another post about it regarding the profile of lead coordinator of ENCODE, Ewan Birney. And I have just run across a great collection of links to stories that more critically examine the ENCODE claims on Ryan Gregory's blog.

Wednesday, September 26, 2012

Vampire squid

Ed Yong is a science writer who's work I often enjoy reading. He has an interesting piece about vampire squid, Vampyroteuthis infernalis, that he has written for his blog "Not Exactly Rocket Science". Vampire squid are not actually squid, although they are related to squid and octopus. They are classified in their own order of cephalopods, the Vampyromorphida, in which they are the only known extant species.

Sunday, September 23, 2012

A little fish makes big sand sculptures

In the ocean off Japan an industrious pufferfish has been crafting elaborate sand sculptures. And they're spectacular!


The sculptures created by the pufferfish (photos Yoji Ookata)
The sculptures appear to be sexually selected. Only the males make them and females prefer to mate with males who make sculptures with more ridges. During mating the eggs are laid into the center of the sculpture where they may receive some protection from the currents preventing them from being dispersed far and wide.

A male pufferfish creating a sculpture (photo Yoji Ookata)
These pufferfish (I can't work out the species) are not the only fish to make sand sculptures. Many species of African cichlids make structures, known as bowers (after the bowerbird), that function in sexual selection too. But, for many species the bowers, although they appear nest-like, do not hold the eggs. The female broods them in her mouth until they hatch and often longer.

A male cichlid patrols his volcano shaped sandcastle in Lake Malawi (photo Justin Marshall)

Tuesday, September 18, 2012

Unflappable albatrosses

ResearchBlogging.orgWandering albatrosses, Diomedea exulans, are among the largest flying birds in the world and are renowned for soaring flights of thousands of kilometers to feed. Several adaptations allow their flight to be extremely energy-efficient. For instance, their extremely long wings allow them to glide remarkably long distances and a modified tendon allows them to hold their wings open without the use of their muscles.

A wandering albatross showing its fight position (photo Wikipedia)
For a long time, it's been clear that albatrosses are using wind energy to power their flight. Indeed, Lord Rayleigh proposed that albatrosses were using wind shear to soar in 1883. Although other mechanisms have been proposed, dynamic soaring in wind shear has since been cited as the principle mechanism that they are able to gain energy from the wind. 

At the ocean surface the wind travels more slowly because of friction, but as you move away from the surface wind speeds get higher. Albatrosses can gain airspeed by rising away from the sea into the faster winds and then dropping back into the slower winds at the surface. They first turn into the wind and rise followed by a turn with the wind as they descend, gaining energy in both directions while losing some to drag.

The dynamic soaring cycle of an albatross. It starts with a turn into the wind, then a climb in altitude, then a turn with the wind and a descent back to the sea surface. The length of yellow arrows to the left of the figure indicate the strength of the wind at different altitudes (Image taken from Sachs 2005).
Penncuick argued that albatrosses couldn't get enough energy from the wind-gradient and must be deriving a large amount of energy from moving in and out of the pockets of almost still air in the lee of wave crests, which he termed 'gust soaring'. Other authors have suggested that they slope-soar off the windward side of wave crests. But, the debate over how albatrosses are gaining enough energy for their long distance flights has played out in the theoretical literature, sometimes accompanied by anecdotal observations of flight behaviour.

The gust soaring cycle of an albatross. As the albatross moves through the 'separated boundary layer' (blue line) from the leeward side of a wave crest it gets a kick of energy from the wind allowing it to gain altitude and potential energy to power its soaring flight (Image taken from Richardson 2011)
With their paper published recently in PLOS One, Sachs et al. have added some empirical data to help resolve the issue. They attached small GPS devices to the backs of 16 albatrosses, which measured the position and altitude of each individual once every second and the velocity 10 times a second. This allowed them to look at the small scale of the flight cycle and draw inferences about the physics of the manoeuver.

A plot of a recorded dynamic soaring cycle. The numbers indicate each stages from the ascent [1], to the turn at peak altitude [2], to the descent [3] and the turn to restart the cycle [4] (Image taken from Sachs et al. 2012).
They used the data to calculate the total energy over the entire dynamic soaring cycle by summing the potential and kinetic energy. Contrary to the expectations of gust soaring and slope soaring, the maximum energy in the cycle was reached on the descent. And the energy accumulation was gradual, without any large spikes that would result from a big kick in energy close to the surface.
A two-dimensional plot of the soaring cycle showing the point at which maximum and minimum energy are reached. The track shown here is the same as the one above (Image taken from Sachs et al. 2012).
Sachs et al. also calculated the energy gain that the albatrosses could achieve throughout the cycle. The maximum energy in the cycle was ~360% of the minimum energy and provided enough surplus to overcome drag forces. Indeed, the energy gain was so large that it far exceeded what the albatrosses could achieve by flapping their wings.

The efficiency that the albatrosses converted the wind into usable energy for flight allowed them to achieve ground speeds higher than the wind speed. On average the 16 birds that they followed traveled at ~60 kilometers per hour, but one bird was clocked traveling at an average of 76 kilometers per hour. If that's not amazing enough, an earlier study that Sachs et al. cite, clocked a grey-headed albatross (Thalassarche chrysostoma) traveling at an average ground speed of 110 kilometers per hour for 9 hours in high winds! 

My only concern about the paper, which isn't a very big one, is that all of the energy calculations are based on a single dynamic soaring cycle (the one in the two figures above). The authors do present three others in their supplementary material, which all look essentially the same. But, I wonder why they don't use them for the calculations. And they tracked 16 birds for at least 176 kilometers, did they really only get four cycles which occur in the space of ~150 meters? They don't say.

References:

Sachs G, Traugott J, Nesterova AP, Dell'omo G, K├╝mmeth F, Heidrich W, Vyssotski AL, & Bonadonna F (2012). Flying at no mechanical energy cost: disclosing the secret of wandering albatrosses. PloS one, 7 (9) PMID: 22957014  

Richardson PL (2011). How do albatrosses fly around the world without flapping their wings? Progress in Oceanography, 88 (1 - 4), 46-58 DOI: 10.1016/j.pocean.2010.08.001  

Pennycuick CJ (2002). Gust soaring as a basis for the flight of petrels and albatrosses (Procellariiformes) Avian Science, 2 (1), 1-12

Friday, September 14, 2012

Top five on Friday

On his website "Why Evolution is True", Jerry Coyne has posted pictures of a pretty spectacular looking snail, Blaesospira echinus. So, I thought that today I would post my top five favourite mollusks. There were two mollusks in last week's list of my top five favourite marine animals. To give the other amazing species in phylum Mollusca a chance, I'll leave them out.


It was hard to keep this one out of last week's list. Like Glaucus atlanticus (who was number 1 last week), it steals cells from the organisms it eats and uses them for its own ends. In Elysia's case, it steals chloroplasts from the seaweed Vaucheria litorea. It's able to keep these alive for up to 9 or 10 months, which indicates that it has acquired genes for this task, probably by horizontal gene transfer.

The beautiful and fascinating Elysia chlorotica (Photo Wikipedia)
2. Giant squid, Archieteuthis dux

It's the second biggest invertebrate, after the colossal squid. And like the colossal squid, it has the biggest eyes of any animal. Eight species of giant squid have been named, but it's almost certain that there are fewer species and there may be only one, A. dux

The first live giant squid ever to be photographed in its natural habitat, the deep sea (photo Kubodera and Mori)
3. Dorytethis opalescens (formerly Loligo opalescens)

Like most cephalopod mollusks, D. opalescens is an amazing colour changer. But, unlike many other cephalopods it uses two different cell types to change colour (see here for an amazing bit of science communication explaining it all). It lives close to the surface and one of the reasons for its colour changing skill is thought to be that it avoids predators by countershading the light-dark patterns of wave lensing.

Doryteuthis opalescens (photo Wikipedia)
Wave lensing pattern on a sandy seafloor (Photo National Geographic)
4. Giant clam, Tridacna gigas

It's big, it's beautiful. Like corals, all of its colouration comes from symbiotic algae living inside its body.
The giant clam, Tridacna gigas (photo Wikipedia)


A bubble rafting snail that lives in the open ocean. The bubble raft is likely to have evolved from an ancestral egg coat.

The bubble rafting snail Janthina janthina (photo Denis Riek)


Sunday, September 9, 2012

ENCODE: Great science, poor communication

Last week the ENCODE project published 30 papers in three different journals, Nature, Genome Research and Genome Biology. In the summary paper, they claimed that they had found a function for 80% of the genes in the genome. However, in order to make this claim it seems they have had to redefine 'function' to have a meaning that most people wouldn't accept as meaningful.

We know that only about 1 to 1.5% is used to make proteins and the ENCODE project's findings didn't change that figure. A lot of DNA is transcribed into RNA and some of that RNA has a regulatory role, that is it regulates gene function by turning them on and off. ENCODE found that adding the amount regulatory DNA to protein ecoding DNA and you get to a figure of 9%. This is higher than was expected and is an exciting result.

Getting from 9% to 20% was all estimation. The ENCODE project looked at 147 different human cell types, but there are at least 210 and possibly many more distinct human cell types. Based on their incomplete coverage of cell types, ENCODE researchers believe that there is at least another 11% of the genome that is regulatory. But, this remains to be demonstrated.

The final 60% is part DNA that's meant to help package the DNA helix, part that has sites that proteins bind to and part DNA that's transcribed into essentially meaningless RNA (I might have missed some things here). The argument for including this 60% in the estimate of how much of the genome is 'functional' seems to boil down to the idea that is does something and evolution wouldn't let it do something if it wasn't useful. Other than this, there seems little merit in including this 60% as functional.

If my suspicions about the argument are correct, it's adaptationist nonsense. The amount of non-coding DNA, also called 'junk DNA', is variable among species. For instance, the genome of the pufferfish, Takifugu rubripes, is ~365 million base pairs, while genome of the lungfish, Protopterus aethiopicus, is orders of magnitude larger at ~133 billion base pairs. Much of the lungfish genome would be functional under the ENCODE definition, but if it's important, how come the pufferfish can get away with 0.3% of the base pairs*?

The media coverage of the ENCODE publications has focused on the 80% figure, without much discussion of what is meant by 'functional'. This is unfortunate because the definition of 'functional' is critical for evaluating the findings. In my opinion, 80% is a fudge that can only be reached by a weaseling use of language. It's clear to me, from the variation in genome size among species and that we can remove large sections of non-coding DNA with no observable effect, that most of our genome has no important function. The ENCODE project has not shown it to be otherwise.

Other coverage that I thought was good:

T. Ryan Gregory - A slightly different response to today's ENCODE hype

Michael Eisen - A neutral theory of molecular function

Sean Eddy - ENCODE says what?

Brendan Maher - Fighting about ENCODE and junk

John Farell - Reports of junk DNA's demise have been greatly exaggerated


* This is Ryan Gregory's "Onion Test".