Increasing levels of carbon dioxide in the atmosphere are turning the oceans more acidic, according to scientists who have been raising alarms for years.

The acidity threatens the marine food web, with the most direct effects on the shells and skeletons of shellfish and corals, since their absorption of calcium carbonate is reduced in a more acidic environment.

Let’s take note of a few new milestones, although nobody has a practical idea for responding to the threat without addressing the entire issue of global warming.

First, and none too soon, the first comprehensive national study of ocean acidity was commissioned last month by the National Oceanic and Atmospheric Administration and the National Science Foundation. See Oct. 20 news release.

The study followed an international symposium in early October, called the “Second International Symposium on the Ocean in a High CO2 World.” The meeting’s chairman, James Orr of the International Atomic Energy Agency, had this to say in a prepared statement:

“Since the industrial revolution, the acidity of ocean surface waters has increased by 30 percent. This change is greater and happening about 100 times faster than for previous acidification events experienced in many millions of years…

“Published research indicates that by 2030, the Southern Ocean will start to become corrosive to the shells of some marine snails that swim in surface waters. These snails provide a major source of food for Pacific Salmon.

“If they decline or disappear in some regions, such as the North Pacific, what will happen to the salmon – and the salmon fishing industry? And what will happen as ocean acidification increasingly affects coral reefs, which are home to one-quarter of the world’s fish during at least part of their lifetime, and which support a multi-billion dollar tourist industry?”

Finally, the Center for Biological Diversity today issued a notice to the Environmental Protection Agency saying it intends to sue the federal government for failure to respond to the threat of ocean acidification. Last year, the environmental group filed a formal petition asking EPA to impose stricter pH standards for ocean water quality and to publish guidance to help states protect U.S. waters.

A press release from the center includes these comments:

The federal Clean Water Act requires the EPA to update water-quality criteria to reflect the latest scientific knowledge. Since the agency developed the pH standard back in 1976, an extensive body of research has developed on the impacts of carbon dioxide on the oceans.

“Ocean acidification is global warming’s evil twin,” said Miyoko Sakashita, an attorney with the Center for Biological Diversity’s oceans program. “The EPA has a duty under the Clean Water Act to protect our nation’s waters from pollution, and today, carbon dioxide is one of the biggest threats to our ocean waters.”

It appears the Center for Biological Diversity is launching a flank attack on the global warming issue via the Clean Water Act, which allows citizen lawsuits. A similar flank maneuver involved the effort to get the polar bear protected under the Endangered Species Act as a result of melting ice caused by global warming. See CBD press release.

Clearly, environmental groups are not waiting for a new administration to move into the White House or to see how President Barack Obama might address the threat of global warming.

ABC World News is reporting that it will feature a story about the seven Puget Sound killer whales that are missing and presumed dead. Locally, watch Channel 4 at 5:30 p.m. A written story with plenty of photos can be seen on the World News Web site.

The Kitsap Sun was the first daily newspaper to report on the missing orcas. For breaking news and regular reports, sign up for e-mail notification or RSS in the right-hand column of “Watching Our Water Ways.”

The draft of the Puget Sound Action Agenda is a bit of a jumble in its initial form, but officials with the Puget Sound Partnership say this wide-ranging report will get better with time.

Valerie Wolf braves the rain Thursday near the Norm Dicks Government Center in Bremerton Carolyn J. Yaschur, Kitsap Sun

It is, after all, a broad list of the actions that need to be taken to move Puget Sound toward a healthy condition. What will help in future versions is a list of possible actions in order of priority. I’m told the final draft will also include additional summaries to help people work their way through the dense 50-page report (not including the “action area profiles” at the back).

State Sen. Phil Rockefeller, D-Bainbridge Island, chief architect of the Puget Sound Partnership structure, told me that he’s pleased to have something down on paper for people to review and make comments about. The issue is complex, he said, and people need to understand that those involved with the Partnership are working very hard.

I get the sense that many people, especially conservationists, would like to see a more forceful, perhaps activist, attack on the problem. So far, the Partnership has taken a rational, scientific approach. It seems there is a strong desire among the leaders to bring the public along with education before asking for the levels of funding needed to turn things around more quickly. Economic times are tough, after all.

Can we afford to go slow while putting an optimistic face on the problem, or do we need to scare people into the realization that salmon and orcas are going extinct? That is the key question that the Puget Sound Leadership Council needs to address with some clear certainty.

In writing about this draft, I found it hard to discuss what might be proposed during the first two years without listing all the “near-term actions” (which I didn’t do), because there won’t be enough money to do the dozens of things listed. Those decisions must be made by the Puget Sound Leadership Council, preferably by Dec. 1. In the meantime, I encourage you to take a look at the list in the draft Action Agenda (PDF 1.7 mb).

Also, it’s not always clear who is going to be responsible for what. That is something to be negotiated with state and local agencies, as well as other entities. Such commitments, along with accountability, is the essence of the Puget Sound Partnership structure.

David Dicks, executive director, said what has been missing in previous efforts to restore Puget Sound is an overall scientific-based plan that puts everyone on the same “songsheet.” It’s the same problem plaguing other ecosystems, such as Chesapeake Bay, he said. Plans by the previous Puget Sound Action Team seemed to be no more than a list of what the agencies said they would do, whether or not those things ever got done, Dicks said.

Bill Ruckelshaus, chairman of the Leadership Council, often talks about the need to obtain cooperation from the other “partners.” The Legislature gave the Partnership new techniques of holding people accountable. One would be recommending that funding be withdrawn from entities that aren’t doing the job. Another would be a report card that essentially grades everyone and holds people up for public ridicule if they aren’t getting the job done.

So feel feel free to read my story in today’s Kitsap Sun, and check out reports from other newspapers in the region: Seattle Times, Seattle Post-Intelligencer and The Olympian.

UPDATE

I revised the story for Friday’s Kitsap Sun.

—————-

I just came off a teleconference where David Dicks and other Puget Sound Partnership officials discussed with reporters the draft of the Action Agenda, which was released today.

Dicks said the number-one problem facing Puget Sound is all the toxic chemicals that drain into the waterway with stormwater, which we have discussed many times before. He also emphasized the need to protect the last remaining fish and wildlife habitat of high quality.

I’ll have more to discuss later, but I’m posting this item for all you e-mail subscribers who like to stay on top of things. Here’s the quick-and-dirty story I wrote this morning about today’s activity. You’ll find a lot more by going to the Puget Sound Partnership Web site:

Report is a “road map” for restoring Puget Sound to health

By Christopher Dunagan

Puget Sound Partnership, tasked with restoring Puget Sound to health, released a draft of its first Action Agenda, a road map for protecting, restoring and cleaning up the waterway.
For the first time, one organization has laid out a strategy to observe the threats and changes to Puget Sound and to direct unified efforts to reverse the long decline in habitat and water quality.

One of the greatest threats to Puget Sound, according to the report, is ongoing stormwater runoff. Each year, some 52 million pounds of toxic chemicals – or nearly 150,000 pounds per day – flow into Puget Sound. That’s equivalent to a spill the size of the Exxon Valdez every two years, officials said.

“These disturbing numbers are putting more than 40 species in Puget Sound at risk, including the Sound’s orca population, where we just saw a decline of nearly 10 percent in the past several months,” David Dicks, executive director for the Partnership, said in a written statement.

Recommendations fall into four strategic areas:

• Protecting sensitive lands, including working forestland, farms and shoreline.
• Restoring degraded areas, such as estuaries, wetlands and marine ecosystems — including the implementation of salmon recovery plans that have already been developed for every watershed.
• Reducing water pollution, including that from stormwater, sewage treatment plants and septic systems.
• Coordinating efforts to restore Puget Sound by encouraging all agencies, organizations and individuals to manage Puget Sound as one complete ecosystem.

For information, including a copy of the Action Agenda and related scientific reports, go to the Puget Sound Partnership’s main page.

Comments on the Action Agenda will be taken until Nov. 20. Two public meetings are planned, both beginning at 9 a.m.:

• Nov. 11: Embassy Suites Seattle-Tacoma International Airport, 15920 W. Valley Highway.
• Nov. 21: Edmonds Conference Center, 201 4th Ave N.

A fungus that can turn cellulose into diesel fuel?

An announcement this week by a Montana State University researcher is either one of the greatest discoveries of the decade or else it could become one of the most disappointing. It will all depend on how the “development” end of the “research-and-development” continuum plays out in the coming years.

Plant pathologist Gary Strobel of MSU announced in the journal “Microbiology” (PDF 176 kb) that he discovered a wood-eating fungus that produces medium-chain hydrocarbon molecules — the kind found in gasoline and diesel fuel.

Science reporters all over the world quickly grasped the potential of this discovery and began reporting the findings in dozens of bulletins, stories and blog entries — all within the last two days.

The hope is that the fungus — Gliocladium roseum — can be perfected through genetic engineering to produce an organism that can break down wood chips, corn stocks and other cellulosic materials that typically go to waste.

There is much uncertainty about whether this discovery can yield a marketable product before fuel cells take over the world. But even fuel cells require raw energy, and part of our national challenge is to get away from imported oil as quickly as possible. This microscopic fungus could fill an important gap.

Strobel is no stranger to discovery. His tiny organisms have been used to fight human and plant diseases. See his discoveries list.

Of all the stories so far on the Internet dealing with this so-called myco-diesel fungus, the seven-minute radio report by Robert Chadwick of National Public Radio is the most entertaining. For my tastes, however, a description by Robert F. Service of “Science Now” holds just the right amount of technical detail and scientific excitement.:

The discovery is “a really great contribution,” says Stephen Del Cardayre, a synthetic biologist and vice president for research and development at LS9, a South San Francisco-based start-up working to use microbes to produce renewable fuels. Even though the new fungus pumps out only small quantities of fuel hydrocarbons, researchers might use its genes to engineer other industrial microbes to do the job more efficiently. “The beauty is that even if the chemical reaction isn’t perfect, you can always improve it,” he says.

The search for fuel-producing microbes is one of the hottest areas in synthetic biology. Strobel, an expert on endophytes–organisms that live within the tissues of other creatures–joined it by accident in 1997, when he discovered a fungus in Honduras that naturally produces volatile antibiotics, now being evaluated as a way to preserve fruit during shipping. Strobel has since identified related fungi around the globe that produce different volatile hydrocarbons.

After discovering the new fungus wedged between cells in a stem from an Ulmo tree (Eucryphia cordifolia), Strobel and colleagues cultured the organism, collected the gaseous compounds it produced, and ran the compounds through a mass spectrometer to identify them. When he saw the printout, Strobel says, “every hair on my body stood up.” The list included octane, 1-octene, heptane, 2-methyl, and hexadecane–all common components of diesel fuels.

If you want more, MSU staff are compiling a growing list of stories from around the world.

Alexandra Morton of Echo Bay, British Columbia, is a fascinating person — part researcher, part activist and 100 percent advocate for killer whales. She is often compared to Jane Goodall and Dian Fossey, who studied complex mammals by essentially living with them.

Morton and a group of salmon-farming opponents — including Anne Mossness of Washington state — are trying to make people aware of their concerns regarding salmon farming, which they say threatens wild salmon, orcas and other predators.

On Sunday, the group signed an ”international declaration” (PDF 856 kb) outlining why salmon farming violates the United Nations “Code of Conduct” regarding sustainable aquaculture.

“Scientific studies show that wild salmon populations are crashing wherever there are salmon farms due to pathogen amplification and genetic pollution, but the damage runs much deeper,” according to a press release issued yesterday.

Meanwhile, reporter Cornelia Dean spent some time with Morton and wrote about the researcher’s personal and somewhat tragic life in a story published yesterday in the New York Times.

The timing of the story may be related to a court challenge last month by Morton and other fish-farming opponents trying to force the federal government in Canada to take authority over fish farms. In an AOL video, Morton explains the legal aspects of the case and talks about how killer whales are at risk from the farms. The seven-minute video is a solid piece of education that illuminates Morton’s point of view, once you ignore the wind on the microphone.

While I may not have a clear perspective of who Morton really is, I think I share a fascination with most people who have read her autobiography, “Listening to Whales: What the Orcas Have Taught Us” Am I right? Maybe I’ll get the chance to meet her one of these days.

It was sad and disturbing to find out that seven Puget Sound killer whales have died so far this year.

We haven’t had that number of deaths since 1998 — the year after 19 orcas visited Dyes Inlet between Bremerton and Silverdale. To those who study these whales, the orcas aren’t just seven animals in a herd; they are individuals with unique characteristics; they are members of an extended family that stays together for life.

Ken Balcomb of the Center for Whale Research believes the deaths are related to a shortage of chinook salmon seen this year from California to Washington to British Columbia. I went into some detail about this in a story in today’s Kitsap Sun. I also included a brief “obit” on the animals that died.

I would like to take a moment to remind myself and others that it is unlikely that the deaths were caused by a single factor. I have long been intrigued by the prospect of synergism in these animals, and I would hope that researchers will one day be able to accumulate enough data to support or deny this hypothesis.

What I’m talking about is this: Researchers have promoted three principal causes of the decline in Puget Sound whales, officially known as Southern Residents. They are toxic chemicals (such as PCBs) that have accumulated in their bodies, lack of prey (chinook primarily), and stresses caused by noise, whale-watching boats and other things. For more info, check out the recovery plan for the Southern Residents.

Follow this train of thought:

• PCBs and other chemicals are believed to damage the orcas’ immune systems and reduce their ability to fight off disease.
• If the animals are not getting enough food, they draw upon fat reserves in their blubber. Metabolizing these fats tend to release the toxic chemicals into their bloodstream, exposing their immune systems to more chemicals and further increasing their risk of disease.
• Although the whales seem accustomed to whale-watching boats, anything that causes them to use up excess energy to replenish their energy supplies by hunting for food cannot be a good thing, especially in times of a food shortage. Uninformed boaters sometimes interfere with the whales’ travel during foraging, and noise caused by boats is believed to decrease their efficiency in finding fish through echolocation (their natural sonar system).

In my mind, all of these factors tend to work together. What is often hard to sort out is whether an animal dies of starvation or disease. When food is in short supply, disease may set in before an animal literally starves to death. Also, especially for a hunting species, a disease can reduce their ability to get food, so the outcome is the same. For many species, a higher-level predator may kill an individual that is starving or diseased. But with an animal at the top of the food web, such as killer whales and humans, the dynamics may be different.

I guess I’m just trying to point out that it could be an oversimplification to say the whales starved to death, even if food were a certain factor.

With regard to news sources, I have to confess that this story of the seven missing whales has been in the wind since Oct. 8, but I missed it. Howard Garrett and Susan Berta of Orca Network put something on their Web site, but I overlooked it. Richard Walker, editor of the Journal of the San Juans had talked to Ken Balcomb about that time, but I missed his story until someone pointed it out to me.

Finally, several people have mentioned the coincidental stranding of a killer whale on the island of Kauai in Hawaii. Diana Leone of the Honolulu Advertiser reported that the 18-foot female was emaciated and had “cookie-cutter shark bites” and whale lice, all signs that it had been sick for some time.

CNN posted a user-generated video about the whale.

I understand that researchers are trying to see if the female orca, who was euthanized, can be connected with previous sightings.

I looked up a 2004 Marine Mammal Stock Assessment Report (PDF 56 kb) for a little background. It says Hawaiian killer whales are rarely seen, but the best population estimate is 430. Minimal genetic data indicate that the animals may be related to Gulf of Alaska transient killer whales.

Construction of a new boardwalk from downtown Bremerton to Evergreen Park is supported by more than a few people, as evidenced by letters sent to the Army Corps of Engineers. But most of the letter writers don’t tackle the thorny environmental issues involved with the overwater structure and its significant impacts on fish habitat.

On the other hand, state and federal agencies and the environmental group People for Puget Sound have raised many more issues than I could cover in Sunday’s Kitsap Sun story.

I would like anybody interested to be able to read the agency letters I’ve seen, so I’m posting them here for you to download. Some agencies, such as the National Marine Fisheries Service and Washington Department of Ecology, are involved directly in permitting, so they have chosen not to comment at this time.

Suquamish Tribe (PDF 208 kb)
U.S. Fish and Wildlife Service (PDF 180 kb)
Washington State Department of Natural Resources (PDF 108 kb)
People for-Puget Sound (PDF 973 kb)

David Parry, Northwest regional president for Camp Dresser & McKee, an engineering and consulting firm, makes a good case for turning sewer gas into energy.

As he explained to commissioners and staff for West Sound Utility District and Silverdale Water District, you need to remove carbon dioxide and impurities from biogas to get a high-quality methane, which is essentially natural gas that can heat buildings, run cars or generate electricity. Read more details in my story published in Sunday’s Kitsap Sun.

Responding to a question, Parry did a quick back-of-the-envelope calculation about the costs and potential of converting biogas generated at West Sound’s sewage-treatment plant near Retsil. Conversion equipment would cost roughly $500,000, he said, and it would produce an amount of natural gas equivalent to about 100 gallons of gasoline a day.

Bonneville Power Administration has removed the last of more than 100,000 capacitors containing PCBs throughout its distribution system, thus reducing the risk of spilling these toxic chemicals that never seem to go away.

Officials with the Environmental Protection Agency recognized the accomplishment, as stated in a press release.

“EPA congratulates BPA for its proactive and voluntary efforts to remove a significant source of PCBs from the Northwest’s largest transmission system,” said Elin Miller, administrator for EPA’s Region 10. “This action by BPA shows their commitment to protect human health and the environment by preventing future releases of toxic PCBs.”

BPA replaced more than 101,000 capacitors at 69 substations. The $102-million cost was spread over a 17-year period beginning in 1991.

Eliminating the chance of spilling PCBs also reduces the financial risk of a costly cleanup hanging over BPA since PCBs were outlawed in the 1970s.

We hear a lot about dangerous levels of PCBs residing in marine mammals, including killer whales, seals and sea lions. These chemicals are considering endocrine disruptors with effects on the immune and reproductive systems of all kinds of animals.

I’m not sure if anyone has identified the predominant sources of PCBs are in the marine environment, but we know it will take a long time to eliminate the problem.

UPDATE, OCT. 10: Eric Robinson of the Vancouver Columbian does a nice job covering this story.