SeaSponge SmartPants

barrel_sponge_ngDr Bernie Degnan and his team have been sequencing the genome of the simple sea sponge here at the University of Queensland and have made some pretty astonishing findings in regards to humans and stem cells:


CARLY LAIRD: For anyone who thought the cartoon character, SpongeBob SquarePants, was a bit far fetched, think again. Bernie Degnan is a professor of marine biology at the University of Queensland. He says although sea sponges certainly can’t talk and don’t have their own apartments under the sea, they are indeed clever marine animals.

BERNIE DEGNAN: Sponges just by their natural biology do things that we only wish we can engineer in a biomedical laboratory.

CARLY LAIRD: Professor Degnan and his colleagues have just completed the first genome sequence of the squelchy organisms. They found that sponges are very similar to our own gene make-up.

BERNIE DEGNAN: Turns out this sponge is the first marine organism in Australian waters to have its genome fully sequenced, assembled and annotated which means it’s been analysed to completion.

By having all that genomic information we’ve been able to start to tease apart the ways sponges actually work and funny, try and relate that back to our own condition. So even though sponges and humans have kind of split off from each over at least 600 million years ago, we can find a whole range of molecular characteristics, genes that are shared between sponges and humans.

Blogging from the Galapagos Islands

John Bruno mentioned this in passing at the bottom of his last post (Climate Literacy), but I thought this deserved a post of it’s own. Check out JB’s blog over at his lab website, bought to you live from the Galapagos Islands – shark surveys, coral monitoring, marine iguanas, seals on the rocky intertidal shores… (and who says the life of a marine biologist isn’t at least slightly glamorous?)

“I’ll be working with a team of scientists on San Cristobal island in the Galapagos for a week.  I am blogging about the trip, mainly to share the things I see and do with family and friends back home.  Especially my nature-crazy daughters, my nephew Joey and my friend Zaim (who is already charting a path to being a marine biologist)!

You can ask questions, make comments, complain about the lousy photos and poor grammar, etc. just by clicking “Add a Comment”

Hope you enjoy it – JB”

7000-year-old corals of Moreton Bay tell their story

Picture 632

The 7000-year-old coral communities of Moreton Bay are telling a curious tale, expanding when sea-levels rise or water quality improves, then declining when current circulation becomes more restricted.

Intriguing new insights into the behaviour of corals and fish under changing climatic conditions will be presented by leading marine researchers at a public forum in Brisbane this coming Friday.

Professor John Pandolfi from the University of Queensland and ARC Centre of Excellence for Coral Reef Studies and his team have been dating the corals of Moreton Bay and finding they have undergone surges of growth, probably triggered by subtle changes in sea level and water conditions.

“We’ve found coral communities up to 7000 years old showing these curious growth episodes – the last one started about 400 years ago. When coral reef growth slows or stops in the Bay, it appears to correspond with a decline in the current circulation and an increase in turbidity.”

The team has also found clear evidence of changes in the types of corals in the Bay from the delicate staghorns to more massive forms, coinciding with European settlement and possibly resulting from declining water quality as nearby catchments were altered.

These and many other aspects of the future of Australia’s corals will be explored at a scientific symposium and public forum in Brisbane this week.

The scientific symposium “Securing Coral Reef Futures” will take place on August 6 and 7 at the Brisbane Customs House.

It will be followed by the Public Forum on the future of the coral reefs worldwide at 6.00pm, Friday 7 August at the Brisbane Convention and Exhibition Centre. Media are welcome to attend both.

This and more from the scientific symposium “Securing Coral Reef Futures” here in Brisbane on the 6th and 7th August, including seminars by Dr Morgan Pratchett (adaptability of fish to ocean acidification and coral loss),Professor Garry Ryss (GBR Marine parks and fisheries stocks), and Professor Ove Hoegh-Guldberg (coral reefs, mangrove forests and global food security). Anyone is welcome to join the Public Forum on the future of the coral reefs worldwide at 6.00pm, Friday 7 August at the Brisbane Convention and Exhibition Centre (click here for more details).


Mixing it up, jellyfish style

With the advent of overfishing of the worlds oceans and climate change, jellyfish are slowly beginning to dominate oceanic ‘deadzones’ (see the ‘never-ending jellyfish joyride‘ for more details). Now, researchers are coming around to the idea that in such high numbers, jellyfish might just be able to stir up the oceans in a similar way to the tides and winds, according to a recent paper published in Nature. Sounds  crazy? Take a look at this video footage of the researchers squirting fluorescent dye into the water column infront of the Mastigias jellyfish. As the jellyfish swims through the watercolumn, the dyed water travels along with the jellyfish rather than being displaced – a mechanism apparently first described by Charles Darwin’s grandson that is enhanced by the viscosity of seawater. Read more at Live Science and over at Wired Magazine, and watch the video footage below:

“As a body moves in a fluid, a high-pressure field is created in front of the body, and a low-pressure field behind. Because fluid moves from high to low pressure, the fluid that’s adjacent to the rear of the body moves along with it,” said Katija. “You get a permanent displacement of the water.”

Katija and CalTech bioengineer John Dabiri have provided the first direct observation of this phenomenon. Using fluorescent dyes and underwater video cameras, they’ve made visible the invisible, producing videos of swimming jellyfish trailed by the water they came from.

If swimming generates tide-scale forces, then “it has an impact on global climate. This is a rather novel twist to the whole climate story,” said William Dewar, a Florida State University oceanographer. “How one would extend existing models to include a biosphere mixing input is not clear, largely because no-one has spent much time thinking about it.”


Short-term declines in global temperature predicted by GCMs

One of the most common climate change skeptic arguments against AGW is that short-term declines in globally averaged temperature completely refute arguments about the occurrence and causes of global warming.  A new paper published in Geophysical Research Letters (Easterling and Wehner  2009)  argues that short term periods of no-trend or even cooling (nested within longer term warming) are in fact predicted by Global Climate Models.

Abstract: Numerous websites, blogs and articles in the media have claimed that the climate is no longer warming, and is now cooling. Here we show that periods of no trend or even cooling of the globally averaged surface air temperature are found in the last 34 years of the observed record, and in climate model simulations of the 20th and 21st century forced with increasing greenhouse gases. We show that the climate over the 21st century can and likely will produce periods of a decade or two where the globally averaged surface air temperature shows no trend or even slight cooling in the presence of longer-term warming.

Globally averaged surface air temperature

Globally averaged surface air temperature

The reality of the climate system is that, due to natural climate variability, it is entirely possible to have a period as long as a decade or two of ‘‘cooling’’ superimposed on the longer-term warming trend due to anthropogenic greenhouse gas forcing. Climate scientists pay little attention to these short-term fluctuations as the short term ‘‘cooling trends’’ mentioned above are statistically insignificant and fitting trends to such short periods is not very meaningful in the context of long-term climate change. On the other hand segments of the general public do pay attention to these fluctuations.

It is easy to ‘‘cherry pick’’ a period to reinforce a point of view, but this notion begs the question, what would happen to the current concerns about climate change if we do have a sustained period where the climate appears to be cooling even when, in the end, the longer term trend is warming?

One realization of the globally averaged surface air temperature from the ECHAM5 coupled climate model forced with the SRES A2 greenhouse gas increase scenario (a business as usual scenario, that assumes little reduction in anthropogenic emissions resulting in large greenhouse gas concentrations by the end of the 21st century.

One realization of the globally averaged surface air temperature from the ECHAM5 coupled climate model forced with the SRES A2 greenhouse gas increase scenario (a business as usual scenario, that assumes little reduction in anthropogenic emissions resulting in large greenhouse gas concentrations by the end of the 21st century.

We highlight two periods in 2001–2010 and 2016–2031 [see bottom figure above]. Both of these periods show a small, statistically insignificant negative trend based on a simple least-squares trend line and there are other periods, such as the last seven years of this simulation, that show a similar lack of trend. This behavior occurs without any simulated volcanic eruptions or solar variability (natural forcing) that could result in a widespread cooling for some period of years and thus is presumed entirely due to natural internal variability. Climate models are often criticized for producing a more or less monotonic-type response to anthropogenic forcing in 21st century simulations. Part of this may be due to the lack of volcanic and solar forcing I the SRES scenarios of anthropogenic forcing increase for the 21st century and part could be due to the fact that largescale oscillatory climate features, such as the El Nino Southern Oscillation are not well simulated. However, even considering these criticisms, it is clear that the models can and do produce sustained multi-year periods of ‘‘cooling’’ embedded within the longer-term warming produced in the 21st century simulations.

Therefore, it is reasonable to expect that the natural variability of the real climate system can and likely will produce multi-year periods of sustained ‘‘cooling’’ or at least periods with no real trend even in the presence of long-term anthropogenic forced warming. Claims that global warming is not occurring that are derivedfrom a cooling observed over such short time periods ignore this natural variability and are misleading.


Easterling, D. R., and M. F. Wehner (2009), Is the climate warming or cooling?, Geophys. Res. Lett., 36, L08706, doi:10.1029/2009GL037810

“National targets give virtually no chance of protecting coral reefs”

A study published in Nature Reports Climate Change on 11 June 2009 reports on the consequences of the emission targets being set by countries, including the US and Australia, in the lead-up to the international climate negotiations in Copenhagen in December.

Joeri Rogelj and colleagues conclude, “National targets give virtually no chance of constraining warming to 2 °C and no chance of protecting coral reefs.”


Citing recent publications of Jacob Silverman and colleagues, they note in relation to ocean acidification and coral reefs:

Acid test
While we have focused on global mean temperature increase here, it is increasingly clear that independent of its effect on temperature, growing CO2 concentrations in the atmosphere will also threaten the world’s oceans owing to acidification. The latest research indicates substantial risk to calcifying organisms at atmospheric CO2 concentrations of 450 ppm, with all coral reefs halting their growth and beginning to dissolve at concentrations of 550 ppm. The best Halfway to Copenhagen emissions pathway would result in CO2 concentrations above this level shortly after 2050.

Unless there is a major improvement in national commitments to reducing greenhouse gases, we see virtually no chance of staying below 2 or 1.5 °C. Coral reefs, in addition, seem to have certainly no chance if the work of Jacob Silverman and colleagues is correct.

Three Really, Really Bad Reasons to Want to Be a Marine Biologist

Because it’s a slow Friday and this was a great read – check out the following piece by the ‘piquant’ Dr Milton Love (who really does exist – check out the ‘Love Lab‘ at the University of California) on why being a marine biologist really ain’t that great:

Reason Number Three: “I want to be a marine biologist because I want to make big bucks.”

Okay, here’s the bottom line. By Federal law, marine biologists have to take a vow of poverty and chastity. Poverty, because you are not going to make squat-j-doodly in this job. Just how squat is the doodly we are talking about? Well, five years after finishing my PhD I was making slightly less than a beginning manager at McDonalds. Ooh, a 36 year old guy with 13 years of college and 5 years of post-doctoral experience making just about as much as a semi-literate 19 year old with pimples the size of Bolivia, who can speak perhaps 3 words at a time before the term “you know” enters the conversation.

Indeed. Read more in Part 1 and Part 2 of the series, direct from the Love Lab, or check out the lab’s blog written by their resident fish, the Cow Cod. In the day and age when scientists are assumed to be revered, it’s great to see someone in a high up position (with a great tattoo none-the-less)  not take themselves too seriously:

Milton Love is a Research Biologist at the Marine Science Institute, University of California, Santa Barbara. He has published simply oodles of scientific papers on the fishes of the Pacific Coast and has written several books on that topic. He thinks he knows more about these fishes than just about anyone. Whether this is true or merely the delusions of an individual with an ego the size Mount Kilamanjaro is still an open question.

Coral almost as genetically complex as humans’


CNN News, May 29th 2009:

Advances in the study of coral in the last few years has led a group of scientists to conclude that corals almost rival humans in their genetic complexity and their relationship to algae is key to their survival.

“We’ve known for some time the general functioning of corals and the problems they are facing from climate change,” said Virginia Weis, a professor of zoology at Oregon State University and an author of a report published in the journal Science.

“But until just recently, much less has been known about their fundamental biology, genome structure and internal communication. Only when we really understand how their physiology works will we know if they can adapt to climate changes, or ways that we might help.”

The study found that corals have sophisticated systems of biological communication that are being stressed by global change. Disruptions to these communication systems, particularly between coral and the algae that live within their bodies are the underlying cause of the coral bleaching and collapse of coral reef ecosystems around the world, say the report’s authors. (Read the full story at CNN News)

Why the existence of ‘heat tolerant’ corals does not mean that coral reefs will be able to resist climate change.

ofuA recent study published by Tom Oliver and Stephen Palumbi from Stanford University in the journal ‘Marine Ecology Progress Series‘ seems to suggest yet another miraculous and novel mechanism by which corals will ‘escape’ the pressures of global warming. In a nutshell, the researchers found that corals from ‘warm pools’ at Ofu Island (American Samoa) hosted ‘heat tolerant’ types of symbiotic algae, whereas corals from cooler lagoons hosted more ‘heat sensitive’ types of algae. When combined with regional data, Oliver & Palumbi suggest that in regions where annual maximum temperatures reached 29 – 31C, coral ‘avoided bleaching’ by hosting higher proportions of ‘heat tolerant’ algal symbionts.  Whilst these findings are interesting, the study is a long way from the suggestion in the paper and accompanying press release that coral reefs are ‘adapting’ and ‘may survive global warming’, and relies mainly on over interpreting their results. There are several issues at hand:

  1. Whilst these results highlight both the diversity of bleaching responses at a community level and the array of algal symbionts, the finding of heat tolerant corals has been shown throughout the Indo-Pacific and Great Barrier Reef on a number of previous occasions. The suggestion that this pattern results from a correlation in local scale heating based upon a limited sampling regime is far from proving causality
  2. The identification of a few remnant tough (‘heat resistant’) corals does not equate to these corals spreading out and maintaining coral reef ecosystems under rapid climate change.  Such coral types are rare, and are likely to have minimal impacts in sustaining reef populations under future climate change scenarios.  In making this argument, the authors are leaping across a myriad of issues that would need to be proven before we could pin our hopes on a few odd-ball corals for building and maintaining functional reef ecosystems into the future.
  3. Although corals have been shown to be able to ‘shuffle’ symbionts (change the proportion of ‘heat sensitive’ to ‘heat tolerant’ types), to date it has never been shown that corals can uptake ‘novel’ symbiont types from external sources. So, corals that are ‘heat sensitive’ can’t acquire ‘heat tolerant’ types from the environment. In light of rapid increases in sea surface temperatures under future climate scenarios, these ‘heat sensitive’ corals will undergo mass mortality, as they are unable to simply ‘adapt’ or switch to more resistant types.
  4. Any successful proliferation of these heat resistant genotypes will depend on a stabilised climate. Continual increases in temperatures means that these genotypes will have a harder time proliferating and stabilising, given that selection pressures will continue to intensify. This is akin to the bar in a high jump competition being placed ever higher.  As time goes on, fewer and fewer ecotypes from the population will be able to pass beyond the barrier.
  5. The authors seem to imply that functional reef ecosystems (and countless ecosystem services) will be ‘saved’, based upon a specific niche of ‘heat resistant’ corals.  The issue here is not the survival of corals species – many of whom will be resistant to extinction under global climate change (albeit as rare organisms) – but the destruction of functional coral reef ecosystems that millions of people depend on. Unfortunately, a few corals in a warm rock pool in Samoa will not save the day or the planet.
  6. These results do not address ocean acidification – the ‘other CO2’ issue along with temperature that threatens all calcifying organisms. To somehow imply that coral reefs are not facing problems from climate change because Oliver and Palumbi found a few tough coral genotypes in a rock pool, verges on the incredible.

These points aside, the study is an interesting one in terms of exploring heat stress in corals. My main issue is that Oliver & Palumbi have massively overextended their conclusions, which is particularly apparent in the associated press release.  Needless to say, these sorts of overblown claims are less than useful in the lead-up to the critically important COP15 negotiations in Copenhagen at the end of year.

Update, 25th May

And here is a classic example of why such media releases are less than useful, courtesy of the detractor Andrew Bolt:

World Ocean Conference (Part II): Scientists urge world leaders to respond cooperatively to Pacific Ocean threats

picture-387More than 400 leading scientists from nearly two-dozen countries have signed a consensus statement on the major threats facing the Pacific Ocean. The threats identified as the most serious and pervasive include overfishing, pollution, habitat destruction and climate change.

“This is first time the scientific community has come together in a single voice to express urgency over the environmental crisis facing the Pacific Ocean,” said Meg Caldwell, executive director of the Center for Ocean Solutions, who will present the statement on Wednesday, May 13 at 6:30 a.m. U.S. Eastern Time to government officials gathered at the World Ocean Conference in Manado, Indonesia. “The scientific community urges governments to respond now, cooperatively, to these threats before their impacts accelerate beyond our ability to respond.”

The consensus statement, entitled “Ecosystems and People of the Pacific Ocean: Threats and Opportunities for Action,” emerged from a scientific workshop in Honolulu hosted by the Center for Ocean Solutions in collaboration with the International Union for Conservation of Nature (IUCN) and Ocean Conservancy. The workshop was part of a broader effort by the three organizations to challenge countries throughout the Pacific region to improve the health of marine ecosystems by 2020.

In the consensus statement, the scientists warn that if left unchecked, the cumulative impacts of overfishing, pollution and habitat destruction—exacerbated by climate change—could have devastating consequences for coastal economies, food supplies, public health and political stability. These threats affect all members of the Pacific Ocean community, said Stephen Palumbi, director of Stanford University’s Hopkins Marine Station and one of the principal organizers of the consensus statement. “Remarkable similarity exists between the major problems experienced in poor and rich countries alike, in populous nations and on small islands,” said Palumbi, a professor of biology and a senior fellow at Stanford’s Woods Institute for the Environment.

In addition to listing the serious environmental challenges facing the Pacific Ocean, the consensus statement also highlighted a set of potential solutions now being applied and tested at various scales throughout the region. Examples include the establishment of marine protected areas and the creation of economic incentives for activities that promote rather than degrade ecosystem health. “These efforts have shown remarkable success at local scales in maintaining biological and human economic diversity, particularly when applied with adequate levels of regulation and enforcement in place,” said Caldwell, a senior lecturer at Stanford Law School and at the Woods Institute. “These solutions are indicators of hope within an ocean of distress.”

The consensus statement was largely based on a synthesis of more than 3,400 scientific papers on the threats and impacts to the Pacific prepared by the Center for Ocean Solutions. The Pacific Ocean Synthesis provides “a roadmap by which governments might chart a new course of policy for the Pacific region,” said Biliana Cicin-Sain, a professor of marine policy at the University of Delaware and coordinator of the Global Forum on Oceans, Coasts and Islands, a multi-stakeholder network committed to advancing ocean issues within international agreements.

“The impacts of misuse of our ocean resources on our economy, our environment and our community can no longer be ignored,” said Gov. Sinyo Harry Sarundajang of the Indonesian province of North Sulawesi, whose capital Manado is hosting the World Ocean Conference. The governor will convene the event with Caldwell on Wednesday. “We must work together at the regional and transboundary levels to find solutions for improved management of our common ocean.”

The scientific consensus statement and synthesis can be found at the Center for Ocean
Solutions website, Scientists interested in signing the consensus statement can send an email to

Based in Monterey, Calif., the Center for Ocean Solutions is a collaboration of three leading marine science and policy institutions—Stanford University (through its Woods Institute for the Environment and Hopkins Marine Station), the Monterey Bay Aquarium and the Monterey Bay Aquarium Research Institute (MBARI). The center focuses on finding practical, enduring solutions to major challenges facing the oceans.

(Photograph courtesy of Flickr)