Big Changes at Small Fish

Small Fish, Big Apple is dead. Long live Small Fish, Big Red!

The holiday is over for me, I have accepted a job in Perth, Western Australia and left the Big Apple.
Perth is one of the most geographically isolated cities in the world. It is more than 2000 km from the next city of >1 million people. It is geographically closer to East Timor, Singapore and Jakarta, Indonesia, than it is to Sydney, Melbourne, and Brisbane. According to Wikipedia, it is the antipode of Hamilton, Bermuda. Living here is going to be an interesting experience, I'm sure.

I'm working as an environmental scientist at a consultancy in Perth now. Some the clients of my new employer are in the oil and gas industry. Client sensitivity may affect what I can blog here from time to time. I guess I'll cross that bridge when I come to it. Apart from the name change and geographical relocation though, the only thing that will change around here is the frequency of posting. Posts can take quite a while to compose, so it remains to be seen how that will fit in with a full-time job. I hope it won't slow me down too much.

Anyway, thanks for reading. Here is a photo of my new city, taken on a beautiful spring afternoon.

Perth from Kings Park, Sep 2009.

Japanese Scientists Publish Results From "Scientific" Whaling Program

Japan has been roundly criticized by many commentators over the past two decades for it's “scientific” whaling program, with many saying the program is no more than commercial whale hunting in disguise. Japanese scientists have finally published data from this program in Popular Biology, and their findings aren’t good: whales are getting skinnier, and global warming might be at fault:

Japan's scientists claim their controversial whaling programme has produced a key finding. Measurements taken from more than 4,500 minke whales slaughtered since the late 1980s reveal the animals have lost significant amounts of blubber, and are getting thinner at a worrying speed. The team says its study offers the first evidence that global warming could be harming whales, because it restricts their food supplies.
It seems equally likely that chronic overfishing has also played some part in the decrease in food available to whales as well, but this is not mentioned in the article.

These aren't the first published results from the "scientific whaling" program, but these are the most high-profile findings so far. In 2005 Australian scientist Nicholas Gale analyzed 43 scientific papers produced by the program and concluded that only a handful were relevant and required the whales to have been killed. The others included descriptions of bizarre experiments to cross-fertilize whales with sheep and cows.

Climate Change "Skeptic" Admits He Was Wrong.

James Hrynyshyn at The Island of Doubt has a post up this morning which describes a rapid about-face performed by climate change denialist Steven Goddard of The Register.

We all make mistakes. And even the most humble among us can be a little self-righteous when it comes to our pet projects. But when was the last time you came across a self-righteous pseudo-skeptic who had the decency to admit to getting it completely wrong? Meet Steven Goddard of The Register, a peculiar little news outlet published in London. Sort of. Goddard wrote a piece that appeared on Aug. 15 under the bold headline "Arctic ice refuses to melt as ordered." As anyone who has been following the plunging arctic sea-ice extent graphs at the National Sea Ice Data Center can attest, this is a rather peculiar interpretation of the data.
Goddard's article was riddled with errors of science and made clear his lack of familiarity with the subject. This prompted actual experts at the National Snow and Ice Data Center (NSIDC) to offer a rebuttal:
The author asserts that NSIDC's estimate of a 10% increase in sea ice compared to the same time as last year is wrong. Mr. Goddard does his own analysis, based on images from the University of Illinois' Cryosphere Today web site, and comes up with a number of ~30%, three times larger than NSIDC's estimate. He appears to derive his estimate by simply counting pixels in an image. He recognizes that this results in an error due to the distortion by the map projection, but does so anyway. Such an approach is simply not valid.

The proper way to calculate a comparison of ice coverage is by actually weighting the pixels by their based on the map projection, which is exactly what NSIDC does.
Thankfully Steven Goddard had the intellectual honesty to admit his error in an addendum to the original article:
"Dr. Walt Meier at NSIDC has convinced me this week that their ice extent numbers are solid. So why the large discrepancy between their graphs and the UIUC maps? I went back and compared UIUC maps vs. NASA satellite photos from the same dates last summer. It turns out that the older UIUC maps had underrepresented the amount of low concentration ice in several regions of the Arctic. This summer, their maps do not have that same error. As a result, UIUC maps show a much greater increase in the amount of ice this year than does NSIDC. And thus the explanation of the discrepancy.

"it is clear that the NSIDC graph is correct, and that 2008 Arctic ice is barely 10% above last year - just as NSIDC had stated."
Unfortunately the original error-riddled article was immediately seized as evidence that the science of global climate change is built on shaky ground and the myth rapidly metastasized around the internet. A quick Google search reveals 55,300 hits for the phrase "Arctic ice refuses to melt as ordered".
I wonder how many of those denialists who trumpeted the original article will have Steven Goddard's intellectual honesty and will print a retraction...

Moving Toward a Global Biodiversity Observation and Measurement System

From Science Magazine:

Biodiversity is a composite term used to embrace the variety of types, forms, spatial arrangements, processes, and interactions of biological systems at all scales and levels of organization, from genes to species and ecosystems, along with the evolutionary history that led to their existence. In part because of this complexity, universally applicable measures of biodiversity have proven elusive. Commonly used measures, such as the number of species present, are strongly scale-dependent and only reveal a change after species have been lost. Indices incorporating several proxy signals are potentially sensitive, but their arbitrariness obscures underlying trends and mechanisms. Integrated measures are both sensitive and achievable, but more research is needed to construct the globally robust relations between population data, genetic variation, and ecosystem condition that they require.
The paper goes on to reiterate the need for national to global-scale biodiversity measurements. This need was highlighted by the adoption of a target to "reduce the rate of loss of biodiversity by 2010" by the 190 countries that are parties to the Convention on Biological Diversity (CBD).
There is no widely accepted and globally available set of measures to assess biodiversity. Consequently, the community has fallen back on a range of existing data sets gathered for other purposes. Currently, in the CBD process alone, there are ~40 measures reflecting 22 headline indicators in seven focal areas... There is no general shortage of biodiversity data, although it is uneven in its spatial, temporal, and topical coverage. The problem lies in the diversity of the data and the fact that it is physically dispersed and unorganized.
The paper states that the solution to this problem is to organise the information currently available and to create systems whereby data of different kinds, from many sources, can be combined. The authors then go on to propose a new network, the Group on Earth Observations Biodiversity Observation Network (GEOBON) designed to help collect, manage, analyse, and report data relating to the status of the world's biodiversity. The new network would be based on the Global Earth Observation (GEO) platform.
The Group on Earth Observations (GEO) was launched in 2002 in response to the widely identified need for adequate information to support environmental decision-making. GEO is a voluntary partnership of 73 national governments and 46 participating organizations. It provides a framework within which these partners can coordinate their strategies and investments for Earth observation. The GEO members are establishing a Global Earth Observation System of Systems (GEOSS) that provides access to data, services, analytical tools, and modeling capabilities through a Web-based GEO Portal.
GEOBON aims to create a global network from multilateral collaborative efforts in the realm of biodiversity by linking and supporting individual efforts within an overarching scientific framework. It is proposed that GEOBON will allow the combination of top-down measures of ecosystem integrity from satellite observations (for example) with bottom-up measures of ecosystem processes, population trends of key organisms and genetic measures of biodiversity from field-based and molecular survey methods. The proposed role of GEOBON will be to guide data collection, standardisation, and information exchange. All participating organizations will retain their mandates and data ownership, but agree to collaborate in making part of their information accessible to others.

Scholes RJ, Mace GM, Turner W, Geller GN, J├╝rgens N, Larigauderie A, Muchoney D, Walther BA, Mooney HA (2008) Toward a Global Biodiversity Observing System. Science 321(5892) 1044-1045.

Teenage DNA Detectives Expose US Fish Fraud

New Scientist magazine is carrying the story of two classmates from New York's Trinity School who collected 60 fish samples from fish stores and restaurants around New York. They then sent their samples off to the University of Guelph in Canada for DNA testing. Of 56 samples that could be identified by the DNA barcoding identification technique, 14 were mislabeled as an entirely different species.

"We never expected these results. People should get what they pay for," said Kate Stoeckle, 18, of the project with Louisa Strauss, 17.
In all cases, the fish was labelled as a more costly type, ruling out simple chance. In the worst cases, two samples of filleted fish sold as red snapper, caught mostly off the southeast United States and in the Caribbean, were instead the endangered Acadian redfish from the North Atlantic. The DNA of fish from a sushi restaurant called "white tuna" revealed the fish to actually to be Mozambique tilapia, a type of cichlid often raised on fish farms. One restaurant offered "Mediterranean red mullet" but the DNA matched spotted goatfish from the Caribbean.

I have highlighted this issue in previous posts here and here, but this is the first time I have seen such an excellent study showing what a widespread problem this is.

New Regulation Would Lessen Influence of Fish and Wildlife Experts

The U.S. Endangered Species Act (ESA) has been at the center of some of the fiercest environmental battles in the history of the United States. It has been the law which has held up big dams, helped bring iconic species such as the bald eagle back from the brink, and been used by environmentalists battling loggers over old-growth forests in the Pacific Northwest. For these reasons the ESA is often demonised by those who prefer business as usual to biodiversity preservation.

The Bush Administration, with only a few months left in government, has just proposed a series of controversial rule changes to the ESA that would prevent the review of many new projects by biologists at the U.S. Fish and Wildlife Service (FWS) and the National Marine Fisheries Service (NMFS).

The departments of the Interior and Commerce have given two main justifications for the proposed rule changes. The first is to prevent the ESA from being used to regulate carbon dioxide (CO2) emissions. That became a possibility after FWS listed the polar bear as a threatened species. Interior Secretary Dirk Kempthorne is reported as saying that:

...the changes were needed to ensure that the Endangered Species Act would not be used as a "back door" to regulate the gases blamed for global warming...
The draft rules would bar federal agencies from assessing the emissions from projects that contribute to global warming and its effect on species and habitats.

The second justification given by the departments of the Interior and Commerce for the proposed rule changes is to reduce the number of "informal consultations" around the ESA. The consultations have caused considerable delays on projects in the past according to a 2004 report by the U.S. Government Accountability Office.

Sen. Barbara Boxer, chairwoman of the Environment and Public Works Committee, called the proposed changes illegal.
This proposed regulation is another in a continuing stream of proposals to repeal our landmark environmental laws through the back door," she said. "If this proposed regulation had been in place, it would have undermined our ability to protect the bald eagle, the grizzly bear and the gray whale.
As the rules currently stand, when an action requiring a permit is proposed the permitting agency responsible must consider whether a listed species or its critical habitat might be affected by the proposed action. If the agency decides that a listed species or its critical habitat may be affected, then the agency must informally consult with staff at the relevant service (FWS or NMFS depending on whether it is a terrestrial or marine matter). If the agency or FWS/NMFS biologists decide that the action is likely to cause harm then a formal consultation is required. If the project is thought to be unlikely to cause harm to a listed species or its critical habitat however, then the agency may proceed with issuing whatever permits are required.

Under the proposed new rules, agencies have to consult the services only if indirect or direct effects of their actions are an "essential cause" of and "significant contributor" to the likely harm. Under the new rule, if the agencies determine that their projects are not likely to harm a species, they would not need to seek an expert opinion from the services at all. If the agencies suspect harm to a species, however, they still must formally consult. Officials at the departments of Interior and Commerce argue that agencies are "fully qualified" to decide on their own whether their projects will harm a species or its habitat.

This isn't the first action by the Bush administration to weaken the ESA. An analysis by FWS and NMFS of newly introduced regulations under the National Fire Plan (similar to those proposed under the ESA) was released in January. These regulations allow the U.S. Forest Service and the Bureau of Land Management to decide whether to consult about prescribed burning and other fire-related actions. NMFS found that in 10 out of 10 cases:
  • The agencies failed to describe spatial and temporal patterns of the action’s direct and indirect environmental effects, including direct and indirect effects of interrelated and interdependent actions;

  • The agencies failed to identify Action Areas clearly;

  • The agencies failed to identify all threatened and endangered species and any designated critical habitat that may be exposed to the proposed action;

  • The agencies failed to compare the distribution of potential effects with the threatened and endangered species and designated critical habitat;

  • The agencies failed to identify to establish, using the best scientific and commercial data available, that (a) exposure is improbable or (b) if exposure is likely, responses are insignificant, discountable, or wholly beneficial; and
  • The agencies failed to base the determination on best available scientific and commercial information
FWS found other flaws in 25 out of 43 cases. It seems unlikely that removing the oversight provided by FWS and NMFS biologists from more projects that are likely to affect ESA listed species will do anything to improve these statistics. It seems immaterial whether agencies are "fully qualified" to decide on their own whether their projects will harm a species or its habitat if they have no will to protect those species and habitats.

The proposed rule is open for public comment until 15 September. From the FWS:
Submit your comments or materials concerning this proposed rule in one of the following ways:

(1) Through the Federal eRulemaking Portal at Follow the instructions on the website for submitting comments.

(2) By U.S. mail or hand-delivery to Public Comment Processing, Attention: 1018-AT50, Division of Policy and Directives Management, US Fish and Wildlife Service, 4401 North Fairfax Drive, Suite 222, Arlington, VA 22203. We will not accept e-mail or faxes.

We will post all comments on This generally means that we will post any personal information you provide us."

Beautiful Sailfish Photographs

Amazing underwater shots of sailfish feeding on a school of sardines, from National Geographic:

More photos here.

The US EPA is Dysfunctional

The U.S. Environmental Protection Agency (EPA) is an agency of the federal government of the United States charged with protecting human health and with safeguarding the natural environment: air, water, and land. The EPA was proposed by President Richard Nixon and began operation on December 2, 1970.

Over the first 30 years of its existence the EPA played an important role and acted decisively to live up to its mandate of protecting human health and safeguarding the natural environment. Today however the EPA is an embattled organization facing criticism from environmental groups that it is powerless to safeguard the environment and is neglecting its responsibilities to protect human health. Among the recent issues that have reflected negatively on the EPA:

  1. Environmental Protection Agency chief Stephen Johnson declined to explain before Congress how a conclusion he made last year that global warming put the public in danger could lead to a decision not to regulate greenhouse gases.
  2. A Federal judge found that the EPA and the state of Florida had dismally failed in their duty to protect the Everglades from harmful phosphorus washing off sugar farms, vegetable fields and suburban streets. In his ruling the judge took EPA to task for repeatedly violating the very Clean Water Act that it is supposed to administer.
  3. A Federal Court in the Northern District of California (Northwest Environmental Advocates v. EPA) found that EPA’s regulation exempting ballast water discharges from the Clean Water Act was “plainly contrary to the congressional intent,” and ordered the Agency to develop new regulations.
  4. Voluntary pollution-reduction programs touted by the Bush administration and supported by EPA as part of the solution to global warming had "limited potential" to reduce greenhouse gases, according to the Environmental Protection Agency's Inspector General's Office.
  5. Senate Environment and Public Works Committee Chairman Barbara Boxer and committee members Sheldon Whitehouse, Amy Klobuchar, and Frank Lautenberg called for the resignation of Environmental Protection Agency Administrator Stephen L. Johnson, charging that Johnson had given misleading testimony before Congress; refused to cooperate with Congressional oversight; and based agency decision making on political considerations rather than scientific evidence or the rule of law.
  6. Five states threatened to sue the Environmental Protection Agency if it did not act soon to reduce pollution from ships, aircraft and off-road vehicles.
  7. Hundreds of Environmental Protection Agency scientists complained they had been victims of political interference and pressure from superiors to skew their findings. In a survey, the EPA scientists described an agency suffering from low morale as senior managers and the White House Office of Management and Budget frequently second-guess scientific findings and change work conducted by EPA's scientists.
Scientists at EPA have repeatedly singled out the Office of Management and Budget (OMB) at the White House for interfering with their work, accusing OMB officials of inserting themselves into decision-making at early stages in a way that shaped the outcome of their inquiries. They also alleged that the OMB delayed rules not to its liking. EPA actions "are held hostage" until changes are made, a scientist from the EPA's Office of Air and Radiation wrote

Even for those who have read Chris Mooney's The Republican War on Science the number of accusations of malpractice and/or incompetence against the EPA in the last few months is staggering. The EPA is clearly a dysfunctional agency no longer able to live up to its mandate. It's time for that to change. Hopefully the political will for that to happen will return after the United States presidential election in November.

More Jonathan Meiburg (Shearwater) Ornithological Geekery

Since I posted about Jonathan Meiburg's (not so) secret life as a bird nerd the other day I have been pointed to this series of videos on YouTube:
Jonathan Meiburg of Shearwater gives a tour of the Falkland Islands. As part of a survey team from Falklands Conservation and the Edinburgh Zoo, he searches for Striated Caracaras or, "Johnny Rook".
There are some lovely shots of all kinds of non-birdy wildlife of the Falklands in these videos.

Murray River Lower Lakes Beyond Salvation

Source: Alex Schrader

The Australian Federal Water Minister, Penny Wong, has announced that due to the extended drought, the Murray River's lower lakes appear to now be beyond salvation. Lying near the mouth of the Murray in SA, the lakes have been listed as internationally protected wetlands under the Ramsar Convention. They host a large number of plants, animals and migratory birds.

Back in July I wrote that:
Australia’s worst drought in 100 years, which has already cost the nation $20 billion dollars since 2002, is likely to become even more severe and cause permanent ecological changes in the country’s breadbasket, the Murray-Darling river basin, government officials said.
Alexandrina Council which manages the environment at the Murray mouth and lower lakes region says emergency water flows are needed or the river system will soon be beyond repair. Neil Schillabeer, from the Lower Lakes and Coorong Infrastructure Committee, says:
"There is a need for probably 200-250 gigalitres of water in the very immediate future to solve the problems we've got there right now. That doesn't seem to have eventuated. Our state Premier hasn't been able to negotiate those sort of volumes of water for the lakes."
Signalling that the Federal Government has given up on saving the drought-stricken lakes, Senator Wong said yesterday that a final decision on whether to flood the lakes with seawater would be made within the next few months.
"Unfortunately, there's just not enough water to do everything we want, so the priority has to be critical human needs," Senator Wong told ABC radio.
The South Australia Government's adviser on drought, Dean Brown, said the fate of the lakes depended on rainfall over the next two months.
"There's a 50% chance that there might be enough flow in the river and enough flow into the lakes to maintain the level where it is," Mr Brown said.