August 2008 Archives

The New York Times is reporting this morning that Mayor Ray Nagin has issued a mandatory evacuation order for New Orleans.

This is the mother of all storms, and I'm not sure we've seen anything like it," Mr. Nagin said at an evening news briefing. "This is the real deal. This is not a test. For everyone thinking they can ride this storm out, I have news for you: that will be one of the biggest mistakes you can make in your life."

The official advisory is a little less dramatic, but not very reassuring.

A HURRICANE WARNING REMAINS IN EFFECT FOR THE NORTHERN GULF COAST
FROM CAMERON LOUISIANA EASTWARD TO THE ALABAMA-FLORIDA BORDER...
INCLUDING THE CITY OF NEW ORLEANS AND LAKE PONTCHARTRAIN. A
HURRICANE WARNING MEANS THAT HURRICANE CONDITIONS ARE EXPECTED
WITHIN THE WARNING AREA WITHIN THE NEXT 24 HOURS. PREPARATIONS TO
PROTECT LIFE AND PROPERTY SHOULD BE RUSHED TO COMPLETION.

Gustav is currently rated as category 3 with maximum sustained winds of 125mph, and it has New Orleans in its sights. Fortunately, people seem to be getting out of the way this time. 

Last fall a small group of people called for the presidential candidates to a debate focused on issues relevant to science, technology, and innovation. None of the candidates answered that call, but more recently Innovation 2008 issued 14 questions for the two remaining candidates to answer.

Today Senator Obama has responded, but John McCain has also promised to respond. I'll post a link to his answers as soon as they're available.

I've posted several times about proposed changes to rules implementing the Endangered Species Act. On Tuesday, John Kerry, Barbara Boxer, Chris Dodd, Sheldon Whitehouse, Hillary Clinton, Bernie Sanders, and Frank Lautenberg sent a letter to Secretary of Interior Dirk Kempthorne.

The proposed changes are inconsistent with the letter and spirit of the ESA, contradicted by federal judicial precedent, and would reduce rather than strengthen protections for imperiled fish and wildlife.

They ask Kempthorne to withdraw the proposal. Failing that, they ask that the comment period be extended to six months, allowing time for a series of public hearings on the proposal.

You can read the full text of the letter at JohnKerry.com.

On Tuesday a group of Senators wrote to Dirk Kempthorne asking that he withdraw his recently proposed changes in regulations implementing the Endangered Species Act. Joe Lieberman was not among them.

On his Senate website, Lieberman has this to say about environmental oversight:

In April 2007, Senator Lieberman led four Senate colleagues in writing the US Secretary of the Interior to oppose draft changes to the regulations that implement the Endangered Species Act. Their letter noted that the draft changes would reduce dramatically the current scope and positive impact of the Act. The letter posed fifteen detailed questions about the draft rule changes and requested that the Department not move any closer to promulgating any revisions until it answered the Senators' questions.

Senator Lieberman. Please join your colleagues in asking Secretary Kempthorne to withdraw the changes Endangered Species Act regulations proposed on 15 August.

In 2007 the extent of ice in the Arctic Sea reached a new low. Last year it reached a low of 4.24 million square kilometers. Yesterday the National Snow and Ice Data Center reported that it has dropped below the minimum level of 2005, and the minimum is not normally seen until late September.

With several weeks left in the melt season, sea ice extent dipped below the 2005 minimum to stand as the second-lowest in the satellite record. The 2005 minimum, at 5.32 million square kilometers (2.05 million square miles), held the record-low minimum until last year.

Juliet Eilperin has additional information in a Washington Post story this morning.

The Ecological Society of America just released a statement on the proposed changes in federal regulations implementing the Endangered Species Act. The bottom line?

The Society believes that independent scientific review is a critical part of the Endangered Species Act and that eliminating this part of the process will result in environmental neglect at best and species extinctions at worst. The administration's proposal would compromise our ecosystems' capacity to provide essential services, such as mitigating pollution, regulating climate and providing natural resources. Exposing the most vulnerable species to the threats that will result from the Bush proposal will endanger our ecological support system.

I encourage you to read the full text of the statement at the ESA's web site. The American Institute of Biological Sciences submitted comments last week requesting that the public comment period be extended to at least 90 days.

I just learned that the American Association for the Advancement of Science released this video, Evolution, education and the integrity of science, last spring. Take a look, and and pass it along.¹

I have enormous respect for high school biology teachers, especially those like David Campbell who teach evolution in communities where many parents (and even some biology teachers) are hostile to it. Campbell was part of the committee that drafted Florida's new science standards, standards that require evolution to be taught.

Today's New York Times has an article describing the challenges Campbell faces teaching evolution in Orange Park, Florida. You should read the whole thing. It shows how Campbell achieved a small victory by being firm on what science tells us about the natural world, while being sensitive to the religious beliefs many of his students bring to class.¹

In his first exam on evolution, Campbell asked students to provide two pieces of evidence for evolution and natural selection. One of his student, Bryce Haas, refused to answer. Bryce plays football and regularly attends prayer meetings of the Fellowship of Christian Athletes that are held at 6:00am in the school gymnasium.

Faced with a challenge like that, I probably would have given up.² But David Campbel isn't me. He's a much better teacher. He pressed on through a difficult, challenging lecture in which he presented some of the evidence that humans and apes share a common ancestor.

When the bell rang, he knew that he had not convinced Bryce, and perhaps many of the others. But that week, he gave the students an opportunity to answer the questions they had missed on the last test. Grading Bryce's paper later in the quiet of his empty classroom, he saw that this time, the question that asked for evidence of evolutionary change had been answered.

Tim Whitehead links to this story from yesterday's New York Times in which two high school  students found that 25% of the fish sold as sushi in New York are misidentified.

[O]ne-fourth of the fish samples with identifiable DNA were mislabeled. A piece of sushi sold as the luxury treat white tuna turned out to be Mozambique tilapia, a much cheaper fish that is often raised by farming. Roe supposedly from flying fish was actually from smelt. Seven of nine samples that were called red snapper were mislabeled, and they turned out to be anything from Atlantic cod to Acadian redfish, an endangered species.

Tim headlines his entry "More fake fish", which is true, but it's not what interests me.

In 2007 universities and colleges in the United States spent just over $49.4 billion in scientific research and development. Of that total, more than 60% ($30.4 billion) came from federal sources. Although total federal support increased by a little less than $300M from 2006, that represents a 1.6% decline when adjusted for inflation. Its the second year in a row when federal support for scientific research and development failed to keep pace with inflation. Total research and development expenditures increased by only 0.8% from 2006 to 2007 when adjusted for inflation.

According to figures from the Bureau of Economic Analysis the Gross Domestic Product of the United States increased by almost 2.4% from the fourth quarter of 2006 to the fourth quarter of 2007. In other words, the U.S. economy grew at three times the rate of overall U.S. investment in scientific research and development at colleges and universities.

I'm not going to claim that federal and non-federal funding for university-based scientific research should increase at the same rate as the overall economy, but surely we're eating our seed corn when the economy is growing three times as fast as our investment in university-based scientific research.

Hey, maybe this is something we should ask John McCain and Barack Obama about. Oh wait. It sounds a lot like question 13 of the fourteen questions both candidates have been invited to answer. Shawn Otto reported in a recent e-mail that both campaigns have said they will respond. I, for one, am looking forward to their answers.

I've mentioned before the changes that Secretary of the Interior Dirk Kempthorne is proposing to regulations that implement the Endangered Species Act. The Union of Concerned Scientists has just posted a brief analysis of the proposed changes. They conclude that the proposed changes would:

• Transfer much analysis away from the scientists at the Services and instead give the action agencies enormous discretion to determine whether or not their own project will affectimperiled species.
• Make action agencies the gatekeepers to the consultation process, effectively transferring decision-making based solidly in science to agencies that severely lack the biological expertise to make them.
• Impose an arbitrary deadline of 60 days for the Services to respond to a consultation requestfrom action agencies. If the Services do not reply in 60 days, the action agency is free to move forward with their desired action.

I mentioned last month that Michael Mann and Lee Kump from RealClimate.org have a new book out, Dire Predictions: Understanding Global Warming. I ordered shortly after learning about it, and I finished reading it this weekend. It is a very, very, very good book. Mann and Kump explain the current state of climate science very well. They identify those features of the global climate that we understand well (e.g., the greenhouse effect), those we don't understand so well (e.g., the surface warming expected if CO₂ levels increase to 560ppm), and  those where the uncertainties are even larger (e.g., how fast will the major ice sheets melt). More importantly, they do a good job of explaining why action to curb climate change makes sense even though there are parts of the climate system we don't understand well.

Clearly, we must work to diminish the uncertainty where possible, particularly when it impacts on our ability to make appropriate policy decisions or choose an optimal strategy for mitigating climate change. Recent history has taught us that uncertainties are not adequate justification for avoiding action. We know enough today to understand how vital it is that we act now. (emphasis mine)

Biology is a very, very different discipline from the one I began to study thirty years ago when I started graduate school at Stanford.¹ Entire genomes are sequenced routinely where once we were lucky to know the sequence of a single gene. Theoreticians, like me, depended on computers in our research, but for everyone else the only time they used a computer was when they needed to do a complicated statistical analysis in SAS.² Now it's difficult to imagine any biologist surviving without a computer and an internet connection, whether downloading sequences from Genbank, inferring phylogenies,³, or inferring rates of gene flow, computers are an essential part of the modern biologists toolkit. Writing in Nature Genetics Lincoln Stein outlines a vision of the future for cyberinfrastructure in biology. The whole article is worth reading, but if you can't wait for the punchline, here it is:

This is an exciting time for biology. The projects that are now in progress or just getting under way point towards a future in which scientific collaborations will be unimpeded by geographic constraints or by limited access to data. Just as it is now inconceivable to do science without access to a personal computer and e-mail, in a decade the cyberinfrastructure will be an absolutely indispensable part of the biological researcher's equipment.

A few days ago we learned that DNA from the "bigfoot" specimen in Georgia came from a human and an opossum. Today we learn that Tom Biscardi, the guy who sponsored the news conference in Palo Alto announcing the "discovery" and paid "a substantial amount of money" for the corpse, admits that he was duped. "It was just a total scam," he said.

Well, Mr. Biscardi, my offer still stands. If you really did pay "a substantial amount of money" for a frozen gorilla suit, there's a bridge in Brooklyn you might be interested in buying. I'm sure I could get you a good deal.

USA Today has more details.

A new ad from our friends at wecansolveit.org. It will run nationally on cable news channels with concentrated efforts in Denver during the Democratic convention and Minneapolis during the Republican convention.

Maybe converting to renewable sources of energy won't be as difficult as some people think.

When Colorado voters were deciding whether to require that 10 percent of the state's electricity come from renewable fuels, the state's largest utility fought the proposal, warning that any shift from coal and natural gas would be costly, uncertain and unwise.

Then a funny thing happened. The ballot initiative passed, and Xcel Energy met the requirement eight years ahead of schedule. And at the government's urging, its executives quickly agreed to double the target, to 20 percent.¹

100% of our energy from sources with zero net carbon emissions in ten years may sound impossible, but Colorado is showing the way. Let's get on with it.

According to Glassbooth

Ralph Nader shares a 83% similarity with your beliefs.

Sorry Ralph. Obama's 71% is good enough for me, and he has a chance of winning.

I mentioned yesterday that "bigfoot hunters" were going to present evidence that they have a dead bigfoot in a freezer back home in Georgia. Well, according to a report from Reuters in the New York Times.

One of the two samples of DNA said to prove the existence of the Bigfoot came from a human and the other was 96 percent from an opossum, said Curt Nelson, a scientist at the University of Minnesota who performed the analysis.

If you're surprised that the DNA evidence didn't hold up, there's a bridge in Brooklyn that I'd like to sell you.

That's the title of the proposed changes to regulations that would eliminate independent scientific review of actions by federal agencies that could affect endangered or threatened species. The National Wildlife Federation posted its analysis of the proposed changes on Monday. The Federal Register Notice was just posted today (HTML version, PDF version).

Comments on the proposed changes must be received by 15 September 2008, either through the Federal eRulemaking Portal at www.regulations.gov or by US Mail. I urge you to file comments on the rule. If you do file comments, I suggest that you ask that the comment period be extended to at least 90 days. and that you point out that the changes would have the fox guarding the henhouse.

Among the provisions included in the proposed changes is one that would allow federal agencies to avoid consultation with the Fish & Wildlife Service when the effects on a listed species or its designated critical habitat "[a]re not capable of being meaningfully identified or detected in a manner that permits evaluation." And who gets to make the decision about whether that criterion is met? You guessed it. The agency who wants to do something that will affect a listed species.

Larry Moran quotes this excerpt from a recent O'Leary post at Uncommon Descent:

Having reported news on the ID scene for about five years now, I could give a number of reasons why I think ID is slowly winning the intellectual battle, but let me focus on just one for now ...

Let's see, didn't Michael Medved tell us recently that "intelligent design is not a theory"? And last year didn't Philip Johnson reveal that "I also don't think that there is really a theory of intelligent design at the present time"?

That's winning? When two of your strongest supporters admit that you don't even have a theory? Boy, the sixties must have been good to Denyse.

Last week John Holdren published an op-ed in the Boston Globe bemoaning the undue attention paid to the tiny group of scientists who dissent from the findings of the Intergovernmental Panel on Climate Change.

The few climate-change "skeptics" with any sort of scientific credentials continue to receive attention in the media out of all proportion to their numbers, their qualifications, or the merit of their arguments. And this muddying of the waters of public discourse is being magnified by the parroting of these arguments by a larger population of amateur skeptics with no scientific credentials at all.

Apparently, he's been receiving a lot of nasty e-mail in response. He's written a short commentary in response to those e-mails, You can find the whole thing at DotEarth, but here's one of his key observations:

Appreciation for this positive role of scientific skepticism, however, should not lead to uncritical embrace of the deplorable practices characterizing what much of has been masquerading as appropriate skepticism in the climate-science domain. These practices include refusal to acknowledge the existence of large bodies of relevant evidence (such as the proposition that there is no basis for implicating carbon dioxide in the global-average temperature increases observed over the past century); the relentless recycling of arguments in public forums that have long since been persuasively discredited in the scientific literature (such as the attribution of the observed global temperature trends to urban-heat island effects or artifacts of statistical method); the pernicious suggestion that not knowing everything about a phenomenon (such as the role of cloudiness in a warming world) is the same as knowing nothing about it; and the attribution of the views of thousands of members of the mainstream climate-science community to "mass hysteria" or deliberate propagation of a "hoax".

In a sentence cut from the op-ed piece Holdren wrote,

We should really call them "deniers" rather than "skeptics", because they are giving the venerable tradition of skepticism a bad name.

Exactly! Hence the title of this post.¹

on Friday at a hotel in Palo Alto, Calif., a pair of Bigfoot hunters say they will present what they contend is the most definitive proof yet of an animal that science says does not exist: DNA evidence and photographs of a dead specimen they say they found in a remote swath of woods in northern Georgia. "Two Georgians say they have bigfoot's body," by Jesse McKinley, New York Times, 15 August 2008.

The photo in the Times is not at all convincing. It looks like a bad gorilla suit. If I learn anything about the DNA evidence they present, I'll report back.

I mentioned last week that the National Center for Atmospheric Research (NCAR) closed its Center for Capacity Building in response to continuing budget cuts. Today's Nature has more details about the closure and its consequences. Here are a couple of the key paragraphs.

[T]he lay-off of Mickey Glantz, a high-profile researcher who has chalked up some 34 years at the institution, has raised questions about whether NCAR is turning its back on the social sciences at a time when international efforts are focusing on mitigation and adaptation. Certainly Glantz believes this is the case, saying budgets are just an excuse and that the leadership is defensively "circling the wagons". His dismissal is tied to NCAR's announcement last week that it is shutting its Center for Capacity Building, the highly respected outreach programme that Glantz has run since 2005.

But others associated with the programme say they believe the NCAR leadership still backs them despite its budgetary problems. "I don't think this has anything to do with shutting down social science at NCAR," says Linda Mearns, who recently stepped down as director of the Institute for the Study of Society and Environment there. Mearns says social scientists within the institute will continue to work with physical scientists at NCAR on integrated research projects. "And that's the proper role for an institute in social science at NCAR."

The American Psychological Association begins its 116th annual convention today in Boston. Writing in USA Today, Sharon Jayson reports that among the findings to be discussed are these:

• Walking outside rather than inside -- even for just 15 minutes -- makes you feel happier, more energetic and more protective of the environment.
• Negative feedback can backfire. In two studies, psychologist Amara Brook of California's Santa Clara University and colleague Jennifer Crocker of the University of Michigan asked 212 undergraduates about their ecological footprint. For those not heavily invested in the environment, negative feedback about their ecological footprint actually undermines their environmental behavior.
• News stories that provided a balanced view of climate change reduced people's beliefs that humans are at fault and also reduced the number of people who thought climate change would be bad.

That third point deserves a little comment.

John Wilbanks has been traveling, and he noticed something:

As I was driving through the Wasatch-Cache Forest at night, it struck me that the vision required to start the protection of lands in 1891 was the kind of vision we need now in intellectual property. If nearly 10% of this country's physical property can be reserved as a commons - which is so much harder to provide dual-use, public and private - why not for IP?

It's a very interesting analogy, one I've used myself.¹ If we push the analogy, though, it suggests that immediate open access won't be the long-term solution we're looking for.

If you want to camp in a National Forest, hike in some of them (like the Red Rock region around Sedona, Arizona), or simply enter a National Park, you have to pay a fee. We pay taxes to fund the National Forest Service, the Bureau of Land Management, and the National Park Service whether we visit their properties or not. And we often pay a fee when we want to use them.

The analogy would be that we pay taxes to fund research by the National Institutes of Health, the National Science Foundation, and other federal agencies, whether expect to use the results of that research directly or not. And that if we want to use the research directly, it wouldn't be unreasonable to pay a fee, just as we pay a fee to enter Grand Canyon National Park.

The Redfish Lake sockeye salmon (Oncorhynchus nerka) were listed as endangered in 1991. In 2007 only two made the 900-mile journey from the mouth of the Columbia River, through the Snake River, through the Salmon River, and up Redfish Lake Creek to Redfish Lake. This year there could be 700!

Such a run this summer would be a remarkable improvement above single-digit or non-existent sockeye returns to the scenic Idaho lake during the past several decades. In all, just 352 wild and hatchery-origin sockeye have migrated back to the Redfish Lake area since 1985, Fish and Game information indicates.

Between 1991 and 1998 only 16 wild sockeye returned to Idaho.

One year does not a species recovery make, but this is very, very good news.

Neither McCain nor Obama agreed to a science debate, but I recently received an e-mail from Shawn Otto suggesting that both have promised to answer the fourteen questions put to them by Innovation 2008.

Yesterday there was a report on National Public Radio suggesting that science will play a quite different role in a new administration than it has in the current one.

The last eight years have brought multiple charges that the White House has politicized science -- from muzzling federal climate scientists to ignoring advice on clear air and endangered species.

Both Republican John McCain and Democrat Barack Obama say that if they are elected, things will be different. And although the two differ on how much money should be promised to basic research, they say they will restore integrity to federal science agencies.

An administration that bases its policy on evidence rather than twisting the evidence to fit policy will be a welcome change.

This just in from the National Center for Science Education:

The defendants in Association of Christian Schools International et al. v. Roman Stearns et al.have prevailed. The case, originally filed in federal court in Los Angeles on August 25, 2005, centered on the University of California system's policies and statements relevant to evaluating the qualifications of applicants for admission. The plaintiffs -- the Association of Christian Schools International, the Calvary Chapel Christian School in Murrieta, California, and a handful of students at the school -- charged that the university system violated the constitutional rights of applicants from Christian schools whose high school coursework is deemed inadequate preparation for college; they objected to the university system's policy of rejecting high school biology courses that use textbooks published by Bob Jones University Press and A Beka Books as "inconsistent with the viewpoints and knowledge generally accepted in the scientific community."

If you're one of the dozen people who subscribe to my RSS feed and if you are interested in what I write, ¹ you might want to click through to the site and see what's there. For some reason, Feedburner missed about four entries between last Friday and yesterday morning. Or if you'd rather not visit the site. Here are titles and links to the posts that Feedburner missed:

• Finding patterns
• More NSF grant applications
• Climate resilient cities
• Intelligent design is not a theory
  

I don't have a link to the Federal Register yet,¹ but Mike Dunford provides a link to the National Wildlife Federation press release about the proposed changes, where you can find a draft of them. Mike also provides a brief analysis of a couple of the proposed changes. I'll report back with more details tomorrow, but I agree with Mike:

I've looked at the proposal, and NWF description is, if anything, an understatement of the effects that this rule change could have.

The U.S. Endangered Species Act contains the following provision:

Each Federal agency shall, in consultation with and with the assistance of the Secretary, insure that any action authorized, funded, or carried out by such agency (hereinafter in this section referred to as an "agency action") is not likely to jeopardize the continued existence of any endangered species or threatened species or result in the destruction or adverse modification of habitat of such species which is determined by the Secretary, after consultation as appropriate with affected States, to be critical, unless such agency has been granted an exemption for such action by the Committee pursuant to subsection (h) of this section.

I'm not a lawyer, but it seems pretty clear to me that the act requires federal agencies to consult with the Secretary (in practice the U.S. Fish & Wildlife Service or the U.S. National Marine Fisheries Service) to determine whether their actions might imperil listed species. Well, according to this morning's Washington Post the Bush administration doesn't agree.

The Bush administration yesterday proposed a regulatory overhaul of the Endangered Species Act to allow federal agencies to decide whether protected species would be imperiled by agency projects, eliminating the independent scientific reviews that have been required for more than three decades. 

The new rules, which will be subject to a 30-day per comment period, would use administrative powers to make broad changes in the law that Congress has resisted for years. Under current law, agencies must subject any plans that potentially affect endangered animals and plants to an independent review by the Fish and Wildlife Service or the National Marine Fisheries Service. Under the proposed new rules, dam and highway construction and other federal projects could proceed without delay if the agency in charge decides they would not harm vulnerable species.

In a telephone call with reporters yesterday, Interior Secretary Dirk Kempthorne described the new rules as a "narrow regulatory change" that "will provide clarity and certainty to the consultation process under the Endangered Species Act."

Clarity!!?? Certainty!!?? What's clear is that the Bush administration thinks they can change the law by administrative fiat. What's certain is that the change will result in less protection for endangered species.

If you're a regular reader of this blog, you probably know the story of brown tree snakes. In case you don't, here's how how the United States Geological Survey describes it:

Shortly after World War II, and before 1952, the brown Treesnake was accidentally transported from its native range in the South Pacific to Guam, probably as a stowaway in ship cargo.  As a result of abnormally abundant prey resources on Guam and the absence of natural predators and other population controls, brown Treesnake populations reached unprecedented numbers.  Snakes caused the extirpation of most of the native forest vertebrate species; thousands of power outages affecting private, commercial, and military activities; widespread loss of domestic birds and pets; and considerable emotional trauma to residents and visitors alike when snakes invaded human habitats with the potential for severe envenomation of small children.

As bad as that is, it appears that the situation is even worse.

Nick Matzke points to a